Senate Bill No.: 0405-29
UNIVERSITY SENATE
UNIVERSITY AT ALBANY
STATE UNIVERSITY OF NEW YORK
Introduced by:
University Planning and Policy Council
Date:
May 9, 2005
PROPOSED GEN*NY*SIS CENTER FOR EXCELLENCE IN CANCER GENOMICS
IT IS HEREBY PROPSED THAT THE FOLLOWING BE ADOPTED:
The Senate finds the proposed Gen*NY*Sis Center for Excellence in Cancer Genomics to be
consistent with the University's educational and research mission. The Senate endorses its
establishment at the University at Albany.
That this be forwarded to the President for approval.
Gen*NY*Sis Center for Excellence in Cancer Genomics
OPERATING PLAN
Title and Leadership:
The Gen*NY*Sis Center for Excellence in Cancer Genomics, East Campus, University at
Albany, SUNY
Dr. Paulette McCormick, Director
University at Albany, East Campus
One University Place A202
Rensselaer, N.Y. 12144
518-591-8300
pmc@albany.edu
Abstract:
Last year, the Gen*NY*Sis Cancer Center for Excellence in Cancer Genomics (hereafter the
“Gen*NY*Sis Cancer Center”) received provisional approval from the Vice President for Research as a
University ‘Center’. We now apply to receive formal, permanent ‘Center’ status, and submit the
following document in accordance with the University’s policies and procedures for establishing,
operating and reviewing organized research units. We trust that all the answers to all questions and
considerations regarding permanent ‘Center’ status are adequately addressed within the body of this
document.
Background:
Mission & Strategic Goals of the Gen*NY*Sis Cancer Center
The mission of the Gen*NY*Sis Center for Excellence in Cancer Genomics is to conduct cutting-edge
high-throughput cancer research. We are especially focused on translational research – i.e., that which
can be “translated” into clinical benefits sooner rather than later. Such research is already being
performed by the Center’s own scientists, all of whom have faculty appointments with the University’s
School of Public Health or College of Arts and Sciences.
The Cancer Genomics Center has short-term, medium-term and long-term goals corresponding
to various types of research programs and centers recognized by the National Cancer Institute
(NCI). Our ultimate long-term goal is to become a NCI Comprehensive Cancer Center,
integrating excellence in basic, clinical, and population sciences research.
Our short-term-term is to first conduct a series of early-stage interventions to establish the
feasibility or proof of principle of specific approaches in cancer. Modeled after the NCI’s
Specialized Programs of Research Excellence (SPOREs), such programs promote
interdisciplinary research and speed the exchange between basic and clinical science to move
basic research finding from the laboratory to applied settings involving patients and populations.
We have already agreed with NY Oncology and Hematology, the region’s leading oncologist
network, to jointly develop two pilot SPORE-like programs and will soon submit the proposals
to private foundations for funding. If these are successful, we will then look at ways to establish
formal NCI SPORE projects as a step toward obtaining our medium-term goal of becoming an
NCI generic research center that has a somewhat narrower research agenda that may focus, for
example, on certain basic sciences. Our long-term goal to ensure that the basic research done at
the Cancer Center is eventually developed into clinically relevant technologies and therapies is to
obtain designation as a Comprehensive Cancer Center in conjunction with other institutions in
the area (e.g., Albany Medical College, Ordway, RPI, Wadsworth), a status granted to certain
high-caliber institutions by the NCI.1
Rationale and Need for the Center
1 of 2 men and 1 of 3 women in America will develop cancer. Due to advances in medicine, the
incidence rate of the #1 killer of Americans, heart disease, is rapidly declining, and cancer is
quickly replacing it as the country’s leading cause of death.
Despite these sobering facts, cancer-related death rates have not significantly declined even after
20 years of intense research, reflecting a gap between basic research and clinical efficacy.
Therefore, new approaches are needed to ensure that the discoveries of cancer researchers are
applied and used to treat patients. That is the reason that entities such as the Gen*NY*Sis
Cancer Center, which focuses on translating science into medicine, are so desperately needed.
This is particularly the case in the Capital Region where the gap is so wide and where the
activities at the Gen*NY*Sis Cancer Center can certainly help speed the adoption of science into
local clinical practice.
Benefits to the University; how the Cancer Center will Advance the University’s Mission
The establishment of the Center also meets an important educational need, as biomedical
research is currently one of the most active fields of study and funding in science, and as there
are limited opportunities for students to work in this field locally. In fact, the Gen*NY*Sis
Cancer Center will be housed in the only building dedicated solely to cancer research in the
Capital Region. Featuring world-class, pioneering research (which is attracting other high-
caliber faculty members to the University), the Gen*NY*Sis Cancer Center already has several
post-docs (6), undergraduate (3) and graduate students (5) working in its labs, and Gen*NY*Sis
Cancer Center faculty members are now offering UAlbany students several new, much needed
courses in cancer biology and bioinformatics – classes of great interest to our students. As the
centerpiece of the University’s East Campus, the new building housing the Gen*NY*Sis Cancer
Center is also attracting biopharmaceutical companies to the region (such as Acceptys, Inc.,
Malvern , PA) that are specifically focusing on cancer and that are intending to establish R&D
facilities on the East Campus, thereby increasing the University’s local economic impact. Thus,
the establishment of this Center will be of great benefit to the University in its efforts to recruit
and retain the highest caliber faculty and students and will advance the University at Albany’s
1 There are three components to a Comprehensive Cancer Center that must be in place before the NCI grants that designation: 1)
vibrant basic research, such as that presently taking place at the Gen*NY*Sis Cancer Center 2) population studies, including
epidemiological assessments of the prevalence and incidence of cancer in the local area, as well as preventative intervention and
prevention education, which is being done or will be done by the University’s School of Public Health. This School is housed on
the East Campus next door to the cancer center; and 3) clinical treatment of cancer patients. Two of these three components of a
comprehensive cancer center are already in place, but are certainly in need of expansion. As for the third component, we are
exploring opportunities to work with area cancer clinicians at Albany Medical Center, St. Peter’s, Samaritan Hospital, and NY
Oncology and Hematology associates.
stated mission of creating a “university that is not only a leader, but relevant to a new century
and cause for pride among its students, alumni, faculty, friends and fellow citizens.”
Differences Between Gen*NY*Sis Cancer Center and Other University Units
While other cancer research facilities exist in the SUNY system (at Buffalo and Stony Brook), the State of
New York, and around the country, the individual laboratories in these centers often focus on a single
form of cancer (such as breast or prostate cancer); a single molecule or pathway linked to cancer; or use
mainstream or traditional technologies and approaches. The Gen*NY*Sis Cancer Center, the only one
affiliated with U Albany, takes a unique multimodal approach based on the use of genomic and proteomic
technologies. The aim of all our cancer research is the identification and functional validation of
therapeutic targets for the development of small molecule inhibitors or other therapeutics to be tested in
the clinic. Thus, our approach is advantageous compared to other research models in that it combines the
expertise of all our labs to look in a high-throughput fashion at all type of molecule (DNA, RNA, protein)
that when aberrantly regulated can drive cancer progression. The access to high-throughput tools
empowers us to rapidly generate this information across various types of cancer and with the use of
bioinformatics and powerful computer analysis integrate it into a working model to identify common
targets for all types of cancer. This approach means that the results of our research programs may be
broadly applicable to several forms of cancer, and if needed we will be able to identify targets that will
allow us to tailor therapies for a specific cancer. We believe that this approach will lead to the accelerated
compilation of knowledge critical to understanding and defeating cancer through the discovery of new
drugs and treatments.
The Gen*NY*Sis Center for Excellence in Cancer Genomics differs from all other University at
Albany Centers because of its unique biomedical and translational focus on cancer with the goal
of transferring this information to the clinical setting. It is our intention that it one day will be
one of New York’s leading centers for studies leading to improved prevention, prognostic and
diagnostic analyses and treatment of cancer. It is the foundation for the eventual establishment
of a NCI (National Cancer Institute) Comprehensive Cancer Center, filling a critical need for a
high standard and comprehensiveness of care and research that is currently only available in New
York City and Buffalo, New York. The buildup of a critical mass of top senior faculty and young
scientists will allow us to obtain NCI designation and along with Albany’s unique demographic
composition (which accurately reflects the demographic make-up of the entire U.S.), will enable
the Center to further recruit top senior faculty members, attract students, and offer faculty
members unique opportunities to apply their research in a relevant clinical setting.
The cancer center is also supported by the U Albany faculty members and staff who operate the state-of-
the-art research facilities of the University at Albany’s Center for Functional Genomics (CFG) – another
University Center. The unique set of core laboratories maintained by the faculty/Core Directors focus on:
1) molecular genetics 2) proteomics 3) transgenesis, 4) cell culture and analyses 5) microscopy and
histology, and 6) bioinformatics. These laboratories are staffed by approximately 15 well-trained
scientists including six PhDs and two MS degree holders with over 175 years combined experience in
molecular and cell biology.
Relationship with Other Entities
The center is designed to accommodate the basic and translational cancer research groups of both
the University at Albany and the 15 different cancer scientists at Albany Medical College,
making it the largest and most experienced cancer research group in the Capital District.
Members of the Gen*NY*Sis Cancer Center research team are faculty at the University at
Albany’s Department of Biology or the School of Public Health (SPH)’s Departments of
Biomedical Sciences or Biometry and Statistics and collaborate extensively with other SPH
faculty members who have dual appointments at U Albany and the State’s Wadsworth Research
Center. Relationships and Memorandums of Understanding (MOUs) are under development
with the Ordway Institute (in Albany) and other Institutions both within the U.S. and in other
countries. A Gen*NY*Sis grant was awarded to RPI recently for a Center of Bioengineering and
Medicine, which specializes in drug discovery, biosensors, and tissue repair, categories that are
not the focus of UAlbany’s Gen*NY*Sis Cancer Center. The Ordway Institute is also largely
focused on drug discovery, thus making the programs at these two institutions complementary to
ours, rather than directly competitive.
Activities:
The cancer center faculty and leadership have already started working on a number of activities and
research programs, a portion of which are listed below:
I. Current Research Programs
Following is a summary the research taking place at the Gen*NY*Sis Center by each of our eight core
faculty members:
A. Mechanistic and Systems Biology Based Studies of Cellular Response to Chemotherapy – Dr. Thomas
Begley (Assistant Professor, Department of Biomedical Sciences, School of Public Health)
High throughput systems biology techniques and computer modeling to gain insight into genetic
requirements and cellular strategies used to process macromolecular damage caused by
chemotherapy
Molecular interaction technologies, along with kinetic and thermodynamic analysis, to construct
and evaluate input and output modulators of DNA repair activities, known modulators of
chemotherapeutic efficacy
Modern genetic and biochemical methods to study stress induced methylation and demethylation
signaling pathways within the cell.
B. Functional Genomics Using RNA Interference Technology – Dr. Douglas Conklin (Assistant
Professor, Department of Biomedical Sciences, School of Public Health)
Using short hairpin RNAs (shRNAs) to silence suspect genes, we are systematically assessing the
importance of each of the human tyrosine kinase genes to the tumor cell phenotype in a variety of
cancers.
By systematically removing or reducing the expression of each, we expect to gain insights into
which ones in particular contribute to various steps in carcinogenesis.
A second, related project is designed to test, in depth, the significance of genetic lesions that have
been identified in tumor cells by expression profiling or mapping studies.
C. Cell-Specific Gene Expression Profiling – Dr. Scott Tenenbaum (Assistant Professor, Department of
Biomedical Sciences, School of Public Health)
RNA-binding proteins are essential in regulating posttranscriptional gene-expression and are
thought to be responsible for generating much of the diversity of the proteome.
Unlike traditional genomic methods, the use of tumor specific RNA binding proteins excludes
expression profiling of normal stroma such as fibroblasts and endothelial cells commonly
associated with complex solid tumors.
As additional cell type specific RNA binding proteins are discovered, further specific profiling of
these associated normal tissues may be possible. In this manner, intercellular communication
pathways affecting gene expression within the microenvironment of tumors and other complex
tissues may be identifiable.
D. Inducing Tumor Cell Dormancy – Dr. Julio Aguirre-Ghiso(Assistant Professor, Department of
Biomedical Sciences, School of Public Health)
More than half of cancer patients will die from metastatic disease that develops months, years or
even decades after primary tumor removal. It appears that during these periods disseminated cells
are in a dormant, non-proliferative state.
We are exploring the mechanisms that force proliferating cells into dormancy to design strategies
to induce dormancy or to maintain cells dormant. This strategy would be highly beneficial for
patients.
Our lab is also committed to uncovering the programs that govern metastatic growth and survival
of metastatic dormant cells. We have found that these dormant cells display a remarkable
chemotherapy resistance and we have identified ways to overcome it.
Overall, our research efforts are designed to identify which protein signaling pathways are
advantageous for metastatic growth and dormant cell survival. Targeting these mechanisms will
enable the eradication of metastatic disease.
E. DNA Repair – Dr. Richard P. Cunningham (Professor, Department of Biological Sciences, College of
Arts and Sciences)
Biochemistry of DNA Repair Enzymes
DNA Repair in Bacteria
Structure and Function of DNA Lyases
Structure and function of DNA Nucleases
Structure and Function of DNA Glycosylases
Genetic Analysis of DNA Repair Pathways
F.
Bioinformatics – Dr. Igor Kuznetsov (Assistant Professor, Department of Epidemiology and
Biostatistics, School of Public Health)
Due to the recent technological advances in genomic data acquisition, bioinformatics has become
a crucial element of genomics.
Our laboratory is focused on developing bioinformatics tools (methods and software) for the analysis
of genomic data and applying these tools to genome research.
Our lab is particularly interested in understanding the languages in which genetic texts are written so
that we can read and use the information encoded in DNA, RNA and protein sequences, with a focus
on the identification of patterns in biosequences of:
o
Patterns associated with structural and functional properties in proteins.
o
Patterns involved in transcriptional and post-transcriptional gene regulation.
G. Cancer Biology – Dr. Paulette McCormick (Professor, Department of Biological Sciences, College of
Arts and Sciences)
Our laboratory’s research has been continuously funded by the NIH and focuses on cancer, metastases
and developmental genetics.
Laboratory projects include:
Analysis of retinoids and histone deacetylase inhibitors in cytodifferentiation therapy with a focus
on microarray studies;
Identification of a novel tumor promoting gene in the mouse;
Examination of the role of myoR in development;
Analysis of the role of cell surface LAMP in promoting metastasis; and
Determination of the extent of differential global gene expression between different mouse
strains, mice of different ages, different tissues, etc.
H. Bioinformatics – Dr. Chittibabu Guda (Assistant Professor, Department of Epidemiology and
Biostatistics, School of Public Health)
Primary research focus of our laboratory is to develop computational algorithms, databases and
web servers for DNA and protein data analysis.
Current research projects include:
o
Reconstruction of metabolic pathways associated with human mitochondria
o
Developing new methods in structure alignment, automated target selection protocols for
proteins likely to be used as potential drug targets in several disease conditions including
cancer.
o
Developing novel computational algorithms for functional annotation of proteins,
phylogenetic analysis, protein structure data analysis etc.
o
Comparative proteome analysis to understand the functional modules (domains) of
protein structure and function.
II. Collaborations
Gen*NY*Sis Cancer Center researchers have already established collaborations with respected scientists
at a number of institutions locally and around the world, such as General Electric Life Sciences, the
Wadsworth Center, Albany Medical College, McGill University, RPI, Duke, and Mt. Sinai. Working
relationships exist between Gen*NY*Sis Cancer center faculty and U Albany faculty in the School of
Public Health, the Chemistry department, the Nanotechnology College, and the Biological Sciences
Department, ranging in nature from collaborative research projects to graduate-level course development.
The Center benefits from such collaborations and intends to continue fostering collaborative relationships
that are strategically aligned with our mission.
As a specific example, the Center’s Directors recognize that its cancer researchers bring with them
knowledge of both the latest technological advances and the underlying genetics and mechanisms of
tumor initiation and progression. Clinical oncologists, on the other hand, bring a depth of understanding
of both the course of disease in the context of the patient and of the limitations in our efforts at detection
and treatment (they also provide the crucial clinical specimens). It is only through the combination of
these two skill sets in basic and clinical research that true progress in the “War on Cancer” will be made.
Based on the novelty and importance of their research and the resources of the Center for Functional
Genomics, Gen*NY*Sis Center faculty members are highly desirable collaborators, and in fact, have
already established a wide network of relationships in the local area and around the world. For example,
in one venture with the Capital Region’s largest hematology and oncology physician group, we are
initiating a series of pilot projects that will test and validate the clinical relevance of certain genetic and
proteomic markers we identify here at the Center. We have identified and anticipate funding this
endeavor with Foundation, federal and/or state grants.
Collaborations already in existence include work with:
Ben Szaro (UAlbany)
James Castracane (UAlbany)
Imed Gallouzi (McGill University)
Sandy Wollen (Yale University)
Georg Stroaklin (Harvard University)
Ken Alexander (Duke University)
Roland Green (NimbleGen)
Tom Gingeras (Affymetrix)
Mike DiPersio (AMC)
David Housler (UCSC)
Rich Maria (NIH)
Mike Zuker (RPI)
Mark Embrechts (RPI)
Liliana Ossowski, (Mount Sinai School of Medicine)
Conly Rieder, (UAlbany)
Andres Melendez (AMC, Albany)
Thomas Hollis (Wake Forest Medical Center)
Robert Sobol (University of Pittsburgh Cancer Center)
Trey Ideker (University of California, San Diego)
Shalom Rackovsky (Mount Sinai School of Medicine)
San Diego Supercomputer Center (University of California, San Diego)
and others.
III. National Cancer Symposium
Given the University’s location 2.5 hours from Boston and New York City, we believe the Gen*NY*Sis
Cancer Center is ideally suited to host a national, annual symposium that will bridge the geographic
separation between two of the top research hubs in the U.S. and help establish the University in a pivotal
role among the country’s top echelon of cancer researchers.
Starting with a small symposium, the kick-off event will include presentations by nationally-recognized
leaders in cancer research with whom the Center has existing relationships. Additional scientific seminars
and sessions will be held by U Albany faculty and invited speakers. The focus of the meeting will be on
translational research. The rationale for this is that it supplements the two most significant cancer
meetings that take place annually: the American Association for Cancer Research (AACR), which
primarily focuses on basic research and early clinical studies, and the American Society for Clinical
Oncology, which primarily focuses on the clinical treatment of patients. We are currently working with
the Albany County Convention and Visitor’s Bureau to plan the logistics, theme, and look and feel of this
event.
III. Journal Club
Every Friday, Cancer Genomics Center faculty members host a “journal club” that features invited
presenters or a discussion about an important new research study. All Cancer Genomics Center faculty,
technicians, and lab personnel are invited as are members of the local research community.
IV. Meetings with Genomics Institute
Gen*NY*Sis Cancer center faculty meet regularly with members of the nearby Genomics Institute, a part
of the Wadsworth Center of NY State’s Department of Health, to share ideas, research, and identify areas
to collaborate.
V. Healthcare Professionals Lecture Series
The Gen*NY*Sis Cancer Center is working with medical provider NorthEast Health and Troy’s
Samaritan Hospital on a lecture series to educate healthcare professional across the Capital Region about
the latest biomedical research and biotechnologies that might be applied to their practice and improve the
care of their cancer patients. The series is planned to take place in Spring ’05.
Organization/Staffing:
The Gen*NY*Sis Cancer Center is directed by U Albany Professor Dr. Paulette McCormick, a Professor
who reports to the Vice President of Research and other U Albany executives. Professor Richard
Cunningham, Biological Sciences, U Albany, is the Center’s Associate Director. Junior faculty (currently
six in number) are all affiliated with U Albany’s School of Public Health and report to the Associate
Director, who in turn reports to the Director.
Current CVs for all personnel are included in the attached appendix. Faculty are responsible for
conducting research; mentoring post-docs, University graduate and undergraduate students; formal
teaching; service; and upholding the University’s other expectations of faculty members. The Director
and Associate Director are responsible for oversight of the Center, particularly strategic focus and
operations.
Director
Associate Director
Faculty
Faculty
Faculty
Faculty
Faculty
Faculty
Center for Functional Genomics
VP for
Research
VP for
Research
All are responsible for coordinating efforts among faculty on joint projects and grants, fundraising,
relationship-building between the center and other entities, and recruitment of additional faculty. The
Center for Functional Genomics is also directed by Dr. McCormick, and provides the scientific
infrastructure (e.g., equipment, expertise) that supports the cancer center’s research faculty.
An Advisory Committee has been proposed consisting of seven members:
Dr. Paula McKeown-Longo, co-director of the Center for Cell Biology and Cancer Research,
Albany Medical Center.
Dr. Paul Higgins, co-director of the Center for Cell Biology and Cancer Research, Albany
Medical Center
Dr. Walter Robb, former head, GE Imaging Systems; Principal, Vantage Management, Inc.
Dr. Gary Lyman, M.D., M.P.H., Professor of Medicine, Associate Center Director for Health
Services and Outcomes Research and Director of Biostatistics, James P. Wilmot Cancer Center,
University of Rochester Medical Center, Rochester, NY
Dr. Richard Cunningham, Associate Director of the Center for Functional Genomics and
Professor, U Albany, Department of Biological Sciences
Dr. Chittibabu Guda, Assistant Professor, School of Public Health, Department of Epidemiology
and Biostatistics
Dr. Thomas Begley, Assistant Professor, School of Public Health, Department of Biomedical
Sciences
The roster of Advisory Committee members drawn from Gen*NY*sis Center faculty will be rotated bi-
annually to allow each faculty member an opportunity to serve on the Committee.
Past Collaborations:
Every Cancer Genomics Center faculty member, other than the Director and Associate Director, are new
recruits to the University at Albany and none knew each other personally until arriving at the University
in 2003 or 2004. However, the Cancer Genomic Center’s strategy and approach to cancer is to leverage
the methodologies and expertise of every faculty member in a common effort to arrive at new treatments
and understandings of the disease. Accordingly, every faculty member is now working with other
members of the faculty on a variety of projects, including a recent grant proposal written jointly by every
one of the faculty, and it is typical to see at least three of our faculty member’s names on grants going out
from the Center, showing just how closely they are working together.
The viability of this approach can already be measured by the success of grants funded by federal and
state agencies and private foundations: Every new faculty member who joined a year ago is funded, 75
percent with two grants, and the total amount of grants awarded so far, in just one year, is in excess of $3
million.
Financial Plan
Inputs
The Gen*NY*Sis Center for Excellence in Cancer Genomics program will be the first and possibly the
largest tenant to occupy the new Cancer Center building under construction on the East Campus (private
property owned by the University at Albany Foundation). The Foundation has obtained the primary
funding for the Cancer Center Building from a $22.5 million seed grant from the New York Gen*NY*Sis
program, and expects to recover the difference in building costs from state and University sources.
As part of the conditions for the award of the Gen*NY*Sis grant, the University agreed to match the
$22.5 million through fundraising, grants, and any other sources of revenue, which will be used to support
the cancer research program itself.
Towards that end, U Albany launched a 5-year fundraising effort in October 2004 that, if existing
faculty grants are included, has raised $7,638,890 as of November 10, 2004 (reflects grant totals,
not annual amounts). Further, if all grants submitted by our existing faculty are awarded in the
next 12 months, this amount will rise to $11.1 million, not counting any grants from our new
bioinformatics faculty members, who arrived in 10/04. In addition, we are anticipating
additional contributions to the fund from at least four other sources that could add between
$400k and $2 million to the total. Finally, in discussions with representatives from the State
Legislature, it was indicated that U Albany may receive an additional $2 million in fiscal ’04-’05
and $1 million in ’05-’06 to support the Center during its initial years of operation. Based on
the above, following is the projected annual income we anticipate:
Total Estimates, by Fiscal Year:
’04-‘05 Externally Generated Income
Grants total $1,322,413.10 and will remain at least that much for the subsequent fiscal
year
Direct state support, separate from support through UAlbany, is anticipated to be $2
million
Fundraising support, as of December 3, 2004, is $795,000.
TOTAL: $4,117,443.10, with 6 months left in fiscal year for other grants, donations
’05-‘06 Externally Generated Income
Assumes annual grants income totals $1,322,413.10 and we anticipate approximately
$1,500,000 additional grant money (over 5 years) based on current submissions and
discussions. This yields a total for ’05-’06 of $1,622,413.10
Direct state support, separate from support via UAlbany, anticipated at $1million
Fundraising support is anticipated to exceed prior year as building is completed and
outreach to corporate, private foundation donors intensifies: $1,000,000
Estimated Total: $3,622,413.10
’06-‘07 Externally Generated Income
Assumes annual grants income totals $2,500,000 based on additional grants from faculty
hired in ’04-05
Direct state support, separate from support through UAlbany, is TBD
Assumes fundraising support to be the same level as outreach to corporate, private
foundation donors intensifies: $1,000,000
Estimated Total: $3,500,000 + State TBD
Outputs
Following is a breakdown of the foreseen expenses:
One-Time Expenses
Faculty Recruitment (2 proteomics @ $750k, 2 cancer biology@$500k): $2.5 million
Faculty search funds (4 x $10,000) = $40,000
o
Subtotal: $2,540,000
Operations
Animal facilities, husbandry and housing: $150,000
Two administrative staff, one for cancer center operations, one for faculty support. Current salary &
benefit estimates for both are $117,000.
Faculty retention / enhancement: discretionary, as needed
Travel for Director and co-Director to NCI, necessary specialty meetings, meetings to establish
collaborative grants with other institutions, etc.: $20,000
Graduate student stipends: 4 x $18,000 + tuition waivers: $100,000
Seed money for pilot projects (particularly clinical) for IP development 2x$25,000/year=$50,000
New equipment & service contracts = $500,000/year
Online journal subscriptions (specialized journals on informatics and cancer): $5,000
o
Subtotal: $942,000
Journal Club
Food, beverages for small weekly seminars: $2,000
Distinguished Speaker Seminar Series
2 times/month (7 months per year) = 14 speakers
o
Honorarium $500 x 14 = $7,000
o
Travel= 14@$1,000 = $14,000
o
Room=$150x2 nights x 14 = $4,200
o
Dinner=$50x 4 people at dinner x 14 speakers=$2,800
o
Breakfast, lunch=3 attendeesx14x$20=$840
o
Subtotal: $28,840.00
Annual Meeting
Specifications:
Venue: Gen*NY*Sis Cancer Center auditorium or similar facility
Attendees: 150 researchers and health care professionals with an interest in bridging
cancer research and clinical practice
Three meeting rooms—one for general session (meeting room); one for reception
and plated lunch; one for rotating poster session
AV requirements: rear screen projection, LCD projector (provided by facility);
audiotaping/microphones/sound board provided by outside vendor
Tentative timing : 9:30 a.m.–10 a.m. coffee/reception; 10 a.m.– 12 p.m. morning
session; 12 p.m.-1 p.m. lunch; 1 p.m.-3 p.m. afternoon session; assumes five to six
30-minute presentations followed by Q&As for each session; consider inviting guest
speaker for lunch
o
Detailed Budget:
Food and Beverage
Coffee/reception
(150 @ $20; could vary based on menu selections)
$3,000
Lunch (150 @ $20; could vary based on menu selections
$3,000
Parking
N/A (assumes no cost)
Room rental
N/A (assumes no cost)
Audiovisual
Rear screen projection/LCD projector
N/A (assumes no cost)
Audiotaping/microphones/sound board
$8,000
Material Development and Production
$3,500
Abstract booklet (assumes Cancer Center to lead content develop’t)
$3,500
Invitations
$3,000
Posters, tent cards, name badges, and pens
$1,300
Speaker honorarium @ $1500 each x 6=$9,000
$9,000
Speaker travel, housing ($1300) x 6 speakers
$7800
Speaker/host dinner ($75x12=$900); breakfasts ($25x9)=($225)
$1125
Miscellaneous administrative expenses (phone, fax, conf.calls, overnight mail) $1,500
Subtotal for Annual Meeting
$44,725
TOTAL EXPENSES:
$3,557,565.00
TOTAL YEARLY (- $2,500,000 for one-time faculty start-up expenses):
$1,017,565.00
How will the University’s Investment be Leveraged?
Income from grants
One of the major benefits the University is already enjoying from the Cancer Center is income in
the form of indirect grant allowances (i.e., monies going directly to the University to cover
administrative costs). Totaling millions of dollars already, the grants awarded to Cancer Center
researchers have an average rate of return of 36.7% if all grants are awarded; an extremely high
rate that matches or exceeds even the best-performing academic institutions in the nation.
Drawing Biopharmaceutical Companies to the Area
At the time of this writing, thirteen companies have expressed their interest in taking space in the
building housing the Gen*NY*Sis Cancer Center or the East Campus’ biotechnology incubator in
order to be near the Center for Function Genomics and the researchers with the Gen*NY*Sis
program. This boon to economic development in the Capital Region helps ensure that the
University will enjoy ongoing investments and support from the state and local governments, and
by increasing the number of well-paying jobs, be an economic catalyst for the entire community.
In addition, the co-location of these companies in University-affiliated buildings furthers the
likelihood that joint ventures, spin-offs and collaborations will increase, thus yielding valuable
Intellectual Property that will benefit the University.
Increasing the University’s National Visibility
By specifically selecting faculty members who are pioneers in high-throughput technologies, the
Gen*NY*Sis Cancer Center has established a team of scientists who are sought after as
collaborations and resources for the local and international scientific communities. Their
activities are making invaluable contributions to the University’s reputation and prominence with
the NIH, NSF and other funding entities, and other institutions globally. Finally, by sponsoring
an annual conference, the Gen*NY*Sis Cancer Center will attract the attention of thought-leaders
and their attendance, furthering the University’s status among the SUNY system.
Grant Application Protocol
All junior faculty members have been asked to list the Gen*NY*Sis Cancer Center in their grants when
appropriate and we coordinate directly with grant coordinator Beth Quackenbush to ensure that proper
attribution is given to the Cancer Center on the campus impact statement.
Other Resources Required by the Unit
Gen*NY*Sis Cancer Center personnel will initially require ~21,100 square feet of space in the new
building funded by New York State’s Gen*NY*Sis program. Additional space may be needed as other
faculty and staff members are added.
Educational
Mission
The Gen*NY*Sis Cancer Center covers a gap in the educational mission within the University because it
focuses on the multidisciplinary field of cancer cell biology and genomics. This is an underrepresented
field in the UAlbany research community. Therefore, the educational input of the Gen*NY*Sis Cancer
Center will have a significant impact on current students and postdocs as well as on the recruitment of
new ones wanting to specialize in cancer biology/genomics studies. Further this will expand the
educational interactions with departments such as Biology, Chemistry, Biomedical Sciences and with
bioengineering efforts in the Nanosciences School.
The Gen*NY*Sis Cancer Center educational duties involve:
Training of specialized human resources as evidenced by the active training of three graduate
students, six postdoctoral fellows and two rotating graduate students. We also had a visiting
graduate student from the University of Buenos Aires, Argentina as part of a training program
offered by the Bunge y Born Foundation from the aforementioned country. Two more postdoctoral
fellows are being recruited.
The Gen*NY*Sis Cancer Center faculty is currently developing, with the faculty in the BMS
department of the SPH a specialized second year graduate course in cancer biology to be offered
in Spring 2006. It will consist of a whole semester with 26 lectures and, in synchrony with the
mission of the SPH, it will cover basic mechanisms of cancer biology as well as clinical and
epidemiological aspects of the disease.
A Cancer Biology Journal Club Course for the BMS graduate program will be offered in spring
2005. This will be the first time graduate courses specialized in cancer biology are offered.
Faculty in the Gen*NY*Sis Cancer Center currently teach in various courses in the BMS graduate
program, expanding the scope and depth of the topics offered to students. These include:
BMS500B Introduction to Biomedical Sciences
BMS601B Cancer Biology
BMS632 Molecular & Cell Biology of Prokaryotes
Faculty also will teach a six week class in Genetics via the Biology Department
The Gen*NY*Sis Cancer Center offers a seminar series with local and national invited speakers,
which is open to all member of the local scientific community. Since April 2004, when these
series were inaugurated, we have had twelve invited speakers.
The Gen*NY*Sis Cancer Center will develop, in the near future, a symposium that will bring
world renowned experts in the field to present and discuss recent advances in cancer research.
The unit offers weekly the Gen*NY*Sis Cancer Center journal club where students and postdocs
discuss recent top publications in life sciences research or present and discuss their ongoing
research. This is an instrumental educational exercise.
Faculty also have coordinated or are co-coordinating the following courses:
BMS 601A Bioinformatics in Public Health
BMS551 Introduction to Public Health Genetics and Genomics
Our bioinformatics faculty members are planning:
o
A Bioinformatics Seminar series course (4-5 lectures) in Spring, 2005 offered through
Epidemiology and Biostatistics
o
A series of half-day 'Bioinformatics Workshops' in Summer 2005 for the University and
Industry
o
Initiation of Bioinformatics degree programs (MS, Ph.D) at UAlbany.
Service Mission
The implicit mission of the Gen*NY*Sis Center for Excellence in Cancer Genomics is to further the
understanding of cancer with the long term goal of contributing to improved methods of treatment.
Success will require continuously advancing research and educational programs in a manner that can be
communicated to and approved by other professionals within the field. Similarly, public support of the
center will be key. As a prominent cancer research institution in the region, it is incumbent upon the
center to promote public awareness of its work and mission through community outreach.
In the last year, GCECG faculty have given invited professional presentations at a number of
universities, companies and scientific meetings. These include: Roswell Park Cancer Institute,
McGill University, Mount Sinai School of Medicine, General Electric, Taconic Laboratories, the
American Association for Cancer Research, Cold Spring Harbor Laboratories, IBC Life
Sciences, the International Conference on Protein Expression in Animal Cells, the 2004 Second
Chianti Meeting on Proteases, the Gordon Conference on DNA Repair, and others. Several
collaborative projects have been undertaken as the result of these presentations. More
importantly, these presentations communicate to our peers the quality of the research that is
being carried out and the importance of the institution as a whole. It is expected that this level of
interaction with the professional community will continue.
The Gen*NY*Sis Center for Excellence in Cancer Genomics also firmly believes in an informed public.
We plan to develop an outreach program to inform citizens of all ages about cancer. Presentations will be
provided locally to inform the public about the research taking place at the Gen*NY*Sis Cancer Center as
well as general questions about cancer and its treatment and prevention. Although we plan to host public
seminars at our facility, we can also make visits to classrooms, philanthropies, support groups, church
groups, and other community groups. Several such visits have occurred already.
Faculty in the Gen*NY*Sis Cancer Center also:
Participate in joint seminar series with faculty in other institutions in the community such as
Albany Medical College.
Serve as advisors on PhD committees in Albany Medical College, Rensselaer Polytechnic
Institute, U Albany’s School of Public Health and College of Arts and Sciences.
Serve in the Graduate Academic Committee, the Master in Public Health Program Committee and
Recruitment Committee of the Department of Biomedical Sciences. School of Public Health,
University at Albany-SUNY, Albany, NY.
Serve in the training of high school students from the area that allows them to engage in research
with faculty in the Gen*NY*Sis Cancer Center. This is evidenced by the active participation of at
least four high school students and it involves active mentoring by the faculty as well as
communication with teachers and advisors in the corresponding schools and participating in high
school scientific fairs and related activities.
Furthermore, representatives from the Gen*NY*Sis Cancer Center have been in discussions with cancer
patient support organizations, such as Gilda’s Club (named after the late Gilda Radner) to work with them
and be a resource to their constituents. The Director of the Cancer Center has also agreed to serve on this
organization’s Board of Directors.
Evaluation and Review
Individuals and the Center itself will be evaluated on a yearly basis by the Director and co-Director (for
individuals) and the Scientific Advisory Board (for the Center). Evaluation criteria will include but will
not be limited to: number and amounts of grants submitted and received; number of publications (both
peer-reviewed and invited); number of seminars held and presented, number of individuals trained
(including high school, undergraduate and graduate students as well as postdoctoral fellows); number of
courses taught and/or new courses developed; and the extent of service activities.
###
APPENDIX A – LIST OF CORE FACULTY & AFFILATIONS
Dr. Julio Aguirre-Ghiso, Assistant Professor, Department of Biomedical Sciences, School of Public
Health
Dr. Thomas Begley, Assistant Professor, Department of Biomedical Sciences, School of Public Health
Dr. Douglas Conklin, Assistant Professor, Department of Biomedical Sciences, School of Public Health
Dr. Richard P. Cunningham, Professor, Department of Biological Sciences, College of Arts and Sciences
Dr. Chittibabu Guda, Assistant Professor, Department of Epidemiology and Biostatistics, School of
Public Health
Dr. Igor Kuznetsov, Assistant Professor, Department of Epidemiology and Biostatistics, School of Public
Health
Dr. Paulette McCormick, Professor, Department of Biological Sciences, College of Arts and Sciences
Dr. Scott Tenenbaum, Assistant Professor, Department of Biomedical Sciences, School of Public Health
APPENDIX B – GRANTS AND GRANT APPLICATIONS
Source: Research Foundation Grants Administration, PIs
Grant Analysis as of
09/22/04
PI
RF
Prime
Direct Cost
F & A Cost
Sponsor
Sponsor
(Approximate)
(Approximate)
McCormick
NCI (NIH)
NCI (NIH)
$830,000
$414,170
Taconic Farms
NCRR(NIH)
$727,123
$362,834
Taconic Farms
NCRR(NIH)*†
$933,445
$470,456
NYSTAR
NYSTAR*
$500,000
$75,000
sub-total
$2,990,568
$1,322,460
Aguirre-Ghiso
Samuel Waxman Fdn
Samuel Waxman Fdn
$100,000
$15,000
NCI (NIH)
NCI (NIH)#
$1,250,000
$599,357
NCI (NIH)
NCI (NIH)*
$1,250,000
$598,516
sub-total
$2,600,000
$1,212,873
Begley
NIEHS(NIH)
NIEHS(NIH)
$300,000
$17,660
NYSTAR
NYSTAR
$200,000
$30,000
sub-total
$500,000
$47,660
Conklin
US ARMY
US ARMY
$298,493
$149,949
US ARMY
US ARMY
$250,296
$126,149
Damon Runyon
Damon Runyon*
$300,000
$0
NCI (NIH)
NCI (NIH)*
$1,250,000
$613,132
sub-total
$2,098,789
$889,230
Cunningham
NSF
NSF
$245,253
$114,747
Trevigen, Inc
NIH
$50,034
$24,966
MIT
NIH*
$849,435
$402,915
Trainer
NIH
$540,000
$260,000
NIH
NIH
$463,000
$0
sub-total
$1,607,722
$542,628
Tenenbaum
NHGRI(NIH)
NHGRI(NIH)
$275,000
$138,600
NHGRI(NIH)
NHGRI(NIH)*
$200,000
$100,800
NIMH(NIH)
NIMH(NIH)*
$275,000
$138,600
sub-total
$750,000
$378,000
Aguirre-Ghiso,
Begley, Conklin,
Guda, Kuznetsov,
Tenenbaum
Prostate Cancer
Foundation
Same
$150,000
$0
* Pending (submitted)
# Score within funding range but not yet awarded
† Renewal of existing grant
Gen*NY*Sis Center for Excellence in Cancer Genomics
Income & Budget Projections
April 25, 2005
Financial Plan
I. Inputs
The Gen*NY*Sis Center for Excellence in Cancer Genomics program will be the first and possibly the
largest tenant to occupy the new Cancer Center building under construction on the East Campus (private
property owned by the University at Albany Foundation). The Foundation has obtained the primary
funding for the Cancer Center Building from a $22.5 million seed grant from the New York Gen*NY*Sis
program, and expects to recover the difference in building costs from state and University sources.
As part of the conditions for the award of the Gen*NY*Sis grant, the University agreed to match the
$22.5 million through fundraising, grants, and any other sources of revenue, which will be used to support
the cancer research program itself. A major goal for the program is the establishment of a $10 million
endowment that would generate ~$400,000 per year to cover the programs operational expenses.
Towards that end, U Albany launched a 5-year fundraising effort in October 2004 that, if existing
faculty grants are included, has raised $7,638,890 as of November 10, 2004 (reflects grant totals,
not annual amounts). Further, if all grants submitted by our existing faculty are awarded in the
next 12 months, this amount will rise to $11.1 million, not counting any grants from our new
bioinformatics faculty members, who arrived in 10/04. In addition, we are anticipating
additional contributions to the fund from at least four other sources that could add between
$400k and $2 million to the total. Finally, in discussions with representatives from the State
Legislature, it was indicated that U Albany may receive an additional $2 million in fiscal ’04-’05
and $1 million in ’05-’06 to support the Center during its initial years of operation. Based on
the above, following is the projected annual income we anticipate:
Total Estimates, by Fiscal Year:
’04-‘05 Externally Generated Income
Grants total $1,322,413.10 and will remain at least that much for the subsequent fiscal
year
Direct state support, separate from support through UAlbany, is anticipated to be $2
million
Fundraising support, as of December 3, 2004, is $795,000.
TOTAL: $4,117,443.10, with time left in fiscal year for other grants, donations
’05-‘06 Externally Generated Income
Assumes annual grants income totals $1,322,413.10 and we anticipate approximately
$1,500,000 additional grant money (over 5 years) based on current submissions and
discussions. This yields a total for ’05-’06 of $1,622,413.10
Direct state support, separate from support via UAlbany, anticipated at $1million
Fundraising support is anticipated to exceed prior year as building is completed and
outreach to corporate, private foundation donors intensifies: $1,000,000
Estimated Total: $3,622,413.10
’06-‘07 Externally Generated Income
Assumes annual grants income totals $2,500,000 based on additional grants from faculty
hired in ’04-05
Direct state support, separate from support through UAlbany, is TBD
Assumes fundraising support to be the same level as outreach to corporate, private
foundation donors intensifies: $1,000,000
Estimated Total: $3,500,000 + State TBD
II. Outputs
Following is a breakdown of foreseen one-time and ongoing operational expenses:
Following is a breakdown of foreseen expenses:
One-Time Expenses (Associated with Moving to New Building)
One Shared Tissue Culture Facility:
Biological Safety Renovation
$20,000
Shared tissues culture incubators and safety hoods
$35,000
Tissue culture centrifuges, microscopes, pipettes, liquid nitrogen storage
$45,000
Other Shared Equipment:
Incubator Shaker
$ 8,000
Ice Machine
$ 2,000
Water Purification System
$40,000
Shared Bioinformatic Resource Center (Students, Postdocs ):
Eight Computers
$20,000
Administrative Assistant Initial Office Setup:
Supplies
$10,000
Subtotal:
$180,000
Operations
Animal facilities, husbandry and housing:
$100,000
Two staff, one administrative for faculty support, one lab assistant for cancer center operations.
Current salary & benefit estimates for both are:
$90,000.
Travel for Director and co-Director to NCI, necessary specialty meetings, meetings to establish
collaborative grants with other institutions, etc.
$20,000
Graduate student stipends: 4 x $18,000 + tuition waivers
$100,000
Seed money for pilot projects (particularly clinical) for IP development
2x$25,000/year=
$50,000
New equipment service contracts/year:
$12,000
Online journal subscriptions (specialized journals on informatics and cancer)
$15,000
Subtotal:
$387,000
Distinguished Speaker Seminar Series
7 speaker per year
o
Honorarium, travel, housing (2 nights), breakfast (2); lunch, dinner, and general reception for
seminar attendees
Subtotal:
($2,154 x 7) $14,664
Biennial Meeting
6 Internationally renowned scientists as major participants
Honoraria, travel, housing (2 nights), breakfasts (2), lunch, dinners
~100-125 attendees
o
Coffee breaks, lunch, and reception
Media, marketing and administration
Miscellaneous items (posters, badges, etc.)
Subtotal: $39,150 ($19,575/yr)
YEARLY OPERATING COSTS
$421,653
ONE TIME SET-UP COSTS:
$180,000
TOTAL
$601,653
APPENDIX C – Gen*NY*Sis Cancer Center Researcher CVs
Gen*NY*Sis Center for Excellence in Cancer Genomics - CVs
Director
Dr. Paulette McCormick
Associate Director
Dr. Richard Cunningham
FF
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Paulette J. McCormick
POSITION TITLE
Professor
EDUCATION (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
YEAR(s)
FIELD OF STUDY
Barnard College, New York, NY
University at Albany, SUNY, Albany, NY
B.A.
Ph.D.
1972
1979
Biology
Cell Biology &
Developmental
A. Positions and Honors
Positions and Employment:
1972-74:
Senior Research Assistant in Tumor Virology, Department of Pathology,
Harvard Medical School.
1975-79:
Graduate Student in laboratory of Dr. Albert Millis, University of New
York at Albany.
1976-79:
Predoctoral Fellow of the National Science Foundation.
1979-82:
Postdoctoral Fellow in the Laboratory of Developmental Genetics,
Sloan-Kettering Institute for Cancer Research.
1982-85:
Senior Research Associate in the Laboratory of Developmental Genetics
and Instructor, Developmental Genetics Training Program, Sloan-Kettering
Institute for Cancer Research.
1985-91:
Assistant Professor, University at Albany, SUNY, Center for Cellular
Differentiation, Department of Biological Sciences.
1991-98:
Associate Professor, University at Albany, SUNY, Center for Cellular
Differentiation, Department of Biological Sciences.
1997-date:
Professor, University at Albany, SUNY, Department of Biological Sciences
1998-date: Director, University at Albany Center for Functional Genomics
2000-date: Co-Director of UA/Taconic Farms NIH Mutant Mouse Regional
Resource Center.
2003-date: Director, New York State Gen*NY*Sis Center for Excellence in Cancer
Genomics
2003-date: Founding Member and Steering Committee: Bioconnex
2004-date: Member, Board of Directors, Gilda’s Club, Capital Region, New York
2004-date: Member, Scientific Advisory Committee, Barnard College, Columbia
University
Other Professional Experience, Honors and Awards:
1968: National Merit Scholarship Semi-Finalist; 1968: New York State Regents Scholarship;
1968-72: Barnard College of Columbia University Scholarship 1976-79: National Science
Foundation Predoctoral Fellowship; 1980-82: National Institutes of Health Postdoctoral
Fellowship; 1985-present: Reviewer for numerous journals including Cancer Research, JNCI,
JCI, etc.; 1990: Dr. Nuala McGann Drescher Fellowship for Meritorious Service in Affirmative
Action; 1994: National Association of Science/National Research Council Howard Hughes
Medical Institute, Genetics and Molecular Biology Fellowship Panel, (Co-chair,1993 and Chair,
1994); 1992-96 and 1999-2003: Member of National Institutes of Health, National Cancer
Institute Pathology B Study Section (on molecular genetics of cancer and metastasis); 1995:
Distinguished Lecturer in Cancer and Metastasis, Wayne State University & Michigan Cancer
Center; 1996-present: member of numerous NIH Special Emphasis Panels; 1997: NIH Special
Panel on Germ Line Tumors; 1997: Distinguished Lecturer, Imperial College, London, UK; 1998
Organizer 50 years of Methylation (a symposium to honor Rollin Hotchkiss), Albany, NY; 2001-
present: Editorial Board, Technology in Cancer Research and Treatment; 2004: New York State
Roundtable on Prostate Cancer; 2004 Scientific Advisory Board, Barnard College of Columbia
University.
B. Selected peer-reviewed publications (in chronological order).
McCormick, P.J., Keys, B.J., Pucci, C. and Millis, A.J.T. (1979) Human fibroblast conditioned
medium contains a 100K dalton glucose-related cell surface protein. Cell 18:173-182.
McCormick, P.J., Babiarz, B. and Millis, A.J.T. (1982) Distribution of a 100K dalton
glucose-regulated cell surface protein in mammalian cell cultures and sectioned tissues. Exp.
Cell Res. 138:63-72.
Artzt, K., McCormick, P.J. and Bennett, D. (1982) Gene mapping with the T/t-complex of the
mouse. 1. t-lethal genes are non-allelic. Cell 28:463-470.
McCormick, P.J., DiMeo, A., Neuner, E. and Artzt, K. (1982) Characterization of the F9
antigen isolated from teratocarcinoma cell culture medium. Cell Diff. 11:135-140.
Shin, H.-S., McCormick, P.J., Artzt, K. and Bennett, D. (1983) Cis-trans test shows a
functional relationship between non-lethal allelic lethal mutations in the T/t complex.
Cell 33:925-929.
McCormick, P.J. and Babiarz, B. (1984) Expression of a glucose-regulated cell surface
protein in early mouse embryos. Dev. Biol. 105:530-534.
Gummere, G.R., McCormick, P.J. and Bennett, D. (1986) Effects of overall
genetic background and the homologous chromosome on transmission
ratio distortion in t-haplotypes. Genetics 114:235-245.
McCormick, P.J. and Alton, A.K. (1988) The mouse T/t complex: T mutations and
t-haplotypes. In Developmental Genetics of Higher Organisms (G. Malacinski, ed.)
Macmillan, N.Y. p. 459-475.
McCormick, P.J. and Shin, H.-S. (1990) Analysis of a nontumorigenic embryonal
carcinoma cell line. Exp. Cell Res. 189:183-188.
McCormick, P.J. (1991) Characterization of a developmentally regulated mouse
embryonic antigen. In Vitro Cell. Dev. Biol. 27A:260-266.
Dietrich, J., Shin, H.-S. and McCormick, P.J. (1992) Retinoic acid induced differentiation
of a nontumorigenic embryonal carcinoma cell mutant created through retroviral
insertion. Exp. Cell Res. 199:305-313.
Deckert, J., Dietrich, J. and McCormick, P.J. (1993) A comparative analysis of the activity
of retinoic acid and cyclic AMP in the induction of differentiation of embryonal cells.
International J. of Oncology 2:403-412.
Aziz, N., Dietrich, J., Shin, H.-S., and McCormick, P.J. (1993) Analysis by somatic cell
fusion of the phenotypic properties of a mutant embryonal carcinoma cell line.
International J. of Oncology. 3:313-318.
Dietrich, J., and McCormick, P.J. (1994) Analysis of the factors involved in the retinoic
acid induced differentiation of a retinoid-hypersensitive embryonal carcinoma cell
mutant. Exp. Cell. Res. 210:210-208.
Gama, R.E., Du, Y.L., Bauman, J., Chan, T., and McCormick, P.J. (1996) Novel Mouse
Repetitive Element Structures in an Embryonal Carcinoma Mutant Cell Line. Oncology
Reports 3:171-174.
Gama, R.E., Du, Y.L., Bauman, J., and McCormick, P.J. (1996) Identification of Exons in a
Novel Embryonal Locus Using the GRAIL Program. Oncology Reports, 3:371-374.
Gray-Bablin, J., Acevedo-Schemerhorn, C., Gama, R.E., and McCormick, P.J. (1997)
t-complex associated embryonic cell surface antigen homologous to mLAMP-1: I
Biochemical and Molecular comparisons. Exp. Cell Res. 236:501-509.
Acevedo-Schermerhorn, C., Gray-Bablin, J., Gama, R.E., and McCormick, P.J. (1997)
t-complex associated embryonic surface antigen homologous to mLAMP-1: II
Expression and Distribution and Analyses. Exp. Cell Res. 236:510-518.
McCormick, P.J., Finneran, A., and Bonventre, E. (1998) LAMP-1/ESGP appears on the cell
surface of fertilized mouse eggs subsequent to fertilization. In vitro Dev. Biol.–Animal
34:353-355.
Yu, L-M, Zhang, F., and McCormick, PJ. (2000) An embryonal carcinoma multiple
phenotype locus maps to the proximal portion of the mouse X chromosome.
Oncology Reports, 7: 509-513.
Yu, L-M, Mikloucich, J., Sangster, N., Perez, A. and McCormick, PJ. (2003) Myo R is
expressed in nonmyogenic cells and can inhibit their differentiation. Exp. Cell Res.,
289: 162-173.
Yu, L-M, Eifert, C., Sangster, N., Chittur, S., Tine, J. and McCormick, PJ.
Retinoic acid induced alterations of global gene expression in embryonal
carcinoma cells. (Submitted to Molecular Biology of Reproduction and
Development)
Sangster, N., Yu, L-M, and McCormick, P.J. Molecular Profiling of Embryonal Carcinoma
Cells Following Retinoic Acid or Histone Deacetylase Inhibitor Treatment (Submitted
to Molecular Cancer Research)
Yu, L-M., Perez, A.V. and McCormick, P.J. The bHLH protein MyoR inhibits endodermal
differentiation. (Submitted to Differentiation)
C. Research Support
Ongoing Research Support
“Mutant Mouse Regional Resource Center” (Preserve, distribute and characterize mutant
mice)
Co-Principal Investigator: PJ McCormick, PhD
Agency: National Center for Research Resources
Type: RFA (1.U42 RR 14820) Period: February 1, 2000 to January 31, 2005
$4.5 million (total)
Our long term overall objective is to assist in the characterization and delivery of mutant
mice to the research community so that such mutants may become even more valuable
tools in the elucidation of the mechanisms governing mammalian homeostasis and
disease.
“Analyses of a Non-Tumorigenic Embryonal Carcinoma Cell Line” (determine the molecular
causation of a retroviral insertion mutation regulating multiple phenotypes)
Principal Investigator: PJ McCormick, PhD
Agency: National Cancer Institute
Type: R01 (CA49466, years 11-15) Period: April 1, 2001 to March 31, 2005
$1,200,000 (total)
The long term objectives of this project are to identify and characterize the gene disrupted
by the retroviral insertion as well as any downstream genes whose activity is affected by
loss of the insertion site encoded transcript.
“New York State Gen*NY*Sis Grant for Center for Excellence in Cancer Genomics”
Principal Investigator: PJ McCormick, PhD
Agency: New York State
Period: September 2002 to August 2005
Award: $22.5 million
The objective of this project is to establish a state-of-the-art cancer research center.
Technology Transfer Award
PI: PJ McCormick, PhD
Agency: New York Science, Technology and Academic Research
Period: 2/1/04 – 1/31/05
Award: $500,000
The major goal of this project is to begin a feasibility study for the creation of a National VA
Molecular Medicine Resource
Health Care Reform Act Award
Principal Investigator: PJ McCormick, PhD
Agency: New York State
Period: 2/1/04 – 7/31/05
Award: $1,420,000
Faculty Recruitment to UAlbany School of Public Health
The major goal of this project is to recruit new faculty
Completed Research Support
“Analyses of a Non-Tumorigenic Embryonal Carcinoma Cell Line” (determine the molecular
causation of a retroviral insertion mutation regulating multiple phenotypes)
Principal Investigator: PJ McCormick, PhD
Agency: National Cancer Institute
Type: R01 (CA49466, years 11-15) Period: April 1997 to March 31, 2001
The long term objectives of this project are to identify and characterize the gene disrupted
by the retroviral insertion as well as any downstream genes whose activity is affected by
loss of the insertion site encoded transcript.
“Transgenic Facility Grant”
Principal Investigator: PJ McCormick, PhD
Agency: Research Foundation of the University at Albany and the Albany Medical College
Period: February 1, 1999 to Jan 31, 2001
The objective of this project is to establish a staffed, state-of-the-art core facility for the
generation of transgenic mice and the maintenance of ES cells for targeted homologous
recombination.
“Center for Comparative Functional Genomics Core Facilities”
Principal Investigator: PJ McCormick, PhD
Agency: State of New York
Period: June 1, 1999 to March 31, 2000
The objective of this project is to establish staffed, state-of-the-art core facilities in
biochemistry and molecular biology, cell biology and imaging, and bioinformatics to
support studies in comparative functional genomics.
Principal Investigator/Program Director (Last, first, middle):
Cunningham, Richard P.
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed for Form Page 2.
Follow the sample format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Richard Cunningham
POSITION TITLE
Professor
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
Brown Univ., Providence RI
BA-BS
1966-1971
Biology
Johns Hopkins Univ., Baltimore MD
PhD
1971-1977
Biology
Yale Univ. School of Medicine, New Haven CT
Post-doc
1977-1980
Biochemistry
Johns Hopkins School of Medicine, Baltimore MD
Post-doc
1980-1982
Genetics
A.
Positions and Honors:
Assistant Professor of Biological Sciences, SUNY at Albany, 1982-1988
Associate Professor of Biological Sciences, SUNY at Albany, 1988-1993
Professor of Biological Sciences, SUNY at Albany, 1993-present
Associate Director of the Center for Functional Genomics, SUNY at Albany, 2001-present
Research Scientist, Stratton VA Medical Center, Albany, NY, 2003-present
Associate Director, Gen*NY*Sis Center for Excellence in Cancer Genomics, 2003-present
B.
Selected peer-reviewed publications:
Mol, C.D., Kuo, C-F., Thayer, MM, Cunningham, R.P. and Tainer, J.A. (1995) Structure
and function of the multifunctional DNA repair enzyme exonuclease III. Nature 374,
381-386.
Barzilay, G., Mol, C.D. Robson, C.N. Walker, L.J. Cunningham, R.P., Tainer, J.A., and
Hickson, I.D. (1995) Identification of critical active-site residues in the
multifunctional human DNA repair enzyme HAP1. Nature Structural Biology 2, 561-
568.
Thayer, M.M., Ahern, H., Xing, D., Cunningham, R.P., and Tainer, J.A. (1995) Novel
DNA binding motifs in the DNA-repair enzyme endonuclease III structure. EMBO J. 4,
4108-4120.
Zuo, S., Boorstein, R.J., Cunningham, R.P. and Teebor, G.W. (1995) Comparison of
the effects of UV irradiation on 5-methylsubstituted and unsubstituted pyrimidines
in alternating Py-Pu sequences in DNA. Biochemistry 34, 11582-11590.
Hilbert, T.P., Boorstein, R.J., Xing, D., Kung, P.H., Bolton, P.H., Cunningham, R.P. and
Teebor, G.W. (1996) Purificatiion of a mammalian analog of E. coli endonuclease
III: Identification of a calf thymus pyrimidine hydrate/thymine glycol/AP lyase by
crosslinking the enzyme to a thymine glycol-containing DNA-oligonucleotide.
Biochemistry 35, 2505-2511.
Purmal, A.A., Rabow, L..E, Lampman, G.W., Cunningham, R.P.and Kow Y.W. (1996) A
common mechanism of action for the N-glycosylase activity of DNA
N-glycosylase/AP lyases from E. coli and T4. Mutat. Res. 364, 193-207.
Milligan J.R., Ng J.Y., Wu C.C., Aguilera J.A., Ward J.F., Kow Y.W., Wallace S.S. and
Cunningham R.P. (1996) Methylperoxyl radicals as intermediates in the damage to
DNA irradiated in aqueous dimethyl sulfoxide with gamma rays. Radiat. Res. 146,
436-443.
Hilbert, T.P., Chaung, W., Boorstein, R.J., Cunningham, R.P., and Teebor, G.W. (1997)
Cloning and expression of the cDNA encoding the human homologue of the DNA
repair enzyme, Escherichia coli endonuclease III. J. Biol. Chem. 272, 6733-6740.
Jen, J., Mitchell, D.L., Cunningham, R.P., Smith, C.A., Taylor, J-S., and Cleaver, J.E.
(1997) Ultraviolet irradiation produces novel endonuclease III-sensitive cytosine
photoproducts at dipyrimidine sites. Photobiol. Photochem. 65, 323-329.
Milligan, J. R., Aguilera J. A., Nguyen, T-T. D., Ward, J. F., Kow, Y. W., He, B. and Cunningham, R. P.
(1999) Yield of DNA strand breaks after base oxidation of plasmid DNA. Radiat. Res. 151, 334-342.
Begley, T. J. and Cunningham R.P. (1999) Methanobacterium thermoformicicum Thymine DNA
mismatch glycosylase: conversion of an N-glycosylase to an AP lyase. Protein Engineering, 12, 333-340.
Haas B.J., Sandigursky, M., Tainer, J.A., Franklin, W.A. and Cunningham, R.P. (1999) Purification and
characterization of Thermotoga maritima endonuclease IV; a thermostable apurinic/apyrimidinic
endonuclease and 3-repair diesterase. J. Bacteriol. 181, 2834-2839.
Begley, T.J., Haas B.J., Noel, J., Shekhtman, A., Williams, W.A., and
Cunningham, R.P. (1999) A new member of the endonuclease III family of
DNA repair enzymes which removes methylated purines from DNA. Current
Biology 9, 653-656.
Bazar, L.S., Collier, G.B., Vanek, P.G., Siles, B.A., Kow, Y.W., Doetsch, P.W.,
Cunningham, R.P., and
Chirikjian, J.G. (1999) Mutation identification DNA analysis system (MIDAS) for
detection of known mutations. Electrophoresis 6, 1141-1148.
Shekhtman, A., McNaughton, L., Cunningham, R.P., and Baxter, S.M. (1999) Identification of the
Archaeoglobus fulgidus endonuclease III-DNA interaction surface using heteronuclear NMR methods.
Structure 7, 919-930.
Hosfield, D.J., Guan, Y., Haas, B.J., Cunningham, R.P., and Tainer J.A. (1999) Structure of the DNA
repair enzyme endonuclease IV and its complex with DNA: double-nucleotide flipping at abasic sites and
three-metal-ion catalysis. Cell 98, 397-408.
Chheda, A.D., Teebor, G.W. and Cunningham, R.P. (2000) Identification, characterization,
and purification of DNA glycosylase/AP lyases by reductive cross-linking to 2-deoxyribooligonucleotides
containing specific base lesions. Methods, 22, 80-187.
Hashimoto, H., Greenberg, M. M., Kow, Y. W., Hwang, J.-T. and Cunningham R.P. (2001) The
2-deoxyribonolactone lesion produced in DNA by neocarzinostatin and other damaging agents
Forms cross-links with the base-excision repair enzyme endonuclease III. J. American Chem.
Soc. 123, 3161-3162.
Marenstein, D.R., Ocampo, M.T., Chan, M.K., Altamirano, A., Basu, A.K., Boorstein, R,J.,
Cunningham, R.P. and Teebor G.W. (2001) Stimulation of hNth1 by YB-1 (DbpB): Interaction
between a base excision repair enzyme
and a transcription factor. J. Biol. Chem. 276, 21242-21249.
Mol, C.D., Arvai A. S., Begley, T. J., Cunningham, R. P., and Tainer, J. A. (2002) Structure and Activity
of
a Thermostable Thymine-DNA Glycosylase: Evidence for Base Twisting to Remove Mismatched Normal
DNA Bases. J. Mol. Biol. 315:373-384
Ocampo, M.T.A., Chaung, W., Marenstein, D.R., Chan, M.K., Altamirano, A., Basu, A.K.,
Boorstein, R.J., Cunningham, R.P., and Teebor, G.W. (2002) Targeted deletion of mNth1 reveals
a novel DNA repair enzyme activity. Mol. Cell. Biol. 22, 6111-6121.
Begley, T.J., Haas, B.J., Morales, J.C., Kool, E.T., and Cunningham, R.P. (2003) Kinetics and binding of
the thymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substrates. DNA
Repair 2, 107-120.
Marenstein, D.R., Chan, M.K., Altamirano, A., Basu, A.K., Boorstein, R.J., Cunningham, R. P., and
Teebor, G.W. (2003) Substrate specificity of human endonuclease III (hNth1): Effect of human AP
endonuclease 1 (APE1) on hNTh1 Activity. J. Biol. Chem. 278, 9005-9012.
Burgis, N.E., Brucker, J, J. and Cunningham, R.P. (2003) A repair system for non-canonical purines in
Escherichia coli. J. Bacteriol. 185, 3101-3110.
Aramini, J.M., Cleaver, S.H., Pon, R.T., Cunningham, R.P., Germann, M.W. (2004) Solution
structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate
recognition by endonuclease IV. J. Mol. Biol. 338, 77-91.
PHS 398/2590 (Rev. 05/01)
Page
Biographical Sketch Format Page
Number pages consecutively at the bottom throughout the application. Do not use suffixes such as 3a, 3b.
Laboratory of Dr. Julio Aguirre-Ghiso
Julio A. Aguirre-Ghiso
Principal Investigator
Sharon J Sequeira
Graduate Research Assistant
Aparna C Ranganathan
Postdoctoral Fellow
Lin Zhang
Research Assistant
Curriculum Vitae
Name: Julio A. Aguirre-Ghiso
Position title: Assistant Professor
EDUCATION/TRAINING
INSTITUTION AND LOCATION
DEGREE
YEAR(s)
FIELD OF
STUDY
University of Buenos Aires, Buenos
Aires, Argentina
MSc.
1989-1994
Biological Sciences.
Track: Molecular
Genetics and
Biotechnology
University of Buenos Aires, Buenos
Aires, Argentina
Ph.D.
1994-1997
Molecular Cell Biology
Mount Sinai School of Medicine, New
York, USA
Postdoctoral
Training
1998-2003
Molecular and Cell
Biology
Date of Birth: October 25th, 1969.
Place of Birth: Buenos Aires, Argentina
Citizenship: Argentine (US Permanent Resident)
PROFESSIONAL POSITIONS:
1992-1995: Student Research Assistant, University of Buenos Aires, Argentina.
1994-1995: Teaching Assistant, University of Buenos Aires, Argentina.
1996-1998: Graduate Research Associate, University of Buenos Aires, Argentina.
1998-2003: Postdoctoral Fellow, Mount Sinai School of Medicine-NYU, New York
USA.
2003-date: Assistant Professor, The University at Albany, State University of New York,
USA.
AWARDS:
1996 -Best Basic Research Paper. XII Multidisciplinary Sessions of Oncology of the
Institute of Oncology " Angel H. Roffo" of the University of Buenos Aires, Argentina.
1998-“Florencio Fiorini Foundation Award” from the Argentine League for the Fight
Against Cancer (LALCEC), Argentina.
1999- Best Basic Research Paper. XV Multidisciplinary Sessions of Oncology of the
Institute of Oncology " Angel H. Roffo" of the University of Buenos Aires, Argentina.
2002:“Jorge Oster Fellowship”, Bunge y Born Foundation, Argentina. (Trainee in the
USA. Hernan Farina, PhD).
2003:“Jorge Oster Fellowship”, Bunge y Born Foundation, Argentina. (Trainee in the
USA, Alejandro Adam, MSc.)
2003:“Florencio Fiorini Foundation”, Argentine League for the Fight Against Cancer
(LALCEC), Argentina.
FELLOWSHIPS:
1993- Student Research Fellowship of the University of Buenos Aires, Argentina
1996- Graduate Research Fellowship of the University of Buenos Aires, Argentina.
1996- Graduate Research fellowship of the National Council for Science and Technology
Research (CONICET). Declined
1997- Senior Research fellowship of the National Council for Science and Technology
Research (CONICET). Declined
2001- Charles H. Revson Postdoctoral Fellowship in Biomedical Research, Charles H. Revson
Foundation, New York, USA.
GRANT SUPPORT:
TRAVEL GRANTS:
1995- THE "ANGEL H. ROFFO” FOUNDATION, to develop collaborative research at Dr.
Carlos Arregui’s laboratory at the Biochemistry Department of the School of Chemistry, of
the National University of Cordoba, Argentina .
1996- THE FOUNDATION FOR CANCER RESEARCH AND PREVENTION (FUCA) to attend
the 87th Congress of the American Association for Cancer Research (AACR) in
Washington DC, USA.
1996- BAGÓ LABORATORIES INC. to attend the 4th Brazilian Symposium on Extracellular
Matrix. 8-11 of September Angra dos Reis, Rio de Janeiro, BRAZIL.
1997- THE "ANGEL H. ROFFO” FOUNDATION, to attend the 88th Congress of the American
Association for Cancer Research (AACR) in San Diego CA, USA.
RESEARCH GRANTS:
ONGOING:
-2003-2006. PI: Julio A. Aguirre-Ghiso
Type: Startup Funds from THE STATE UNIVERSITY OF NEW YORK AT ALBANY
-2004-2006 . PI :Julio Aguirre-Ghiso, Co-PI: Douglas Conklin
Title: Functional genomics approach to discover cancer dormancy regulating genes.
Agency: SAMUEL WAXMAN CANCER RESEARCH FOUNDATION. New York.
PENDING
PI: Julio A. Aguirre-Ghiso
Title :Functional determinants of metastatic dormancy.
Type: 1 R01 CA109182-01, Agency: NCI/NIH. 04/01/05-03/30/10
Score 130, percentile 0.9.
PUBLICATIONS:
Julio A. Aguirre-Ghiso, Liliana Ossowski and Sarah K. Rosenbaum. GFP tagging of ERK and p38
pathways reveals novel dynamics of pathway activation during primary and metastatic growth.
Cancer Res (2004); 64(20):7336-45.
Esteban Mazzoni, Alejandro Adam, Elisa Bal de Kier Joffe and Julio A. Aguirre-Ghiso. Immortalized
mammary epithelial cells overexpressing PKC acquire a malignant phenotype and become
tumorigenic in vivo. Molecular Cancer Res. (2003); 1:776-787
Julio A. Aguirre-Ghiso, Yeriel Estrada, David Liu and Liliana Ossowski. ERK(MAPK) activity as a
determinant of tumor growth and dormancy; regulation by p38(SAPK). Cancer Res. (2003);
63(7):1684-95.
Puricelli L, Proiettii CJ, Labriola L, Salatino M, Balana ME, Aguirre Ghiso J, Lupu R, Pignataro OP,
Charreau EH, Bal de Kier Joffe E, Elizalde PV. Heregulin inhibits proliferation via ERKs and
phosphatidyl-inositol 3-kinase activation but regulates urokinase plasminogen activator
independently of these pathways in metastatic mammary tumor cells. Int. J. Cancer. (2002);
100(6):642-53.
David Liu, Julio A. Aguirre-Ghiso, Yeriel Estrada and Liliana Ossowski. EGFR is a transducer of the
urokinase receptor initiated signal that is required for in vivo growth of a human carcinoma.
Cancer Cell (2002); 1: 445-457 (Cover).
Julio Aguirre-Ghiso. Inhibition of FAK signaling activated by urokinase receptor induces human
carcinoma dormancy in vivo. Oncogene (2002); 21(16):2513-24.
Virginia Ladeda , Paul Frankel , Larry A. Feig, David A. Foster, Elisa Bal de Kier Joffe,
Julio A. Aguirre-Ghiso. RalA mediates v-Src, v-Ras, and v-Raf regulation of CD44 and
fibronectin expression in NIH3T3 fibroblasts. Biochem Biophys Res Commun. (2001);
283(4):854-61.
Julio A. Aguirre Ghiso, David Liu, Andrea Mignatti, Katherine Kovalski and Liliana
Ossowski. Urokinase receptor and fibronectin regulate the ERKMAPK to p38MAPK activity
ratios that determine carcinoma cell proliferation or dormancy in vivo. Mol. Biol. Cell
(2001); 12, 4, 863-879.
Liliana Ossowski and Julio A. Aguirre Ghiso. Urokinase receptor and integrin partnership:
coordination of signaling for cell adhesion, migration and growth. Review Article. Current
Opinion in Cell Biology (2000); 12(5):613-20.
Elisa Bal de Kier Joffe, Esteban O. Mazzoni, Julio A. Aguirre Ghiso. Signaling pathways regulating
the expression of proteases during tumor progression. (in Spanish) Medicina (B Aires) (2000);
60:34-40
Julio A. Aguirre Ghiso, Katherine Kovalski and Liliana Ossowski. Tumor dormancy due to
urokinase receptor down-regulation in human carcinoma involves integrin and MAPK
signaling. J. Cell Biol. (1999); 147, 89-103.
Liliana Ossowski, Julio A. Aguirre Ghiso, David Liu, Wen Yu and Katherine Kovalski. The role of
plasminogen activator receptor in cancer invasion and dormancy. Review Article. Medicina
(Buenos Aires) (1999) vol. 59, 547-552.
Julio A. Aguirre Ghiso, Paul Frankel, Eduardo Farías, Zhimin Lu, Hong Jiang, Amanda Olsen,
Larry Feig, Elisa Bal de Kier Joffé and David Foster. Ral-A requirement for v-Src- and v-Ras-
induced tumorigenicity and overproduction of urokinase-type plasminogen activator.
Involvement of metalloproteinases. Oncogene (1999), 18, 4718-4725.
Julio A. Aguirre Ghiso, Daniel F. Alonso, Eduardo Farías, Daniel E. Gomez and Elisa Bal de Kier
Joffé. Deregulation of the signaling pathways controlling urokinase production. Its relationship
with the invasive phenotype. Review Article. Eur. J. Biochem. (1999) vol. 263, 2, 295-304.
(Cover)
Alejandro J. Urtreger, Julio A. Aguirre Ghiso, Santiago Werbahj, Lydia Puricelli, Andrés Muro,
Elisa Bal de Kier Joffé. Involvement of fibronectin in the regulation of urokinase production
and binding in murine mammary tumor cells. Int. J. Cancer, (1999), vol. 82, 748-753.
Virginia Ladeda, Julio A. Aguirre Ghiso, Elisa Bal de Kier Joffé. Function and Expression of CD44
During Spreading and Migration of Murine Carcinoma cells. Exp. Cell Res. (1998); 242:515-
527.
Julio A. Aguirre Ghiso, Eduardo F. Farías, Daniel F. Alonso, and Elisa Bal de Kier Joffé. Secretion
of urokinase and metalloproteinase-9 induced by staurosporine is dependent on a tyrosine-
kinase pathway in mammary tumor cells. Int. J. Cancer (1998); 76: 362-367.
Eduardo F. Farías, Julio A. Aguirre Ghiso, Virginia Ladeda and Elisa Bal de Kier Joffé. Verapamil
Inhibits Proteases Production, Local Invasion and Metastasis Development of Murine
Carcinoma Cells. Int. J. Cancer. (1998); 78 (6): 727-734.
Julio A. Aguirre Ghiso, Eduardo F. Farías, Daniel F. Alonso, Carlos Arregui and Elisa Bal de Kier
Joffé A Phospholipase D and Protein Kinase C Inhibitor Blocks the Spreading of Murine
Mammary Adenocarcinoma Cells Altering F-Actin and Integrin Point Contact Distribution.
Int. J. Cancer. (1997);71: 881-890.
Julio A. Aguirre Ghiso, Daniel F. Alonso, Eduardo Farías and Elisa Bal de Kier Joffé.
Overproduction of urokinase-type plasminogen activator is regulated by phospholipase D and
protein kinase C pathways in murine mammary adenocarcinoma cells. Biochim. Biophys. Acta
(1997); 1356: 171-184.
Julio. A. Aguirre Ghiso, Miriam Diament, Isabel D'elia, Elisa Bal de Kier Joffé and Slobodanka
Klein. Effect of in vivo culture of murine mammary adenocarcinoma cells on tumor and
metastatic growth. Tumor Biol. (1997); 18: 41-52.
Julio A. Aguirre Ghiso, Eduardo Farías, Diego M. Fernandez, Daniel F. Alonso and Elisa Bal de
Kier Joffé. Down modulation of tumor cells-associated proteolytic activity by n-butanol
treatment in cultured murine mammary adenocarcinoma cells. Int. J Oncol. (1996); 8: 35-39.
S. Klein, María Adela Jasnis, Miriam Diament, Lilia Davel, Julio Aguirre Ghiso, Yolanda P. de
Bonaparte. Immunomodulation by soluble factors from tumor cells cultured in vivo in diffusion
chambers. Tumor Biol. (1994); 15: 160-165.
BOOK CHAPTER.
2004- Julio Aguirre-Ghiso. Opposing roles for mitogenic and stress signaling pathways in the
regulation of cancer dormancy: a balancing act. Contemporary Cancer Research, 2004, Humana
Press.
ORIGINAL REPORTS SUBMITTED OR IN PREPARATION
2004- Aparna C Ranganathan, Alejandro P Adam, Lin Zhang, Sharon J. Sequeira and Julio A.
Aguirre Ghiso. Functional coupling of endoplasmic reticulum signaling to drug resistance of
dormant carcinoma cells. Submitted.
2004- Aparna C. Ranganathan, Timothy Baroni, Michele Lastro, Scott Tenenbaum,
Douglas Conklin and Julio Aguirre-Ghiso. Investigating functional gene programs using
ribonomic profiling and genomic scale shRNA targeting: application to cancer dormancy.
Cancer Genomics and Proteomics. Methods Protocols. Methods in Molecular
Biology, Humana Press. In preparation
REVIEWER FOR SCIENTIFIC JOURNALS AND ORGANIZATIONS:
1998-date:
Reviewer for the following journals: The Journal of Cell Science, Clinical
Experimental Metastasis, Cancer Letters, International Journal of Cancer,
Microscopy Research and Technique, Oncogene, Current Cancer Drug Targets,
Cancer Research, Biochemical Pharmacology, Expert Opinion in Pharmacology,
Biomed Central-Gastroenterology.
2001-02
Reviewer: Samuel Waxman Cancer Research Foundation.
2002
Reviewer: John Simon Guggenheim Memorial Foundation
2003
Reviewer: AIRC. Italian Association for Cancer Research
2004
Reviewer: Science and Technology Sponsored Programs, University of Buenos
Aires, Argentina
2004
Reviewer: Area Medicina del FONCYT- Agencia Nacional de Promocion Cientifica y
Tecnologica -Argentina. (Argentine National Agency for the Funding of Science and
Technology).
LECTURES:
1997 Anti-invasive and Anti-signaling strategies to fight cancer. Session of Biological
Therapies for Cancer. XIII Multidisciplinary Sessions of Oncology of the Institute of
Oncology “Angel H. Roffo”, University of Buenos Aires, Buenos Aires, Argentina.
Reviewed and published in Oncología Clínica (Clinical Oncology, in spanish) Vol.2-N°4 pp-
52-55-1997.
1999 Tumor dormancy due to urokinase receptor (uPAR) downregulation ids dependent on
signaling and activation of p42/p44 ERK in vitro and in vivo. Institute of Oncology
“Angel H. Roffo” University of Buenos Aires, Argentina.
1999 Same title as previous. National University of Quilmes (UNQ), Argentina.
1999- Tumor dormancy due to urokinase receptor (uPAR) downregulation ids dependent on
signaling and activation of p42/p44 ERK in vitro and in vivo at the Minisymposium:
Cell signaling in Tumor Invasion and Metastasis of the American Association for Cancer
Research (AACR) Annual Meeting, Philadelphia, USA.
2000 Regulation by urokinase receptor and fibronectin of ERK and p38 signaling regulates
human carcinoma tumorigenicity or dormancy in vivo. Institute of Oncology “Angel H.
Roffo” University of Buenos Aires, Argentina.
2000 MAPK pathways regulated by urokinase receptor for the onset of tumorigenicity or
dormancy of a human carcinoma. Department of Hematology Research Seminars,
Department of Medicine, Mount Sinai School of Medicine, USA.
2001 FAK signaling and cancer dormancy. Department of Hematology Research Seminars,
Department of Medicine, Mount Sinai School of Medicine, USA.
2001 Urokinase receptor and integrin interaction: a novel mechanism of mitogenic signaling
for tumor growth. Department of Biological Sciences, Hunter College of the City Univeristy
of New York, USA.
2001 Lecture: Urokinase receptor and integrin interaction: a novel mechanism of mitogenic
signaling for tumor growth. Co-chair of the Session: Defining new staging markers, Meeting
on Molecular Staging of Cancer, Section Clinical Research, Molecular Oncology, Dept.
Surgery, Klinikum Grosshadern, Ludwig Maximilians University, Munich, Germany.
2002 Balance between ERK and p38-SAPK activities as a determinant of tumor growth and
dormancy. Department of Hematology/Oncology Research Seminars, Department of Medicine,
Mount Sinai School of Medicine, USA.
2002 Urokinase Receptor and Integrin Partnership: a Novel Mechanism of Mitogenic Signaling
in Tumor Growth. Department of Pathology, Albert Einstein College of Medicine, Yeshiva
University, Bronx, New York, USA.
2002 Urokinase Receptor and Integrin Partnership: a Novel Mechanism of Mitogenic Signaling
in Tumor Growth. Center for Cell Biology & Cancer Research Department. Albany Medical
College, Albany, New York, USA.
2002. Regulation of tumor growth and dormancy by urokinase receptor (uPAR): role of focal
adhesion kinase (FAK), Rac and Cdc42 activation. Julio A. Aguirre-Ghiso, Luciana Giono and
Liliana Ossowski. Gordon Research Conference: Signaling by Adhesion Receptors.
Connecticut College, CT, USA July 14-19, 2002. (Poster)
2003 ERKMAPK and p38SAPK signaling balance as a determinant of cancer dormancy. Department
of Oncology, Montefiore Medical Center/ Albert Einstein College of Medicine, Yeshiva
University, Bronx, New York, USA.
2003 ERKMAPK and p38SAPK signaling balance as a determinant of cancer dormancy.
Department of Biomedical Sciences, School of Public Health and Center for Functional
Genomics, State University of New York (SUNY) at Albany/ University at Albany,
Albany, New York, USA.
2003 Functional determinants of metastatic dormancy. Roswell Park Cancer Insitute- Albany
Symposium, Albany, New York, USA.
2004 Functional Genomics Approach to Discover Cancer Dormancy Regulating Genes,
Institute of Biology and Experimental Medicine, University of Buenos Aires, Argentina.
2004 Functional Genomics Approach to Discover Cancer Dormancy Regulating Genes, The
Genomics Institute, Wadsworth Center and Department of Biomedical Sciences, School pf
Public Health, University at Albany-SUNY, Albany, New York, USA.
2004 uPAR signaling through MAPK modules: clues to the mechanisms regulating the
induction and escape from tumor dormancy. David Axelrod Institute, Wadsworth Center
and Department of Biomedical Sciences, School pf Public Health, University at Albany-
SUNY, Albany, New York, USA.
2004 Involvement of ER-stress and hnRNP shuttling in p38SAPK-dependent carcinoma cell
dormancy. Minisymposium on Genetic Regulation of Metastasis American Association for
Cancer Research Meeting, Orange County Convention Center, Orlando, FL. USA
2004 Spatial-temporal imaging of growth regulatory pathways-controlled GFP expression in
primary and metastatic tumors. Minisymposium on Signaling and Tumor Invasion,
American Association for Cancer Research Meeting, Orange County Convention
Center, Orlando, FL. USA
2004 uPAR signaling through MAPK modules: clues to the mechanisms regulating the
induction and escape from tumor dormancy. Second Chianti Meeting on Proteases, "CROSS-
TALK BETWEEN PROTEINASES AND THE EXTRACELLULAR ENVIRONMENT" Certosa
di Pontignano, Siena-Italy, May 16-20,2004
2004 Functional Genomics Approach to Discover Cancer Dormancy Regulating Genes,
Samuel Waxman Cancer Research Foundation, Mount Sinai School of Medicine-NYU,
New York, USA.
2004 uPAR signaling through MAPK modules: clues to the mechanisms that regulate tumor
dormancy. GE Global Research Center, Niskayuna, NY.
2004 Stress signaling and the induction of cancer dormancy. Department of Biology, School
of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA.
TEACHING EXPERIENCE (LECTURES AND COURSES):
1994-1995. Teaching assistant position at the Division of Molecular Genetics and
Biotechnology, Department of Biological Sciences, School of Exact and Natural Sciences,
University of Buenos Aires, Argentina.
1995- Tumor-Associated Antigens and the Immune Response to Tumor Antigens, Allergy and
Immunology Course, School of Medicine, University of Buenos Aires, Argentina.
1995- Regulation of cellular Immune response. Cytokines, Mechanisms of cytotoxicity. Master
in Animal Health, Cell Biology Course. School of Veterinary Sciences. University of Buenos
Aires, Argentina.
1995-1998-Laboratory training of permanent and rotating undergraduate and graduate students
at the Institute of Oncology "A.H. Roffo", University of Buenos Aires, Argentina
1996- Molecular and cellular mechanisms of the metastatic cascade. Course on "Tumor
Markers". Clinical Chemistry Course, School of Pharmacy and Biochemistry, University of
Buenos Aires. Argentina.
1996- Function and structure of the Cellular Membranes. Updates in Oncology, Molecular
Biology course. Radiotherapy Oncology Service, Italian Hospital of Buenos Aires,
Argentina.
1996- Function and structure of the Cellular Membranes. Oncology Fellows Course, Institute
of Oncology "Angel H. Roffo", School of Medicine, University of Buenos Aires, Argentina.
1996- Cell Cycle and cellular synchronization. Course: Animal Tissue Culture. Applications
for Biotechnology. Institute of Oncology "Angel H. Roffo". University of Buenos Aires.
Argentina.
1997- Cell Cycle and cellular synchronization. Course: Animal Tissue Culture. Applications to
Biotechnology. Institute of Oncology "Angel H. Roffo". University of Buenos Aires,
Argentina.
1998-2003 Laboratory training of M.D./PhD. and Ph.D. permanent and rotating graduate
students from Mount Sinai School of Medicine-NYU
2004- Cancer Genetics Lectures in the BMS500b and BMS601 courses, PhD and MPH
programs, Department of Biomedical Sciences, School pf Public Health, State University of
New York (SUNY) at Albany/ University at Albany, Albany, New York, USA.
SERVICE and MENTORING
2004-2007: Member of the Graduate Academic Committee. Department of Biomedical Sciences.
School of Public Health, University at Albany-SUNY, Albany, NY
2004-2007: Member of the Master in Public Health Program Committee. Department of
Biomedical Sciences. School of Public Health, University at Albany-SUNY, Albany, NY
2003-present: Member of the PhD Thesis Committee for Elisabeth Monagh. Center for Cell
Biology and Cancer Research, Albany Medical College, Albany NY.
2003-present: Member of the PhD Thesis Committee for Mio Shinohara. Department of
Biomedical Sciences. School of Public Health, University at Albany-SUNY and Wadsworth Institute,
Albany, NY.
2003-present: PhD Mentor for Sharon Sequeira. Department of Biomedical Sciences. School of
Public Health and Center for Excellence in Cancer Genomics, University at Albany-SUNY Albany,
NY
2003-2004 Member of the Faculty Search Committee for Bioinformatics. Department of
Epidemiology and Biostatistics, School of Public Health and Center for Excellence in Cancer
Genomics, University at Albany-SUNY Albany, NY
Associations: Associate Member of the American Association for Cancer Research
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Sharon J Sequeira
POSITION TITLE
Graduate Research Assistant
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
University of Mumbai, Mumbai, India
B.S
1998
Zoology, Biochemistry
University of Mumbai, Mumbai, India
M.S
2001
Biochemistry
A. Positions and Honors
Positions
2001-Present Graduate Research Assistant, Department of Biomedical Sciences,
Wadsworth Center & University at Albany, Albany, NY.
2002-2003
Committee Member, Indian Student Organization, University at Albany,
Albany, NY.
2004-2006
Student Representative, Student Affairs Committee, Department of
Biomedical Sciences, University at Albany, Albany, NY.
Honors
1998 Achieved Distinction & Awarded Scholarship for Highest Rank in
Zoology, University of Mumbai, Mumbai, India.
1999 Awarded 4th Highest Rank Certificate in Biochemistry, University of Mumbai,
Mumbai, India.
B. ORIGINAL REPORTS SUBMITTED OR IN PREPARATION
2004- Aparna C Ranganathan, Alejandro P Adam, Lin Zhang, Sharon J. Sequeira and Julio A.
Aguirre Ghiso. Functional coupling of endoplasmic reticulum signaling to drug resistance of
dormant carcinoma cells. Submitted.
BIOGRAPHICAL SKETCH
NAME
Aparna C Ranganathan
POSITION TITLE
Postdoctoral Fellow
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
University of Madras, Madras, India
B.S
1994
Chemistry
University of Hyderabad, Hyderabad, India
M.S
1996
Chemistry
Albany Medical College, Albany, NY
Ph.D
2002
Biochemistry &Mol
Biology
University of Rochester
Postdoctoral
Research
Associate
2002-
2004
Biochemistry &
Biophysics
B. Positions and Honors
Positions
2002-2004- Postdoctoral Research Associate, Department of Biochemistry and
Biophysics,University of Rochester, Rochester, NY.
2004-present- Postdoctoral Fellow, Department of Biomedical Sciences, University at
Albany, Albany, NY.
Honors
2002- Dean’s Prize for Excellence in Research- Albany Medical College
2000- Dean’s Prize for Excellence in Extramural Research- Albany Medical College
2000- Outstanding Scientific Presentation Award- 7th Annual Meeting of the Oxygen Society
1999- Outstanding Scientific Presentation Award- 6th Annual Meeting of the Oxygen Society
1997-2002- Trustee Scholarship- Albany Medical College
C. Publications
1.
Fabrice Lejeune,
Aparna C Ranganathan
, Lynne E Maquat.
eIF4G is required for the
pioneer round of translation in mammalian cells. Nat Struct Mol Biol. 2004 Oct;11(10):992-
1000.
2.
Shang-Yi Chiu , Fabrice Lejeune ,
Aparna C Ranganathan
, Lynne E Maquat.
The pioneer
translation initiation complex is functionally distinct from but structurally overlaps with the
steady-state translation initiation complex. Genes Dev. 2004 Apr 1;18(7):745-54.
3.
Kristin K. Nelson, Aparna C. Ranganathan, Jelriza Mansouri, Ana M. Rodriguez, Kerwin
M. Providence, Joni L. Rutter, Kevin Pumiglia, James A. Bennett and J. Andres Melendez.
Elevated Sod2 Activity Augments Matrix Metalloproteinase Expression: Evidence for the
Involvement of Endogenous Hydrogen Peroxide in Regulating Metastasis. Clinical Cancer
Research, Vol. 9, No. 1, pp. 424-432, 2003.
4.
Aparna C. Ranganathan, Kristin K. Nelson, Ana M. Rodriguez, Kwi-Hye Kim, Grant B.
Tower, Joni L. Rutter, Constance E. Brickerhoff, Ting-Ting Huang, Charles J. Epstein, John
J. Jeffrey and J. Andres Melendez. Manganese Superoxide Dismutase Signals Matrix
Metalloproteinase Expression via Hydrogen Peroxide- dependent ERK1/2 Activation.
Journal of Biological Chemistry, Vol. 276, No. 17, pp. 14264-14270, 2001.
ORIGINAL REPORTS SUBMITTED OR IN PREPARATION
2004- Aparna C Ranganathan,
Alejandro P Adam, Lin Zhang, Sharon J. Sequeira and Julio A.
Aguirre Ghiso. Functional coupling of endoplasmic reticulum signaling to drug resistance of
dormant carcinoma cells.
Submitted.
2004-
Aparna C. Ranganathan,
Timothy Baroni, Michele Lastro, Scott Tenenbaum, Douglas
Conklin and Julio Aguirre-Ghiso. Investigating functional gene programs using ribonomic
profiling and genomic scale shRNA targeting: application to cancer dormancy.
Cancer Genomics
and Proteomics. Methods Protocols. Methods in Molecular Biology
, Humana Press.
In
preparation
Principal Investigator/Program Director (Last, first, middle): Aguirre-Ghiso, J.A.
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed for Form Page 2.
Follow the sample format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Zhang, Lin
POSITION TITLE
Research Assistant
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
Jining Medical College, China
M.D.
1981
Medicine
NOTE: The Biographical Sketch may not exceed four pages. Items A and B (together) may not
exceed two of the four-page limit. Follow the formats and instructions on the attached
sample.
A.
Positions and Honors. List in chronological order previous positions, concluding with your
present position. List any honors. Include present membership on any Federal Government
public advisory committee.
1981-1988 Internal Medical Residency, Zaozhuang Hospital, China
1988-1996 Physician-in-Charge, Hospital Infection Section, Zaozhuang Hospital, China
1998
Assistant Manager, Panda Express ( fast-food Restaurant), Chicago
2003- present Research Assistant, Department of Biomedical Sciences, School of Publin Health and
GCECG, State University of New York at Albany
B. ORIGINAL REPORTS SUBMITTED OR IN PREPARATION
2004- Aparna C Ranganathan, Alejandro P Adam, Lin Zhang, Sharon J. Sequeira and Julio A.
Aguirre Ghiso. Functional coupling of endoplasmic reticulum signaling to drug resistance of dormant
carcinoma cells. Submitted.
Laboratory of Dr. Thomas Begley
Thomas Begley
Primary Investigator
Ulrike Begley
Research Scientist
Christine Lussier
Research Associate
John Rooney
Research Associate
Thomas J. Begley, Ph.D.
Curriculum vita
Assistant Professor
Department of Biomedical Sciences
Center for Functional Genomics
School of Public Health
University at Albany
One University Place
Rensselaer, NY 12144-2345
(518) 591-8300
tbegley@albany.edu
Education
University at Albany, State University of New York
B.S., Biochemistry and Molecular Biology
December 1993, Magna Cum Laude
University at Albany, State University of New York
Ph.D., Biological Sciences: concentration; Molecular Biology
May 2000
Thesis title: Mechanism of action of Mig.Mth: Substrate recognition by base flipping and
chemical editing
PROFESSIONAL EMPLOYMENT
Harvard School of Public Health
Post Doctoral Associate, Department of Cancer Cell Biology
September 1999 – May 2001
Massachusetts Institute of Technology, Post Doctoral Fellow, Division of Biological
Engineering, Center for Environmental Health
May 2001- December 2003
University at Albany, State University of New York
Assistant Professor, Department of Biomedical Sciences and Center for Functional Genomics,
School of Public Health
JANUARY 2004 - PRESENT
HONORS
2004:
NYSTAR-James D. Watson Fellowship
2003:
Merck-MIT Computational and Systems Biology Fellowship
2002:
National Research Service Award, NIEHS-NIH
2000:
University at Albany Award for Excellence
1996:
Peter Marfry Memorial Scholarship, University at Albany
1993:
Magna Cum Laude, University at Albany
Professional Associations
2004-present:
Environmental Mutagen Society
1998- present:
American Chemical Society
1995- present:
American Association for the Advancement of Science
Manuscripts
Reviews
Begley, T. J. and Samson L. D. Reversing DNA damage with a directional bias.
Nat Struct Mol Biol. (2004) 8: 688-90.
Begley, T. J. and Samson L. D. Network Responses to Damaging Agents, DNA Repair.
(2004) 3:1123-32.
Begley, T. J. and Samson L. D. A Fix for RNA. Nature, (2003) 421: 795-796
Begley, T. J. and Samson L. D. AlkB mystery solved: Oxidative demethylation of N1-
methyladenine and N3-methylcytosine adducts by a direct repair mechanism. Trends in
Biochemical Sciences (2003) 28: 93-96
Refereed
Said, M. R.*, Begley, T. J.*, Oppenheim, A. V., Lauffenburger, D. A. and Samson, L. D.
Global Network Analysis of Phenotypic Effects: Protein Networks and S. cerevisiae
Damage Recovery. PNAS (in press)
Begley, T. J., Rosenbach, A. S., Ideker, T. and Samson, L. D. Hot Spots for Toxicity
Modulation Identified by Genomic Phenotyping and Localization Mapping. Molecular
Cell (2004) 16:117-25.
Begley, T.J., Haas, B. J., Morales JC, Kool, E.T. and Cunningham, R.P. Kinetics and
binding of the thymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing
DNA substrates. DNA Repair. (2003) 2: 107-120
Begley, T. J., Rosenbach, A. S., Ideker, T. and Samson, L. D. Recovery Pathways in S.
cerevisiae Revealed by Genomic Phenotyping and Interactome Mapping. Mol Cancer
Res (2002) 1: 103-112.
Mol C.D., Arvai A.S., Begley T.J., Cunningham R.P. and Tainer J.A. Structure and
activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to
remove mismatched normal DNA bases. J Mol Biol (2002) 315: 373-84.
Begley, T.J., Jelinsky, S.A. and Samson, L.D. Complex Transcriptional responses to
Macromolecular Damaging Agents: Regulatory Responses Specific for Sn2 Alkylation
and the MAG1 Gene. Cold Spring Harbor Symposia on Quantitative Biology, (2000)
383 - 393.
Begley, T.J., Haas, B.J., Noel, J., Shektman, A., Williams, W. A., and Cunningham, R.P.
A New Member of the Endonuclease III Family of DNA Repair Enzymes Which
Removes Methylated Purines from DNA. Curr Biol (1999) 9: 653-656.
Begley, T.J. and Cunningham, R.P. Methanobacterium thermoformicicum Thymine DNA
Mismatch Glycosylase: Conversion of an N- glycosylase to an AP Lyase. Protein Engineering
(1999), 12: 333-340
Fetrow, J.S., Spitzer, J.S., Gilden, B.M., Mellender, S.J., Begley, T.J., Haas, B.J., Boose, T.L.
Structure, function, and temperature sensitivity of directed, random mutants at proline 76 and
glycine 77 in omega-loop D of yeast iso-1-cytochrome c. Biochemistry (1998) 37: 2477-87
*Authors contributed equally to work
Seminars and Presentations
2004:
“From Systems to Molecules, Complex Cellular Responses to
Damage” American Society for Microbiology Conference on DNA
Repair, Host: Prof. Graham Walker
2004:
“From Systems to Molecules, Complex Cellular Responses to
Damage” Netherlands Cancer Institute, Antoni van Leeuwenhoek
Hospital
Host: Prof. Laura J. van’t Veer
2003:
“Network Maps in DNA Repair ”. NIH-EU Conference on Molecular
Signatures of DNA Damage Induced Stress Response: Seminar Host:
Prof. Ben Van Houten, NIEHS-NIH
2003:
“Complex Cellular Responses To Damage: A Systems Overview ”.
Gordon Research Conference: Mammalian DNA Repair
Seminar Host: Prof. Richard Wood
2002:
“Recovery Pathways in S. cerevisiae Revealed by Genomic Phenotyping
and Interactome Mapping”, Whitehead Institute, Massachusetts Institute of
Technology,
Seminar Host: Prof. Susan Lindquist.
2002:
“Damage Resistance Pathways in S. cerevisiae”, American Chemical
Society National Meeting, Boston, M.A.
Seminar Host: Division of Chemical Toxicology
2002:
“Recovery Pathways in S. cerevisiae Revealed by Genomic Phenotyping
and Interactome Mapping”, Gordon Research Conference: Mutagenesis
2002:
“Genomic Phenotyping”, Cancer Center Research Focus, Massachusetts
Institute of Technology,
Seminar Host: Prof. Philip Sharp
2001:
“Genomic Phenotyping in Saccharomyces cerevisiae”, Toxicology Group,
Division of Bioengineering and Environmental Health, Massachusetts
Institute of Technology,
Seminar Host: Dr. Peter Wishnok
2001:
“Coordinated Cellular Responses to Macromolecular Damaging
Agents Identified Using Organized Toxicogenomic Screens”, Gordon
Research Conference: Genetic Toxicology
2000:
“Phenotypic Macroarrays Using DNA Damaging Agents”, Department of
Cancer Cell Biology, Harvard School of Public Health,
Seminar Host: Prof. Karl Kelsey
1999:
“Substrate Recognition by Members of the Endonuclease III Family of
DNA glycosylase”, American Society for Microbiology conference on DNA
repair and mutagenesis
1999:
“Base Flipping and Chemical Editing in the Endonuclease III Family of
DNA Glycosylases”, Department of Cancer Cell Biology, Harvard School of
Public Health,
Seminar Host: Prof. Leona Samson
1998:
“Methanobacterium thermoformicicum Thymine DNA Mismatch
Glycosylase: The Effect of Strand Cleavage on Glycosylase Activity”,
Gordon Research Conference: Mutagenesis
Teaching and Administrative Experience
Feb 2002: “Global Transcriptional Profiling, DNA Chips and Genomics”, Guest
Lecturer, Systems Pharmacology and Toxicology, BEH.201, Division of
Bioengineering and Environmental Health, Massachusetts Institute of
Technology,
1997-1999:
Biological Science Graduate Representative to the Student Legislature,
University at Albany
1998-1999:
Grant Reviewer, Graduate Student Organization, University at Albany
1997-1999:
Genetics Discussion Section, Bio212, Teaching Assistant, Fall Semester,
University at Albany
1997-1999:
Immunology Lab, Bio335, Teaching Assistant, Spring Semester, University at
Albany
1996:
Cell Biology Lab, Bio302, Teaching Assistant, Spring Semester, University at
Albany
Funding / Grants
Active
James D. Watson Fellowship
New York State Office of Science, Technology and Academic Research
$200,000 / 2 years
10/01/2004- 9/30/2006
Alkylating agents are a class of chemotherapeutic compounds that are used to treat a
number of different types of cancers found in the blood, lung, breast and brain. Alkylating
agents can react with nucleophilic centers found in DNA, to generate cytotoxic lesions that
selectively kill fast growing cells associated with some cancers. Most cells have the potential to
influence the cytotoxicity of alkylating agents, and therefore the efficacy of treatment, through
the coordinated action of different DNA repair pathways. Central to the applicants work is the
hypothesis that DNA repair pathways interface with signaling and metabolic processes, via a
network of DNA damage response proteins, and that these interactions influence the efficiency
of repair. The applicant will use computational and systems biology approaches to construct
mouse cell models detailing chemotherapeutic resistance mechanisms. The main goals of his
research are to (1) identify mammalian gene products that influence the cytotoxic potential of
chemotherapeutic compounds and (2) perform targeted genetic and biochemical
characterization of signaling pathways that mediate cellular alkylation resistance. The
applicant’s research plan entails the use of high throughput phenotypic experiments, in
conjunction with gene specific mouse knock downs and selected chemotherapeutic compounds,
to identify novel gene products that influence killing by alkylating agents. In addition, he will use
mass spectrometry based molecular interaction mapping, phenotypic anchoring and
computational methods to build a detailed model of cellular resistance mechanisms. Modern
genetic and biochemical methods will also be employed to analyze specific proteins involved in
damage initiated signaling pathways, with these targeted studies used to gain detailed
mechanistic information about alkylation resistance pathways.
Active
PROTEIN INTERACTION NETWORKS IN DNA REPAIR
1 K22 ES012251-01: National Institute of Environmental Health Sciences
Transition to Independent Research (TIP)
$300,000 / 3 years
07/01/2004- 06/30/2007
DNA alkylation damage caused by environmental agents is recognized as an initiator of
carcinogenesis. Most cells have the potential to avoid this process through the coordinated
action of different DNA repair pathways. These pathways need to be extensively
choreographed at the protein level to insure the proper initiation of DNA repair and processing of
the lesion. We will therefore test the hypothesis that human proteins that interact with
key DNA alkylation repair pathways are critical for preventing agent induced cytotoxicity
and mutagenesis. To test this hypothesis and gain mechanistic insight into the coordination of
human DNA repair pathways we will undertake the following three aims. First, we will
determine the phenotype of RNAi based knock-downs of a limited set of homology identified
DNA alkylation repair genes from humans, after treatment with methyl methansulfonate (MMS)
and methyl nitrosoamide MNU (MNU). This will be done in a human lymphoblastomia cell line
(TK6) to systematically characterize the phenotype of specific protein deficient cells to alkylating
agents. Secondly, we will identify the pre-and post-treatment (MMS and MNU) protein-protein
interacting partners for this core group of important DNA alkylation repair proteins. This will be
done using yeast two-hybrid screens and mass spectrometry based identification of proteins
identified in protein pull-down experiments. Importantly, this will allow us to generate basal and
induced protein interaction maps to analyze the dynamic processes associated with cellular
responses to these mutagens. Lastly, we will build DNA alkylation resistance pathways using
RNAi based phenotyping of interacting partners and targeted DNA repair assays. All data will
be collected in a database, computationally compiled and systematically tested to identify key
components of DNA repair pathways which coordinate their mode of action. Collectively this
study will provide important mechanistic insights into the coordination of human DNA repair
pathways after challenge from an environmental alkylating agent. The combination of two
simple techniques, RNAi based phenotyping and targeted protein-protein interaction mapping,
provides us with a powerful tool to map biological pathways, better understand the coordination
and fidelity factors important for different human DNA repair pathways and systematically
explore the human genome for crucial DNA repair accessory proteins.
TOXICOGENOMIC APPROACHES TO STUDY ALKYLATION RESISTANCE
Completed
F32-ES11733: National Institute of Environmental Health Sciences
04/01/2002-8/31/2003
Individual Post Doctoral National Research
$ ~52,000 / year
Service Award (NRSA)
STATUS:
The major goals of this project were to (1) systematically screen an ordered
library of 4800 S. cerevisiae gene deletion strains for alkylation sensitive or resistant
phenotypes (2) compile the >350,000 data points into a publicly accessible database and (3)
use computational techniques to identify and examine the different cellular pathways that are
important for maintaining viability after exposure to an alkylating agent. Methods used in Goals
1-3 were designed to train the applicant in the use of genomic tools, large data set handling and
computational techniques that would be applicable to mammalian systems. Goals 1 and 2 have
been completed, while goal 3 is in progress.
AIMS: Alkylating agents are found in the form of reactive intracellular metabolites,
environmental carcinogens and chemotherapeutic compounds. After reaction with DNA,
alkylating agents have been shown to produce a number of mutagenic and / or cytotoxic lesions
which include 3-methyladenine, O6-methylguanine, and alkylphosphate moieties. DNA repair
proteins involved in direct, base excision, nucleotide excision, mismatch and recombination
repair have been shown to be extremely important in battling the cytotoxic effects of alkylation
damage. Similarly, proteins involved in cell cycle arrest, signaling and protein degradation have
also been shown to be vital in preventing alkylation induced cytotoxicity. Little is known about
the global coordination of these activities after attack by an alkylating agent or other cellular
processes important for viability after challenge by an alkylating agent. In addition to DNA repair
and cell cycle arrest, the prevention of DNA damage is another viable cellular defense
mechanism. DNA found in the nucleus is arranged around histones and complexed with other
proteins in a structure called a nucleosome. The organization of nuclear packaged DNA
suggests a role for histone and nucleosomal proteins in protecting DNA from damage. The
following specific aims are designed to help identify many of the cellular processes cells
use to combat the effects of exogenous alkylating agents and will focus on the
hypothesis that proteins involved in nucleosome architecture can modulate the effects of
DNA alkylation damage. This hypothesis will be tested using genomic, genetic and
biochemical experiments. First, we will Identify all yeast gene deletion strains sensitive to the
Sn2 alkylating agent methyl methanesulfonate (MMS). The subsequent results will be analyzed
using a number of computational approaches and a database model was designed, which
makes the results easily accessible and useful to the scientific community. Secondly, we will
implement a publicly accessible database for visual querying and data mining of high throughput
experiments performed to identify gene deletion strains sensitive to MMS. This database will
provide the means to efficiently target phenotypically affected gene deletion strains for future
work. Lastly, we will explore the role that proteins involved in histone modification and
nucleosome architecture play in modulating the effect of alkylation induced DNA damage.
References
Available on request from:
Prof. Leona D. Samson
Ellison American Cancer Society
Research Professor
Biological Engineering Division, and
Director of the Center for
Environmental Health Sciences
Massachusetts Institute of Technology
77 Massachusetts Avenue, 56-235
Cambridge, MA 02139
Tel (617) 258-7813
fax (617) 253-8099
lsamson@mit.edu
Prof. Richard P. Cunningham
Professor of Biological Sciences
Department of Biological Sciences
Associate Director for the Center for Comparative
Functional Genomics
SUNY at Albany
1400 Washington Ave.
Albany, NY 12222
Phone (518) 442-4331
Fax (518) 442-4767
moose@csc.albany.edu
Prof. Peter C. Dedon
Associate Professor of Toxicology
Biological Engineering Division, 56-787
Associate Director, Center for Environmental Health
Massachusetts Institute of Technology
77 Massachusetts Avenue, 56-235
Cambridge, MA 02139
Phone (617) 253-8017
FAX (617) 258-0225
pcdedon@mit.edu
Christine M. Lussier
P.O. Box 458
Slingerlands, NY 12159
(401) 954-8118 (Cell)
(518) 475-7685 (Home)
cmlussier6@aol.com
Academic Preparation
M.S. Environmental Science, G.P.A. 3.9 (Aug. 2003)
University of Rhode Island, Kingston, RI
Thesis Research:
The distribution and comparative sampling of mosquitoes associated with West Nile virus
in national parks in the northeastern United States
Non-Thesis Research:
Tested Deer ticks for Lyme Disease using PCR
Investigated the optimal salinity and organic content for larval
Cx. pipiens, Cx. restuans, and Cx. salinarius
Examined the pathogenicity of Entomophthora culicis against
adult and larval Cx pipiens, Cx. restuans, and Cx. salinarius
B.S. Environmental Science; minor in Biology, G.P.A. 3.4
(May 2000)
University of Maine at Machias, Machias, ME
Specializations:
Marine and terrestrial ecosystems
Secondary Education
Study Abroad, Biological Science (Jan.-June 1999)
University of Wales, Bangor, North Wales
Professional Experience
University at Albany, State University of New York (Nov 2004 –
present)
Department of Biomedical Sciences, Rensselaer, NY, 12144
Research Assistant in the Begley Laboratory
Health Research Inc. / NY State Dept. of Health (Nov. 2003-Sept.
2004)
Division of Infectious Disease, Griffin Lab, Slingerlands, NY
Assistant Research Scientist
Performed experiments in biosafety levels 2 and 3 with West Nile
virus and St. Louis encephalitis
Performed plaque assays and titrations on West Nile virus
Supervised and trained insectary staff
Identified mosquito species using PCR techniques
Conducted research on the vector competence of mosquitoes for
West Nile virus
Maintained mosquito colonies and organized the insectary
Performed indirect immunofluorescence assays (IFA) on mosquitoes
for alphaviruses, flaviviruses, and bunyaviruses
RI Department of Environmental Management (May-Sept. 2002,
2003)
Mosquito Abatement, Kingston, RI
Mosquito Technician
Trapped and speciated mosquitoes
Conducted West Nile virus bird surveillance
Performed data entry using the Arbonet database
Participated in public relations regarding mosquito control and West
Nile virus
American Biophysics (Feb. 2002-May 2003)
East Greenwich, RI
Mosquito Consultant
Taught employees to speciate mosquitoes
Speciated mosquitoes caught in Mosquito Magnet traps across
the United States
University of Rhode Island (Sept. 2002-May 2003)
Kingston, RI
Entomology Teaching Assistant
Planned, organized, taught, and evaluated undergraduate laboratory
Tutored undergraduate students
Administered and graded lecture exams
Purchased laboratory supplies
University of Rhode Island (Sept. 2001-May 2002)
Kingston, RI
Entomology Graduate Research Assistant
Organized and purchased supplies for insect pathology laboratory
Analyzed data and prepared a manuscript on the management of the
stinging ant, Myrmica rubra
Conducted pathogenicity trials on the effects of Metarhizium
anisopliae on non-target insects
Maintained mosquito colonies
University of Maine (Sept. 1997-Dec. 1998)
Machias, ME
Tutor
Tutored undergraduate students in English, writing, and literature
Research Skills
Molecular:
PCR, RT-PCR, Gel Electrophoresis, IFA, Northern/
Southern/Western Blots, Cloning recombinant DNA,
E. coli electroporation, Recovery and purification of DNA
fractionated on agarose gels
Virology:
Plaque assays, Mosquito viral inoculations, Vector
competence assays, Titrations
Cell Culture:
EYSMAY and GFBS for Entomophthora culicis,
MacConkey's agar for Serratia marcesens
Computer:
Microsoft Word, Excel, PowerPoint, Adobe InDesign
and Photoshop, Data analysis using SPSS, SAS, SYSTAT,
and BIOMSTAT
Entomology:
Mosquito and tick rearing, Mosquito and tick speciation,
Harvesting tick saliva, Tick dissections, Mosquito
and tick collection
Other:
Biosafety levels 2 and 3 training, Aseptic techniques,
Animal care, Environmental sampling, Writing
research
proposals and scientific papers; Chicken wing
vein bleeds
Presentations
“Distribution and Comparative Trapping of Mosquitoes”
University of Rhode Island, Kingston, RI (2003)
“Peritrophic Membranes as a Barrier to Parasites”
University of Rhode Island, Kingston, RI (2001)
Professional Service
Entomological Society of America
Eastern Branch, URI
Graduate Student Representative (2002-2003)
Publications
Ginsberg, H.S., Lussier, C., Manski, D., and G. Ouelette. 2002.
Management of the stinging ant, Myrmica rubra, using a baited granular
formulation of hydramethylnon, 1997. Arthropod Management Tests
127(J3).
Lussier, C., Ginsberg, H., Lebrun, R., et al. The comparative trapping of
mosquitoes associated with West Nile virus in eight national parks. Journal
of the American Mosquito Control Association. Submitted.
Lussier, C., Ginsberg, H., Lebrun, R. The distribution of mosquitoes
in eight national parks. In prep.
Ulrike Begley
UBegley@tufts-nemc.org
40 Carroll Ct
Tufts New England Medical Center
Westwood, MA 02090
Molecular Cardiology Research Institute
(781) 329 6796
Tupper Building 14
750 Washington Street
Boston, Massachussets 02111
(617) 636 9003
Residency Status: Permanent US Resident
Tufts New England Medical Center
Molecular Cardiology Research Institute
Tupper Building 14
750 Washington Street
Boston, Massachussets 02111
Education
Julius-Maximilian University,
1992-1999
Würzburg, Germany,
Diplom in Biology, Major: Biochemistry, (grade: A); Minor: Microbiology, (grade: A); and Minor:
Plant Physiology, (grade: B+).
M.S. Equivalent
University at Albany,
November 1997 – November 1998
State University of New York
Diploma Thesis Research,
Thesis title: Cloning and Characterization of the Intron Encoded
Endonuclease I-TwoI from Bacteriophage Twort,
(grade: A).
Thesis advisor: Dr. David A. Shub
Professional Employment
Research Scientist, Department
May 2003 - Present
Of Biomedical Sciences,
University at Albany
Dr. Thomas Begley Laboratory
Research Associate Molecular
May 2003 - Present
Cardiology Research Institute,
Tufts New England Medical Center
Dr. Jonas Galper Laboratory
Research Associate, Cardiovascular Division,
August 1999 – May 2003
Brigham and Women’s Hospital /
Harvard University
Supervisor: Dr. Jonas Galper
Language Skills
Fluent in English and German, working knowledge of Spanish. Lived in Germany, USA and
Spain.
Honors
Deutscher Akademischer Austauschdienst DAAD, one year scholarship for
German students to study in the United States, University at Albany, 1996–
1997; Hoechst AG Praktikum (3 month Internship), 1995; Parlamentarisches
Patenschaftsprogramm, one year scholarship organized by German
parliament and the U.S. Congress to facilitate the exchange of high school
seniors between these two countries, Wilmington, Delaware, 1988-1989.
General Statement
Senior researcher seeks an independent laboratory position that offers the opportunity to work
with little guidance from principal investigator. Applicant has the experience to design, perform
and evaluate experiments, implement and maintain quality control protocols, and initiate new
experimental approaches in consultation with principal investigator. In addition, the applicant
has the ability to oversee the daily activity of research assistants and trainees, and coordinate
their lab activities with postdoctoral fellows and the principal investigator.
Demonstrated Duties and Responsibilities
My past duties included the supervision of research assistants and coordination of their
activities between tissue culture, lab maintenance and experiments. I have evaluated and
reviewed the performance of laboratory members. In collaboration with the principal
investigator, I have developed and maintained a laboratory training program that includes
instructions for primary cultures (cardiomyocytes, human dermal cells, and human umbilical vein
endothelial cells), safety protocols, experimental design, data collection and proper statistical
measures of collected data. In addition, the applicant has significant experience in
implementing new research protocols, has produced data to satisfy a number of aims specified
in NIH grants, has played an active role in the preparation of NIH grants for review, contributed
as an author to a number of publications and has presented her work at both regional and
national scientific meetings. Lastly, my duties have also included significant responsibility for
overseeing proposed budgets and monitoring the inventory needs of the laboratory.
Qualifications
Excellent interpersonal skills; significant initiative, the ability to work independently and
supervise the work of others; maintain a harmonious and productive work environment; strong
analytical skills and the capacity to think creatively and conceptually; Excellent oral and written
communicative skills; documented ability to prioritize tasks, achieve deadlines, identify problems
and develop solutions. Advanced computer skills that include Power Point, Excel, Photoshop
and the ability to capture and filter photo-microscopic data.
Manuscripts
Fetrow, J.S., Begley (Dreher), U., Wiland, D.J., Schaak, D.L. and Boose, T.L. (1998)
Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein
interactions for the function of iso-1-cytochrome c. Protein Sci, 4: 994 - 1005
Landathler, M., Begley, U. Lau, N. C. and Shub, D.A. (2002) Two self splicing group I introns in
the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort.
Nucleic Acids Res, 30: 1935-1943
Park, H.J., Begley, U., Kong, D., Yu, H., Yin, L., Hillgartner, F. B., Osborne, T. F. and Galper, J.
B. (2002) Role of sterol regulatory element binding proteins in the regulation of G-alpha(i2)
expression in cultured atrial cells. Circ Res, 91: 32-37
Park, H.J., Kong, D., Iruela-Arispe L., Begley, U., Tang, D. and Galper, J.B. (2002) 3-Hydroxy-3-
methylglutaryl coenzyme A reductase inhibitors interfere with angiogenesis by inhibiting the
geranylgeranylation of RhoA. (2002) Circ Res, 91: 143-150
Presentations
Begley, U. Park, H. J., Kong, D., Yu, H., Yin, L., Hillgartner, F. B., Osborne, T. F. and Galper, J.
B. Sterol Regulatory Binding Protein Coordinately Regulates the Expression of Parasympathetic
genes in cultured chicken heart cells. Poster Presentation, American Heart Association National
Conference, November 2001.
Begley, U. Sterol (SREPB) Regulation of Para-Sympathetic Response Genes in Cultured Atrial
Cells. Seminar, Cardiovascular Division Brigham and Women’s Hospital, October 2001
Technical Skills
Adenovirus and retrovirus preparations and amplification, adenoviral
infection of endothelial cells, HUVECs, HDMECs, BAECs and embryonic
chick cardiomyocytes isolation and culture, monkey kidney cell line
cultures, mouse maintenance, transfections, luciferase reporter assays, in
vitro angiogenesis assay using 3D collagen gels, preparation of lipoprotein
depleted serum, preparation of collagen from rat tails, fusion protein
purifications, Light microscopy, flow cytometry (FACscan), experience with
bacterial and yeast systems, bacteriophage, plasmid and genomic DNA
isolation, cloning, PCR and RT-PCR, restriction mapping, gel
electrophoresis, site directed and random mutagenesis, protein
engineering, protein structure-function relationships, DNA sequencing,
Northern blots, Southern blots, Western Blots, oligonucleotide design and
purification, vector construction, use of pET vectors for protein expression,
cell sonication, SDS-PAGE, large scale protein preparations, UV-VIS
spectrophotometry, experience with endonuclease assays, experience with
STORM phosphoimager, experience with radioactive isoptopes.
Computer Proficiencies
PC / Macintosh / UNIX / Internet based computing, familiar with the GCG
package, MacVector, Microsoft Office, Kaliadagraph, BLAST, CLUSTAL,
INSIGHT, RasMol, ISIS Draw, Aldus Photostyler, Corel Graphics.
Experience and Accomplishments
RESEARCH PROJECTS:
Role of Autonomic Nervous System in Cardiovascular Disease
Role of Ras in the regulation of parasympathetic genes
Role of Ras Dependent Kinases in the Expression of Parasympathetic Response Genes
1999 – Present: Research Assistant, Cardiovascular Division, Brigham and Women’s Hospital,
Harvard University
• Managed daily operations, ordering and administrative responsibilities in a lab
specializing in angiogenesis
• Responsible for initiating and maintaining human, avian and monkey cell cultures
• Purified C3 toxins
• FACscan analysis to monitor apoptosis
1997 – 1998 Masters Thesis Research, University at Albany, Albany, NY, USA
• Delivered 4 presentations of results and research in progress to
members of David Shub’s lab and Marlene Belford’s lab at the
David Axelrod Institute
• Helped train undergraduate students in the Shub lab
• In addition to experiments, performed general lab maintenance and
some ordering responsibilities
1996 – 1997 Diplom Prüfungen, Julius-Maximilian University Würzburg, Germany
• Prepared and passed with high honors for final examinations
in biochemistry, microbiology and plant physiology
1995 – 1996 Studied Abroad, University at Albany, State University of New York,
ALBANY NY, USA
• Worked in the laboratory of Dr. Jacque Fetrow, and contributed to a paper
on structure-function studies for yeast cytochrome C
1992 – 1995 Julius-Maximilian University, Würzburg Germany, Undergraduate Studies
• Hoechst AG Internship, Frankfurt, Germany, worked in a industrial setting that
specialized in recombinant human insulin production.
• Supervised incoming freshman at the University
• Teaching Assistant in Reproduction and Evolutionary Biology
• Field Assistant in Plant Taxonomy
References
Prof. David A. Shub, Biological Sciences,
University at Albany, Albany, NY, 12222;
Phone: 518 442 4324
shub@cnsunix.albany.edu
Prof. Jonas Galper,
Tufts New England Medical Center
Molecular Cardiology Research Institute
Tupper Building 14
750 Washington Street
Boston, Massachussets 02111
(617) 636 9003
Dr. Ho-Jin Park
Tufts New England Medical Center
Molecular Cardiology Research Institute
Tupper Building 14
750 Washington Street
Boston, Massachussets 02111
(617) 636 9003
CV - John P. Rooney
149 Pine St., Kingston, NY, 12401
home:845-339-0948 / mobile:845-430-1196
e-mail: jprooney36@yahoo.com
Education
Bachelor of Science, Biology, minor, Criminal Justice
Rochester Institute of Technology, Rochester, NY, 2003
- Graduated High Honors, G.P.A. 3.68
- Relevant course work includes molecular biology, genetics,
bioinformatics, microbiology, introductory cell biology, analytical
chemistry, and organic chemistry.
Professional Experience
University at Albany, State University of New York, Dec 2004 – present
Research Assistant, Begley Laboratory
Molecular Biology Research Technician, July 2003 – Dec 2004
The Center for Human Genetic Studies, NewPaltz, NY
- Sequenced DNA including PCR products and palsmids on a
fluorescence
based LiCor IR2 sequencer.
- Troubleshot and modified protocol for PCR product sequencing,
resulting
in increased sequence quality.
- Performed mutational analysis by SSCP on genes of interest.
- Immortalized and maintained mammalian cell lines.
- Created cDNA of a gene of interest, ligated it into a T-
Vector, and
transformed E.Coli with the recombinant plasmid.
- Designed and synthesized numerous oligonucleotides on an ABI
3900 DNA
synthesizer.
Laboratory Skills
- PCR ,RT-PCR, and cDNA sythesis.
- DNA sequencing
- Single Stranded Conformational Polymorphism analysis
- Molecular Cloning and plasmid isolation.
- Cell culture
- Bacterial culture
- Oligonucleotide synthesis
- Restriction digests
- DNA and total RNA extraction from both whole blood and cultured cells.
Computer Skills
- Knowledge of most major genetics databases, including the NCBI
databases, PDB and GDB.
- Familiar with bioinformatics programs including GCG's Wisconsin Package,
and internet based programs including GenScan, Grail, ORFinder, 3dPSSM,
ClustalW, and SOSUI.
- Proficient with Microsoft applications including Word, Works, Excel, and
Power Point.
- Basic Unix and LAN skills.
Awards and Honors
- Consistent Dean's List status
- R.I.T. Presidential and Alumni Scholarships
- Honor Student in the Department of Biology
Publications
Higgins, JJ, Pucilowska, J, Lombardi, RQ, Rooney, JP.
Candidate Genes for Moderate Mental retardation: a
non-syndromic recessive type on chromosome 3p26.3 - 3p26.1.
Clin Genet 2004, 65: 496-500.
Higgins, JJ, Lombardi, RQ, Tan EK, Jankovic, J, Pucilowska, J,
Rooney, JP. Haplotype Analysis at the ETM2 locus in a
Singaporean sample with Familial Essential Tremor. Clin Genet
2004;(in press).
Higgins, JJ, Jankovic, J, Lombardi, RQ, Pucilowska, J, Tan EK,
Ashizawa, T, Rooney, JP. Haplotype Analysis at the ETM2 Locus
in American and Singaporean populations with Familial
Essential Tremor. Neurology 2004;62(suppl 5):A27.
References
Joanna Pucilowska, MS
Lab manager, The Center For Human Genetic Studies
Phone: 845 - 256 - 1155
David Germick, Pharm.D., MBA
Pharmacist, Wegman's Food Markets
585 - 426 - 3727
Douglas Merrill, Ph.D
Department head, Biology department, Rochester Institute of Technology
585 - 475 - 2496
merrill@mail.rit.edu (Preferred method of contact)
Laboratory of Dr. Douglas Conklin
Douglas Conklin
Principal Investigator
Matthew Ryan Curley
Research
Assistant
Kate Farley
Research Assistant
Michelle Lastro
Postdoctoral Fellow
Curriculum vitae
Douglas S. Conklin, PhD.
Assistant Professor
Department of Biomedical Sciences
Gen*NY*Sis Center for Excellence in Cancer Genomics
University at Albany
East Campus, B342A
One University Place
Rensselaer, NY 12144-2345
Phone: (518) 591-8333
Fax: (518) 525-2799
Email: dconklin@albany.edu
Education
INSTITUTION AND LOCATION
DEGREE
YEAR(s)
FIELD OF STUDY
University of Pittsburgh
BS
1985
Microbiology
University of Wisconsin-Madison
PhD
1992
Molecular Biology
Cold Spring Harbor Laboratory
Postdoc
1993-1997
Cancer Genetics
Honors
1993
Damon Runyan-Walter Winchell Postdoctoral Fellowship
1993
NIH Postdoctoral Trainee
1985
NIH Predoctoral Trainee
Positions and Employment
1983-1985
Undergraduate research, Univ. of Pittsburgh
1985-1988
NIH Predoctoral Trainee, U. of Wisconsin-Madison
1988-1992
Graduate Assistant, U. of Wisconsin-Madison
1993-1996
Damon Runyan Postdoctoral Fellow, Cold Spring Harbor
1997- 1999
Senior Fellow, Cold Spring Harbor Laboratory
1999-2000
Senior Staff Scientist, Genetica, Inc.
2001-2002
Scientist, Cold Spring Harbor Laboratory
2002-2003
Research Investigator, Cold Spring Harbor Laboratory
2003-pres
Assistant Professor, University at Albany
Selected peer-reviewed publications (in chronological order).
Jacobson, L.A., L. Jen-Jacobson, J.H. Hawdon, G.P. Owens, M.A.Bolanowski, S.W. Emmons,
M.V. Shah, R.A. Pollock and D.S. Conklin. 1988. Identification of a putative structural gene for
cathepsin D in Caenorhabditis elegans. Genetics 119: 355-363
Conklin, D.S., J.A. McMaster, M.R. Culbertson, and C. Kung, 1992. COT1, a gene involved in
cobalt accumulation in Saccharomyces cerevisiae. Mol. Cell. Biol. 12: 3678-3688
Conklin, D.S., C. Kung and M.R. Culbertson, 1993. The COT2 gene is required for glucose-
dependent divalent cation transport in Saccharomyces cerevisiae. Mol. Cell. Biol. 13: 2041-
2049
Conklin, D.S., M.R. Culbertson and C. Kung, 1994. Saccharomyces cerevisiae mutants
sensitive to the antimalarial and antiarrhythmic drug, quinidine. FEMS Letters 119: 221-228
Conklin, D.S., M.R. Culbertson and C. Kung, 1994. Interactions between gene products
involved in divalent cation transport in Saccharomyces cerevisiae. Mol. Gen. Genet. 244: 303-
311
Conklin, D.S., K. Galaktionov and D. Beach, 1995. 14-3-3 proteins associate with CDC25
phosphatases. Proc. Natl. Acad. Sci. 92: 7892-7896
Hannon, G.J., P.Q. Sun, A. Carnero, L. Xie, R. Maestro, D.S. Conklin, and D. Beach, 1999.
MaRX: An approach to genetics in animal cells. Science 283:1129-1130
Durfee, T., O. Draper, J. Zupan, D.S. Conklin, and Zambryski, P.C., 1999. New tools for protein
linkage mapping and general two-hybrid screening. Yeast 15:1761-1768
Paddison P. J. , A. A. Caudy, E. Bernstein, G.J. Hannon and D.S. Conklin, 2002. Short hairpin
RNAs (shRNAs) induce sequence-specific silencing in mammalian cells, Genes Dev. 16:948-58
McCaffrey, A.P., L Meuse, T-T T. Pham, D.S. Conklin, G.J. Hannon, and M.A. Kay, 2002. RNA
interference in adult mice. Nature 418:38-9
Carmell, M.A., L. Zhang, D.S. Conklin, G.J. Hannon, and T.A. Rosenquist. 2003, Germline
transmission of RNAi in mice. Nat Struct Biol 10:91-2
Conklin, D.S., 2003. RNA interference-based silencing of mammalian gene expression
Chembiochem. 4:1033-1039
Kumar, R., D. S. Conklin and V. Mittal, 2003. High throughput selection of effective RNAi probes
for gene silencing. Genome Res. 13:2333-40
Paddison*, PJ, Silva*, JM, Conklin*, DS, Schlabach, M., Li, M., Aruleba, S., Balija, V.,
O’Shaughnessy, A., Gnoj, L., Scobie, K., Chang,K., Westbrook,T., Sachidanandam, R.,
McCombie, WR, Elledge SJ and Hannon, GJ, 2004, A resource for large-scale RNAi based
screens in mammals. Nature 428, 427 - 431
Book chapters
McManus, M.T. and D. S. Conklin, 2003. shRNA-mediated silencing of mammalian gene
expression.
In RNAi: a guide to gene silencing, Cold Spring Harbor Press
Hannon, G. J. and D. S. Conklin, 2003. RNAi by short hairpin RNAs expressed in vertebrate
cells.
In mRNA Processing and Metabolism: Methods and Protocols, Methods in Molecular Biology
Series,
Humana Press
Recent Presentations
RNAi-based mammalian functional genomics, (invited presentation), Taconic Laboratories Inc,
October 2004
RNAi-based mammalian functional genomics, (invited presentation), University at Albany, Dept
of Biological Sciences, September 2004
Applications of RNAi in mammals, (invited presentation), University at Albany, Dept of
Chemistry, September 2004
RNAi-based mammalian functional genomics, (invited presentation), Berlex Corporation, June
2004
RNAi-based mammalian functional genomics, (invited presentation), McGill University, May
2004
RNAi-based mammalian functional genomics, (invited presentation), Roswell Park Cancer
Institute, April 2004
Mammalian applications of RNAi, (invited presentation), GE Global Research, December 2003
High throughput RNAi in Mammals, (invited presentation), IBC's 2nd International Conference
on RNAi, Boston, November 2003
RNAi in mammalian functional genomics, (invited presentation), RNAi Symposium, David
Axelrod Institute, October 2003
Mammalian applications of RNAi, (invited presentation), 6th Annual PEACE Conference, Mont
Tremblant, September 2003
Theory and Applications of RNAi, Gordon Research Conference, 2003
Mammalian applications of RNAi, (invited presentation), University of Pennsylvania, 2003
Mammalian applications of RNAi, (invited presentation), University of Southern California, 2003
Mammalian applications of RNAi, (invited presentation), Dartmouth University, 2003
Mammalian applications of RNAi, (invited presentation), University at Albany, 2003
Mammalian applications of RNAi, (invited presentation), Aventis iLab Workshop, Wiesbaden,
2003
Mammalian applications of RNAi, (invited presentation), Drexel University, 2002
Mammalian applications of RNAi, (invited presentation), Ambion, 2002
Mammalian applications of RNAi, (invited presentation), Pfizer, 2002
Large scale hypomorphic mutation analysis of mammalian genomes, D.S. Conklin, P. J.
Paddison, J-M Silva, R. Sachidanandam, G.J. Hannon, (platform presentation) Genome
Sequencing & Biology Meeting Cold Spring Harbor Laboratory, 2002
Teaching:
Guest lecture in BMS 601 “Tyrosine kinases”
Guest lecture in Biology 248A “Enzymes of RNAi”
Patents:
Beach, D., G.J. Hannon, D.S. Conklin, and P.Q. Sun, Modified retroviral vectors.
Serial No. 6,025,192
Beach, D., G.J. Hannon, S. Hammond, E. Bernstein, A.A. Caudy, D.S. Conklin, and P.J.
Paddison. Methods and Compositions for RNA interference. Serial No. 60/243,097 (pending)
Matthew Ryan Curley
mcurley@bucknell.edu
College Address Permanent Address
Box c0175 Bucknell University 49 Gretel Terrace
Lewisburg, PA 17837 Ballston Lake, NY 12019
(570) 850-6385 (518) 877-7928
Education
Bucknell University, Lewisburg, PA (Expected Date of Graduation May 2004)
Bachelor of Science
Major: Cell Biology/Biochemistry
Minor: Art
Cumulative GPA: 3.42
Relevant Courses: Molecular Biology, Cell Biology, Biochemistry I, Biochemical Methods,
Virology, Immunology, Organic Chemistry, Inorganic Chemistry, Analytical Chemistry, Biological
Physical Chemistry
-
Teaching Assistant (Fall and Spring 2003, Fall 2002)
-
Deans List 4 of 7 Semesters
-
Member of Alpha Lambda Delta Freshman Honor Society (2001)
Relevant Experience
Research Assistant, Bucknell University (Summer 2002, Spring and Fall 2003)
Biology Department, Professor Mary Howe
-
Participated in study of kinetochore proteins in C. elegans
Research Assistant, New York State Dept. of Health Wadsworth Labs (Summer 2001)
-
Studied cell membrane structure/function in single cell organisms
Additional Experience
Intern, CSEA Labor Union
Marketing Department, Employee Benefit Fund (Summer 2000)
-
Data Base maintenance, Filing, Calling on Members
Records Maintenance (Summer 2003)
-
Data Base maintenance, Construct Mailings, Filing
Relevant Skills
-
Biological: Gel electrophoresis, Northern Blot, Southern Blot, DNA Sequencing, PCR, Cell
Culturing, ELISA Assay, Fluorescent Microscopy
-
Computational: Microsoft Office Programs, Sigma Plot, Swiss-Prot
Kate Farley
652 Morris St. Apt. 2
(518) 435-9085
Albany, NY 12206 kmefarley@yahoo.com
Objective
Obtain a position that will utilize my education in the biological sciences.
Education
Fall 2002
University at Albany
Albany, NY
Graduate Student – School of Public Health
1997 - 2002
University at Albany
Albany, NY
B.S. in Biology
B.A. in Psychology
Work Experience
2002 – present
Research Technician I Wadsworth Center Albany, NY
2002 - 2003
Graduate Assistant Peptide Synthesis Facility, Wadsworth Center
Synthesized peptides using ABI 477 synthesizer
Cleaved and deprotected synthetic peptides
Purified peptides using preparative HPLC with System Gold Software
2001–2002
Wadsworth Center
Albany, NY
Student Assistant in the lab of Dr. Erasmus Schneider
Gel electrophoresis and Western blots
Extracted RNA and Performed real time PCR
Analyzed data obtained from experiments
1997–2002
Our Lady of Lourdes Summer Care
Utica, NY
Supervise junior level employees
Supervised children from age 3 through 12
Organized trips and events
Lab Skills:
Western Blotting, Gel electrophoresis, RNA extraction, PCR and real
time PCR, Peptide synthesis, preparative HPLC, Tissue culture and
transfection of mammalian cells, virus titers, DNA plasmid purification,
ELISA, Radio-immuno assays, Radioreceptor assays, Antibody
purification and conjugation
Computer Skills:
Microsoft Windows, Microsoft Word, Excel, PowerPoint, Internet and
Email, Software used to run the Light Cycler for quantitative PCR,
GraphPad software/Prism 3.0
References:
References furnished upon request
Michele T. Lastro
438 Morrison Hall
1126 Trumbull Corners Road
Cornell University
Newfield, NY 14867
Ithaca, NY 14853
Home Phone (607) 564-3380
Phone (607) 255-3030
Email mtl6@cornell.edu
E D U C A T I O N
Ph.D. Cornell University, Department of Animal Science, Degree expected 2004
Minors: Pharmacology and Physiology
Dissertation Topic: Signal transduction pathways involved in the initiation of bovine oocyte
maturation.
M.S. Cornell University, Department of Animal Science, 1/2000
Minor: Physiology
Thesis: Cytoplasmic Polyadenylation and its Role in Bovine Oocyte Maturation: An Analysis of
Cyclin B1 and B2 mRNA Transcripts.
B.S. Cornell University
5/1994
R E S E A R C H E X P E R I E N C E
Graduate Research Assistant
Cornell University Ithaca,
NY
Supervisor: W. Bruce Currie
September, 1997-present
Routinely perform in vitro maturation, fertilization and culture of bovine oocytes/embryos for
use in weekly experiments
Used RT-PCR to develop probes to screen a bovine cDNA library to obtain cyc B2 cDNA
Cloned and sequenced full-length bovine cyclin B2 cDNA GenBank accession # AF080219
Performed mutagenesis to delete 40 bp fragment from bovine cyclin B2 cDNA to perform
quantitative PCR analysis
Adapted RT-PCR protocol to perform cytoplasmic polyadenylation analysis on bovine cyclin
B1, B2, A and mos transcripts
Performed RNA gel-shift assays on 3’ sequence specific oligonucleotides to assess RNA
binding protein behavior during cytoplasmic polyadenylation
Perform cAMP assays to assess adenylate cyclase activity in bovine cumulus-oocyte
complexes in response to pharmacological manipulation
Use confocal microscopy and calcium imaging techniques to assess calcium response in
oocytes during in vitro maturation and to view calcium movement through gap junctions
Also proficient in the following laboratory techniques:SDS-PAGE, immunocytochemistry,
western analysis, immunoprecipitation, RNase protection assays, mammalian somatic cell
culture
Maintain radioisotope records and inventories
Laboratory Technician
Cornell University Ithaca,
NY
2/1995- 8/1997
Technician to graduate students and research associates studying transcriptional regulation
during early embryonic development
Managed embryology laboratory, ordered supplies, made reagents
Routinely performed in vitro maturation, fertilization, culture of bovine oocytes/embryos
Supervised undergraduate students
Laboratory Technician
Cornell University Ithaca, NY
8/1994- 8/1996
Managed large embryology laboratory, ordered supplies, made reagents
Managed large rabbit colony
Performed surgical and non-surgical embryo flushing and transfer in rabbits and cattle
Assisted with ultrasound-guided oocyte pick-up in cows and heifers
Used computer-Assisted Sperm Analysis (CASA) to compare different bovine sperm
separation techniques
T E A C H I N G E X P E R I E N C E
Graduate Teaching Assistant
Cornell University Ithaca,
NY
Courses: Domestic Animal Biology I and II
Domestic Animal Reproduction
Gamete Physiology
Designed laboratories, written exercises and quizzes for basic animal biology and
reproduction courses
Graded labs, quizzes, exams
Graded and critiqued written exercises and provided feedback to students
Maintained records of course grades
Ran review sessions and discussion sections and guided student-led discussions of
scientific papers
Taught undergraduate students how to read and evaluate scientific articles
Invited to deliver in-class lectures on oocyte development, maturation and ovulation and the
cell cycle during early embryo development
Supervised undergraduate teaching assistants
Counseled students individually with academic and personal problems
Additional Teaching Experience
Teach molecular biology techniques to undergraduate researchers
Co-Taught short course in Embryo Transfer
Volunteered to teach science to third-grade students at Northeast Elementary School
P R O F E S S I O N A L E X P E R I E N C E
Business Intern, OptiGen, LLC
Ithaca, NY
1/1999- 8/1999
Developed and wrote organization’s first handbook of personnel policies
Researched and helped secure health insurance and retirement benefits for employees
Used my interest in start-up biotech companies and scientific knowledge to help implement
a detailed marketing plan for a company that performs genetic testing for inherited diseases
in dogs
Assembled detailed binder describing the genetics of eye disease, the technology behind
OptiGen’s tests and laboratory procedures to be used as the primary resource during
meetings with prospective clients
Wrote scientific articles geared towards the lay public
P R E S E N T A T I O N S A N D S E M I N A R S
Cornell University Graduate Student Symposium 2003
Title: Characterization of Bovine Cumulus Cell and Oocyte Adenylate cyclases
Society for the Study of Fertility (SSF) 1999 meetings Aberystwyth, Wales
Title: Preventing Polyadenylation Delays but does not Prevent Maturation of Bovine
Oocytes: Changes in Cyclin B1 and B2 Transcripts
Cornell University Graduate Student Symposium 1999
Title: Cytoplasmic Polyadenylation During Oocyte Maturation
Cornell Department of Animal Science Seminar 1998
Title: B-Cycling: The IVM Trail Cytoplasmic Polyadenylation and its Role During in vitro
Maturation of Bovine Oocytes
P U B L I C A T I O N S
M Lastro, GG Ignotz, WB Currie 1999 Preventing Polyadenylation Delays but does not Prevent
Maturation of Bovine Oocytes: Changes in Cyclin B1 and B2 Transcripts. Journal of
Reproduction and Fertility v 23 p43.
publications in progress:
Characterization of Bovine Cumulus Cell and Oocyte Adenylate Cyclases
Calcium Movement During Oocyte Maturation: An Analysis of Cumulus-Oocyte Gap Junctional
Communication
Calcium as a trigger of Cytoplasmic Polyadenylation During Bovine Oocyte Maturation
I N T E R E S T S A N D A C T I V I T I E S
Volunteer with Cornell Companions
Visit mentally and physically disabled children with my three dogs
Volunteer with Expanding Your Horizons Conference
The conference is designed to introduce junior high-aged girls to career opportunities
available in
math, science, and engineering through hands-on workshops.
Spoke at several area middle schools to describe the conference and recruit attendees.
Rescue and place abused and abandoned dogs
Enjoy traveling, gourmet cooking, running, water sports and an avid sports fan
R E F E R E N C E S
W. Bruce Currie
Jeanette Felix
Department of Animal Science
OptiGen LLC
438 Morrison Hall
Cornell Business & Technology Park
Cornell University
767 Warren Road Suite 300
Ithaca, NY 14853
Ithaca, NY 14850
(607) 255-2888
(607) 257-0301
W. Ron Butler
Department of Animal Science
203 Morrison Hall
Cornell University
Ithaca, NY 14853
(607) 253-3870
Laboratory of Dr. Chittibabu Guda
Chittibabu Guda
Principal Investigator
Purnima Ambati-Guda
Postdoctoral Fellow
CHITTIBABU GUDA, Ph.D.
A208, East Campus
Gen*NY*Sis Center for Excellence in Cancer Genomics
Department of Epidemiology and Biostatistics
1 University Place, Rensselaer, NY 12144
( (518) 591-8339, Fax (518) 525-2799
WORK HISTORY
Assistant Professor (2004-Current)
University at Albany, State University of New York
Gen*NY*Sis Center for Excellence in Cancer Genomics
Department of Epidemiology & Biostatistics
Instructor in Bioinformatics (2000-2004)
BIOINFORMATICS CERTIFICATION PROGRAM
Department of Biosciences, UCSD Extension, La Jolla, CA 92093
Bioinformatics Scientist (2001-2004)
Post-Graduate Researcher (1999-2001)
BIOINFORMATICS CORE @ LIPID MAPS, MITOPROTEOME, JCSG, PDB
University of California San Diego
San Diego Supercomputer Center, La Jolla, CA 92093
Post-Doctoral Research Associate (1996-99)
BIOINFORMATICS & MOLECULAR BIOLOGY
Iowa State University, Ames, IA 50011
Graduate Teaching & Research Assistant, (1992-96)
Department of Botany & Microbiology
Auburn University
, Auburn, AL 36849
EDUCATION
Ph. D., MOLECULAR BIOLOGY, (1996)
Auburn University, Auburn, AL 36849
M. Sc (Ag), GENETICS & PLANT BREEDING, (1992)
AP Agricultural University, Hyderabad, India
B. Sc. (Ag), AGRICULTURAL SCIENCES, (1990)
AP Agricultural University, Hyderabad, India
TEACHING EXPERIENCE
COURSES
*The first two are core courses in the Bioinformatics Certification Program at the UCSD
Extension
*Tools and Algorithms in Bioinformatics, UCSD Extension (2001-2004)
*Advanced Tools and Algorithms in Bioinformatics, UCSD Extension (2002-2004)
Protein Data Analysis and Modeling in Bioinformatics, UCSD extension (2000-2001)
Recombinant DNA techniques-Lab, Auburn University (1995-96)
Introduction to Plant Biology-Lab, Auburn University (1994-96)
TUTORIALS AND WORKSHOPS
Presented bioinformatics training workshops at Pfizer Global R&D, La Jolla, CA, 2003
Taught a tutorial on “Bioinformatics Tools and Algorithms” at the International Conference on
Computer Science and its Applications (ICCSA), July 2003 at National University, San Diego, CA.
Chittibabu Guda …… Page 2
BIOINFORMATICS RESEARCH EXPERIENCE
ALGORITHM DEVELOPMENT
Developed the following new algorithms for protein sequence or structure data analysis.
pTARGET
A new algorithm for predicting subcellular locations of proteins based on functional
domain occurrence patterns and amino acid compositional differences.
This method could predict proteins targeted to nine different subcellular locations in
eukaryotic
cells at high accuracy rate.
MITOPRED
A genome-scale method for predicting nucleus-encoded mitochondrial proteins in
eukaryotes.
Complete proteomes of six eukaryotic species have been analyzed using this
method and
nucleus-encoded mitochondrial proteins were estimated for each species.
CE-MC
A new algorithm for multiple protein structure alignment using Monte Carlo
optimization.
Multiple structural alignment is performed based on the differences in the C-
coordinate distances by iterative exploration of the search space using random
numbers.
About 10,000 lines of code completely written in C and C++.
A standalone version of CE-MC for local installation has been developed and
released. This
tool is accessible at http://cemc.sdsc.edu
WEBSERVER & DATABASE DEVELOPMENT
MITOPRED WEB SERVER
A web server for the prediction of nucleus-encoded mitochondrial proteins
Provides pre-calculated predictions for the entire SwissProt/TrEMBL eukaryotic
proteins
Implemented in PERL/CGI interface, accessible at http://mitopred.sdsc.edu
CE-MC WEB SERVER
A web server for the alignment of multiple protein structures using Combinatorial
Extension (CE) and Monte Carlo (MC) Optimization.
Users could upload local coordinate files and perform multiple alignments against all
structural neighbors in Protein Data Bank (PDB). Implemented in C/C++/CGI
interface, accessible at http://cemc.sdsc.edu
SledgeHMMER WEB SERVER
A web service for batch searching of protein sequences against Pfam database
Provides pre-calculated Pfam search results for all protein sequences in the
SwissProt/TrEMBL databases in three different search modes i.e., merged, glocal
and local
Implemented in PERL/CGI interface, accessible at http://SledgeHMMER.sdsc.edu
DMAPS DATABASE
Database of Multiple Alignments for Protein Structures
Provides pre-calculated multiple structure alignments for all structural neighbors in PDB
Implemented in PERL/C/CGI interface, accessible at http://dmaps.sdsc.edu
GENOME-SCALE DATA ANALYSIS
Through understanding of the commonly used bioinformatics tools
including NCBI-Toolkit, HMMER, INTERPRO, CLUSTALW, PHYLIP, Post-translational
site prediction tools and structure alignment tools etc.
Extensive experience in local installation, testing and seamless
integration of various bioinformatics tools for high-throughput genome-scale data
analysis.
Developed several customized data analysis pipelines for proteome-scale
functional annotation.
Developed several automated pipelines for target identification in protein
structure determination.
Developed methods for domain boundary prediction, profile building and
phylogenetic data analysis
Chittibabu Guda …… Page 3
COURSEWORK IN COMPUTER SCIENCE & BIOINFORMATICS
*Coursework was completed partly at Iowa State University and partly at UC San Diego.
C++ Programming I & II
Java Programming I & II
Programming in PERL/CGI
Relational Database Systems
Data mining and Data Warehousing
Concepts in Computational Molecular Biology
Computer Analysis of Genome Information
Microarray Technologies-Workshop
Biostatistics
Pattern Recognition for Bioinformatics
COMPUTATIONAL & PROGRAMMING SKILLS
Extensive experience in developing bioinformatics algorithms and applications using C/C++, PERL and
CGI, on UNIX environment.
Expert in genome-scale data analysis using UNIX/LINUX clusters, batch processing of high-throughput
data on supercomputers and developing automated pipelines.
Experience in SQL and development of relational databases using mSQL, MS-Access & ORACLE
MOLECULAR BIOLOGY EXPERIENCE
My Ph.D. dissertation work was in plant molecular biology. I have extensive theoretical,
experimental and teaching experience in genetics, biochemistry and molecular biology. I
worked on several wet lab research projects including:
Expression of biodegradable elastomers in bacteria and plants
Expression of foreign genes in tobacco chloroplasts
Transformation and production of transgenic soybean plants for disease resistance
Expression of green fluorescent protein (GFP) and Acetyl CoA Carboxylase (ACCase)
genes in
Arabidopsis.
RESEARCH GRANTS
Project Leader, PACI REU Grant, 2003 to develop a standalone version of the Multiple Structure
Alignment Program based on Monte Carlo Optimization.
INVITED LECTURES
Guest lecture at the Department of Biological Sciences, Cal State University, San Marcos, CA, February,
2004
Panel Member, Panel Discussion on “Challenges in Bioinformatics”, ICCSA, July 2003, San Diego
Speaker, Workshop on Computer Aided Drug Design (CADD), Summer, 2001 at the UCSD
Extension.
CONSULTING EXPERIENCE
External Bioinformatics Consultant on the NIH MARC U*STAR Grant, Office of Biomedical Research
& Training, California State University, San Marcos, CA.
AWARDS
‘Instructor of the Year’ Award presented by the Dept. of Biosciences at the UCSD
Extension, 2002
DOE Travel Award for Oral Presentation at the Pacific Symposium on Biocomputing
(PSB) 2001, Hawaii
Certificate for Academic Excellence by Auburn University, 1995
UNIDO (United Nations Industrial Development Org.) Travel Award for Poster
Presentation in the International Symposium on Plant Molecular Biology and
Biotechnology, New Delhi, 1994
AP Agricultural University Graduate Fellowship, India, 1990-1992
Chittibabu Guda …… Page 4
PUBLICATIONS
1) Guda C. Tools and Algorithms in Bioinformatics. World Scientific Publishing Corporation,
Singapore. (In Preparation)
2) Cotter D, Guda C, Saunders B, Subramaniam S. LMLPD: LIPID MAPS Lipid Proteome
Database (In Preparation)
3) Guda P, Guda C, Fahy E, Subramaniam S. Reconstruction of human mitochondrial
metabolic pathways (In Preparation)
4) Guda C, Chukkapalli G, Bourne PE, Shindyalov IN. DMAPS: A Database of Multiple
Alignments for Protein Structures. (In preparation)
5) Meller N, Guda C, Schwartz MA, Ravichandran KS. CZH proteins - New family of Rho
GEFs. Journal of Cell Science (In preparation)
6) Guda C, Subramaniam S. pTARGET: A domain-based method for predicting protein sub-
cellular localization. Biochemistry (In preparation)
7) Guda C, S. Lu, Scheeff ED, Bourne PE, Shindyalov IN. 2004. CE-MC: A Multiple Protein
Structure Alignment Server. Nucleic Acids Research, 32: W100-W103 [Pubmed]
8) Guda C, Guda P, Fahy E, Subramaniam S. 2004. MITOPRED: a web server for
genome-scale prediction of mitochondrial proteins. Nucleic Acids Research, 32: W372-
W374 [Pubmed]
9) Chukkapalli G, Guda C, Subramaniam S. 2004 SledgeHMMER: A web server for batch
searching of Pfam database Nucleic Acids Research, 32: W542-W544 [Pubmed]
10) Guda C, Fahy E, Subramaniam S. 2004. MITOPRED: A genome-scale method for
prediction of nuclear-encoded mitochondrial proteins. Bioinformatics, 20:1785-1794
[Pubmed]
11) Heine A, Canaves JM, von Delft F, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi
S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock
HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM,
Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Rodrigues K,
Schwarzenbacher R, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez
J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. 2004. Crystal
structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 Å
resolution, Proteins, 56:387-391 [Pubmed]
12) Schwarzenbacher R, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi
S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock
HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM,
Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL,
Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B,
Wolf G, Hodgson KO, Wooley J, Wilson IA. 2004. Crystal structure of an iron-containing
1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 Å
resolution, Proteins, 54:174-177 [Pubmed]
13) Schwarzenbacher R, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi
S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock
HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM,
Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL,
Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B,
Wolf G, Hodgson KO, Wooley J, Wilson IA. 2003. Crystal structure of uronate isomerase
(TM0064) from Thermotoga maritima at 2.85 Å resolution, Proteins, 52:142-145
[Pubmed]
14) Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A,
Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E,
Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller
MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens
RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Taylor SS,
Hodgson KO, Wooley J, Wilson IA. 2003. Crystal structure of a zinc-containing glycerol
dehydrogenase (TM0423) from Thermotoga maritima at 1.5 Å resolution. Proteins,
50:371-374 [Pubmed]
Chittibabu Guda …… Page
5
15) Kuhn P, Lesley SA, Mathews II, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA,
Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Hodgson KO,
Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, McMullan D,
McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K,
Selby TL, Spraggon G, Stevens RC, Taylor SS, Van Den Bedem H, Velasquez J, Vincent
J, Wang X, West B, Wolf G, Wooley J, Wilson IA. 2002. Crystal structure of thy1, a
thymidylate synthase complementing protein from Thermotoga maritima at 2.25 Å
resolution. Proteins, 49:142-145 [Pubmed]
16) Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock
HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller
MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elslinger MA, Wooley J,
Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC. 2002. Structural genomics
of the Thermotoga maritima proteome implemented in a high-throughput structure
determination pipeline. Proceedings of the National Academy of Sciences, USA
99:11664-11669 [Pubmed]
17) Guda C, Scheeff ED, Bourne PE, Shindyalov IN. 2002. Comparative Analysis of Protein
Structure: New Concepts and Approaches for Multiple Structure Alignment. In: Protein
Structure Prediction: Bioinformatics Approach, pp.451-459
18) Guda C, Scheeff ED, Bourne PE, Shindyalov IN. 2001. A new algorithm for the
alignment of multiple protein structures using Monte Carlo optimization. Proceedings of
the Pacific Symposium on Biocomputing (pdf ), pp. 275-286 [Pubmed]
19) Guda C, Lee SB, Daniell H. 2000. Stable transformation of chloroplasts using a
universal integration vector. Plant Cell Reports, 19:257-262 [Abstract]
20) Daniell H, Guda C. 1997. Biopolymer production in microorganisms and plants (Review
Article). Chemistry and Industry, 14: 555-558
21) Brixey J, Guda C, Daniell H. 1997. The chloroplast psbA promoter is more efficient in E.
coli than the T7 promoter for hyperexpression of a foreign protein. Biotechnology
Letters 19: 395-399 [Abstract]
22) Daniell H, Guda C, McPherson DT, Zhang X, Urry DW. 1997. Hyper expression of a
synthetic protein based polymer gene. Methods in Molecular Biology, 63: 359-371
[Pubmed]
23) Urry DW, McPherson DT, Xu J, Daniell H, Guda C, Gowda DC, Jing N, Parker TM.
1996. Protein- Based Polymeric Materials: Syntheses and Properties. In: The Polymeric
Materials Encyclopedia: Synthesis, Properties and Applications, pp. 2645-2699, CRC
Press, Boca Raton
24) Guda C, Zhang X, McPherson DT, Xu J, Cherry JH, Urry DW, Daniell H. 1995.
Hyperexpression of an environmentally friendly synthetic polymer gene. Biotechnology
Letters, 17: 745-750
25) Zhang X, Guda C, Datta R, Dute R, Urry DW, Daniell H. 1995. Nuclear expression of an
environmentally friendly synthetic protein based polymer gene in tobacco cells.
Biotechnology Letters, 17:1279-1284
26) Daniell H, Zhang X, Guda C., Urry DW. 1995. Plastics from Plants. Highlights of
Agricultural Research, 42: 18-19
27) Daniell H, Guda C, Singh NK, Weete JD, Cherry JH. 1994. Photosynthesis, epicuticular
wax and lipid changes in cowpea cultivars grown under hyperthermic conditions. In:
Biochemical and Cellular Mechanisms of Stress Tolerance in Plants (J.H. Cherry ed.)
NATO ASI Series, Vol. H 86: 213-227, Springer-Verlag, Heidelberg.
PURNIMA AMBATI-GUDA
A208, East Campus
Gen*NY*Sis Center for Excellence in Cancer Genomics
1 University Place, Rensselaer, NY 12144
( (518) 591-8339, Fax (518) 525-2799
WORK EXPERIENCE
Programmer Analyst II (2002-2004)
Bioinformatics Core, Mitoproteome Group
San Diego Supercomputer Center
University of California San Diego, La Jolla, CA 92093
Post-Graduate Researcher (2000-2001)
Bioinformatics Core, Protein Data Bank
San Diego Supercomputer Center
University of California San Diego, La Jolla, CA 92093
Senior Research Fellow (1997-1999)
Council of Scientific and Industrial Research
New Delhi, India
Junior Research Fellow (1995)
Indian Council of Agricultural Research
New Delhi, India
EDUCATION
Ph.D., BIOCHEMICAL ENGINEERING, 2000
Dept of Chemical Engineering,
Andhra University, Visakhapatnam, AP 530 003, India
M.Sc., MICROBIOLOGY, 1994
Nagarjuna University, AP 522 510, India
B.Sc. BIOLOGY, 1992
Andhra University, Visakhapatnam, AP 530 003, India
BIOINFORMATICS EXPERIENCE
Advanced PERL programming and developing automated pipelines for data analysis.
Experience in UNIX and shell programming.
Working knowledge in the use of Access database, Oracle, SQL servers, Excel etc
Experience in using different platforms such as SGI, SOLARIS, LINUX.
Reconstruction of mitochondria-associated metabolic and disease pathways.
Extensive experience in curation and annotation of nucleus-encoded mitochondrial
proteins.
Developed new methodology for the analysis of Voltage-Gated Ion Channel Proteins.
Extensive experience in local installation and evaluation of open source bioinformatics
applications.
Expert in using BLAST suite, HMMER suite, SRS, GCG and other bioinformatics
software.
AWARDS
Senior Research Fellowship awarded by the Council of Scientific and Industrial
Research (CSIR), New Delhi, INDIA, 1997
Junior Research Fellowship awarded by the Central Institute of Freshwater Aquaculture,
Indian Council of Agricultural Research (ICAR), New Delhi, INDIA, 1995
Senior Research Fellowship awarded by the Central Institute of Freshwater Aquaculture,
Indian Council of Agricultural Research (ICAR), New Delhi, INDIA, 1995
PUBLICATIONS
1.
Guda P
, Guda C, Cotter D and Subramaniam S. Reconstruction of human mitochondrial
metabolic pathways (In preparation)
2.
Guda P,
Boojala V. B. Reddy, Philip E. Bourne, Maurice Montal. Analysis of voltage-gated
ion channel sequences: conserved and semi-conserved patterns in voltage sensing and
pore forming structural domains (In preparation)
3.
Mendu D, Guda P, Ayyanna C. (2004) Purification and immunological characterization of -
amylase from Bacillus licheniformis. Enzyme and microbial technology (In Press)
4.
Guda C, Guda P, Fahy E and Subramaniam S. (2004) MITOPRED: a webserver for
genome-scale prediction of mitochondrial proteins. Nucleic Acids Research, 32:W372-
W374
5.
Cotter D, Guda P, Fahy E. and Subramaniam S. (2004) MitoProteome : Mitochondrial
protein sequence database and annotation system.. Nucleic Acids Research, 32:D463-
D467
6.
Mendu D, Ambati P, Ramesh, Ayyanna C. (2003) Purification of -Amylase from Bacillus
licheniformis by Chromatofocusing and Gel filtration chromatography. World Journal of
Microbiology and Biotechnology. 18:547-550
7.
Ambati P,
Ayyanna C. (2000) Optimization of medium constituents and fermentation
conditions for citric acid production from palmyra jaggery using Response Surface Method,
World Journal of Microbiology and Biotechnology 17:331-335
8.
Ambati P.
(2000). Studies on physico-chemical and nutritional paramemters for citric acid
production of palmyra jaggery using Aspergillus niger. Ph.D Thesis, Andhra University, India.
ABSTRACTS
1.
Boojala V B Reddy, Guda P, Maurice Montal, Philip E.Bourne. 2001. A profile-based
consensus sequence alignment method for progressive multiple alignment of evolutionary
related protein sequences: Analysis of voltage-gated ion channel proteins. In the PSB
2001, Hawaii. (Poster)
2.
Guda P,
Boojala V B Reddy, Maurice Montal, Philip E Bourne. 2000. Sequence data
analysis of voltage-gated ion channel proteins. In the ISMB 2000 meetings held at SDSC,
UCSD. (Poster)
3.
Ambati P
, Ayyanna C. 1999. Effect of trace metal ions and minerals on citric acid
production, in The 8th Asian Pacific Confederation of Chemical Engineers, Thailand.
(Oral Presentation)
4.
Ambati P
, Ayyanna C. 1998. Effect of alcohols on citric acid production, in CHEMCON-98,
held at Andhra University, AP, India. (Oral Presentation)
5.
Ambati P
, Ayyanna C. 1996. Comparative studies on citric acid production from various
millets using Aspergillus niger, in The First International Symposium on Microbial
Exploitation, held at Banaras Hindu University, MP, India. (Oral Presentation)
6.
Ambati P,
Ayyanna C. 1995. Studies on production of citric acid by solid state fermentation
using Aspergillus niger, in The 47th Indian Pharmaceutical Congress held at Andhra
University, AP, India. (Oral Presentation)
Laboratory of Dr. Igor Kuznetsov
.
Igor Kuznetsov
Principal Investigator
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Photocopy this page or follow this format for each person.
NAME
POSITION TITLE
Igor B. Kuznetsov, Ph.D.
Assistant Professor
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and
include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
Novosibirsk State University
(Novosibirsk, Russian Federation)
M.S.
1992
Cytology and Genetics with
minor in Mathematics
Mount Sinai School of Medicine/NYU, NY, NY
M.Phil.
2001
Biomathematics
Mount Sinai School of Medicine/NYU, NY, NY
Ph.D.
2003
Biomathematics
Mount Sinai School of Medicine/NYU, NY, NY
Postdoctoral
training
2003
Biomathematics
B. Positions and Honors.
Positions:
1992-1993
Research Trainee
Institute of Cytology and Genetics,
Russian Academy of Sciences
1993-1997
Junior Research Associate
Institute of Cytology and Genetics,
Russian Academy of Sciences
1997-2003
Graduate Research
Assistant
Mount Sinai School of Medicine, NYU
2003
Postdoctoral Fellow
Mount Sinai School of Medicine, NYU
2003-2004
Research Associate
University of Kansas
2004-
present
Assistant Professor
Department of Epidemiology and Biostatistics
Gen*NY*sis Center for Excellence in Cancer
Genomics
State University of New York at Albany
Honors and Fellowships:
1987-1992
Novosibirsk State University, Special Stipend Recipient
1992
Award from the State Department of Science of the Russian Federation for the
work presented at the 30th Annual International Conference “Students and
Scientific Progress”
1997-1998
City University of New York Graduate Fellowship Award
2001
Mount Sinai Graduate School of Biological Sciences, Travel Award Recipient
C. Patents and selected peer-reviewed publications
Peer-Reviewed Publications (in reverse chronological order):
I.Kuznetsov and S.Rackovsky, 2004, Comparative computational analysis of prion proteins
reveals two fragments with unusual structural properties and a pattern of increase in
hydrophobicity associated with disease-promoting mutations. Protein Science, 13:3230-3244.
I.Kuznetsov and S.Rackovsky, 2004, Class-specific correlations between protein folding rate,
structure-derived and sequence-derived descriptors. Proteins: Structure, Function and
Bioinformatics, 54:333-341.
I.Kuznetsov and S.Rackovsky, 2003, Similarity between the C-terminal domain of the prion
protein and chimpanzee cytomegalovirus glycoprotein UL9. Protein Engineering, 16(12): 861-
863.
I.Kuznetsov and S.Rackovsky, 2003, On the properties and sequence context of structurally
ambivalent fragments in proteins. Protein Science, 12:2420-2433.
I.Kuznetsov and S.Rackovsky, 2002, Discriminative ability with respect to amino acid types:
assessing the performance of knowledge-based potentials without threading. Proteins:
Structure, Function and Genetics, 49:266-284.
I.Kuznetsov, P.Morozov, Yu.Matushkin, 1998, Alpha-helix retention in prion proteins. Genetika,
34:183-189
I.Kuznetsov, P.Morozov, Yu.Matushkin, 1997, Prion proteins: evolution and preservation of
secondary structure. FEBS Letters, 412:429-432.
I.Kuznetsov and P.Morozov, 1996, GEOMETRY: a software package for nucleotide sequence
analysis using statistical geometry in sequence space. Bioinformatics (CABIOS), 12:297-301.
I.Kuznetsov and S.Rodin, 1995, Comparative computational analysis of thermodynamic
parameters of the transfer RNA secondary structure. Genetika, 31:1566-1574.
S.Rodin and I.Kuznetsov, 1993, Theoretical study of the features of compensatory substitutions
in the stem regions of the transfer RNA. Genetika, 29:1256-1266.
C. Research Support.
Start-up funds from the University at Albany – State University of New York
D. Other
Reviewing for research journals:
PROTEINS: Structure, Function and Bioinformatics
Protein Engineering
Professional Societies:
International Society for Computational Biology (ISCB)
American Society for Biochemistry and Molecular Biology (ASBMB)
Teaching:
Spring, 2004 Co-director, ‘Introduction to Bioinformatics’ graduate course (BIOL 701/EECS 700,
University of Kansas)
Summer, 2004 Bioinformatics workshops at the University of Kansas and Pittsburg State
University
Laboratory of Dr. Scott Tenenbaum
.
Scott Tennenbaum
Principal Investigator
Evelina Loghin
Research Technologist
Georgi G Shablovsky
Research Associate
Christopher Zalesk
Bioinformatics
Timothy Edward Baroni Postdoctoral Fellow
Francis J. Doyle
Bioinformatics
Michael Malak
Postdoctoral Fellow
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Photocopy this page or follow this format for each person.
NAME
POSITION TITLE
Scott A. Tenenbaum, Ph.D.
Assistant Professor
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and
include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
YEAR(s)
FIELD OF STUDY
University of Missouri
B.A.
1986
Liberal Arts and Sciences
Wright State University, Dayton Ohio
M.S.
1989
Microbiology / Immunology
Tulane University School of Medicine
Ph.D.
1994
Microbiology / Immunology
Tulane University School of Medicine
(Post-doc)
1994-1997
AIDS-Research
Duke University Medical Center
(Post-doc)
1997-2003
RNA-Protein interactions
D. Positions and Honors.
Employment
1987-89
Graduate Research Assistan
Wright State University
1989-94
Graduate Research Assistant
Tulane University School of
Medicine
1994-96
Postdoctoral Fellow
Tulane University School of
Medicine
1997-00
Postdoctoral Fellow
Duke University Medical
Center
2000-03
Senior Research Associate
Duke University Medical
Center
2003-present
Assistant Professor
University at Albany-SUNY
Honors and Fellowships:
1988
Wright State University Microbiology Graduate Teaching fellowship.
1989
Tulane University Graduate Student Fellowship.
1992.94
The Mary Bird Perkins Hematology / Oncology Pre-Doctoral Fellowship.
1993
The College of Rheumatology Student Travel Award.
1994
The Roche Laboratories Award for Excellence in Clinical Research.
1994
The American Association of Blood Banks Transfusion Medicine Award.
1994
The American Society for Microbiology Student Travel Award.
1994-96
The National Hemophilia Foundation Judith Graham Pool Fellowship.
1997
NIH Postdoctoral Research Fellowship (Viral Oncology).
1998
NIH Postdoctoral Research Fellowship (Autoimmune Immunology).
1999
NIH Postdoctoral Research Fellowship (Viral Oncology).
2000
The Duke University Comprehensive Cancer Center James A. Wilson, M.D.
Fellow in Cancer Award.
2001
The Duke University Comprehensive Cancer Center Robert M. and Barbera
R. Bell Basic Science of Cancer Award.
Teaching Experience:
1988
Instructor, Medical Technologist Microbiology. Wright State University,
Dayton, OH.
1989
Instructor, Nursing Microbiology. Wright State University, Dayton, OH.
1991-92
Instructor, Nursing Microbiology and Immunology. Delgado College, New
Orleans, LA.
1992-96
Instructor, Medical Microbiology and Immunology. Tulane University, New
Orleans, LA.
1997-03
Instructor, Microbiology Workshop. Duke University Medical School, Durham,
NC.
2004
Instructor, BMS632/AMC603 Prokaryotic Genetics. Wadsworth Center,
UAlbany-SUNY
Consulting:
1996
Lucent Technologies Inc. Coral Gables, FL.
1995-96
Louisiana Land and Exploration Inc., New Orleans, LA.
1995-99
Autoimmmune Technologies, LLC, New Orleans, LA.
2001-Present
Taproot Ventures LLC, San Mateo, CA
2001-Present
Ribonomics Inc., Research Triangle Park, NC
Presentations:
2004
The Ninth Annual RNA Society Conference. Madison, WI.
2004
McGill University, Department of Biochemistry. Montreal, Quebec.
2004
GI-CFG Symposium, Rensselaer, NY
2003
The Symposium on RNA Biology V. RNA, Tool and Target. Research Triangle Park,
NC.
2002
Beyond the Identification of Transcribed Sequences. Washington, D.C.
2002
The Third Annual Northwest Microarray Conference. Seattle, WA.
2002
MOLECULAR EVOLUTION AND BIOINFORMATICS CONFERENCE.
SORRENTO, ITALY.
2002
The Seventh Annual RNA Society Conference. Madison, WI.
2001
The Triangle Array Users Group Meeting. Research Triangle Park, NC.
2001
The Symposium on RNA Biology IV. RNA: Target and Tool. Chapel Hill, NC.
2001
The Second Annual Northwest Microarray Conference. Seattle, WA.
2001
The Sixth Annual RNA Society Conference. Banff, Canada.
1999
The Fourth Annual RNA Society Conference. Edinburgh, Scotland.
1996
Children Afflicted by Toxic Substances (CATS), Santa Fe, NM.
1995
The American College of Rheumatology Conference, San Francisco, CA.
1994
The ATLA Silicone Toxicity Symposium, Dallas, TX.
1994
Pediatrics AIDS Clinical Trial Unit, TUMC, New Orleans, LA.
1994
The American Rheumatology Conference, San Antonio, TX.
1994
The American Society for Microbiology Meeting, Shreveport, LA.
1993
Louisiana State University, Department of Rheumatology, New Orleans, LA.
1993
Department of Clinical Immunology and Allergy, TUMC, New Orleans, LA
1993
Department of Pediatrics, Tulane Medical Center, New Orleans, LA.
1993
Association for Research in Otolaryngology, St. Petersburg, FL.
Scientific Interests:
1)
The role of mRNA-binding proteins in regulating post-transcriptional gene regulation
2)
The biology and etiology of autoimmunity
3)
Viral-host interactions at the molecular level and
4)
Understanding the organization of the mRNP infrastructure in the cell and how it
relates to global gene expression regulation in cancer
Scientific Organization Memberships:
The American Association for the Advancement of Science
The RNA Society
American Society of Microbiology
American Society of Virolgy
Patents:
1) Keene, J.D., Carson, C.C. and Tenenbaum, S.A. Methods for the Endogenous Isolation
and Identification of Messenger RNA Subsets. USP# 6,635,422
2) Garry, R.F., Tenenbaum, S. A., and Plymale, D. R. A Method For Detecting Anti-Polymer
Antibodies and a Diagnostic Test Kit For Use in the Aid Of Diagnosis of Fibromyalgia and
Chronic Fatigue Syndrome. (International patent pending).
3) Garry, R.F., Tenenbaum, S. A., and Plymale, D. R. A Method for Detecting Anti-polymer
Antibodies and Diagnosing Silicone Related Disease, Fibromyalgia, and Chronic Fatigue
Syndrome. USP# 5,834,215
4) Garry, R.F., Tenenbaum, S. A., and Plymale, D. R. A Method to Aid in the Diagnosis of
Silicone Related Disease. USP# 5,620,859
Publications:
1)
Tenenbaum, S. A., Leissinger, C. A., and Garry, R. F. (1993). Seroreversion of HIV-1
antibodies in seroreactive individuals. Journal of the American Medical Association
270; 2178-2179.
2)
Garry, R.F., Hart, D. J., Tenenbaum, S. A., Luo-Zhang, H., Breeding, S. A. L. and
Alexander, S. S. (1993). Sjogren's syndrome and assays for retroviral proteins. Arthritis
& Rheumatism 35:1405-1406.
3)
Tenenbaum, S. A., Voss, T. G., Garry, R.F., and Gallaher, W. R. (1994). Sequence
similarities between retroviral proteins and components of the spliceosome- AIDS
Research & Human Retroviruses 10:521-523.
4)
Jaspan, J. B., Luo, H., Ahmed, B., Tenenbaum, S., Voss, T., Sander, D. M, Bollinger, K.,
Baquet, T., Garry, R. F. (1995). Evidence for a retroviral trigger in Graves' disease.
Autoimmunity 20:135-142.
5)
Cuellar, M. L., Scopelitis, E., Tenenbaum, S. A., Garry, R. F., Silveira L. H., Gonzalo, C.
and Espinoza, L. R. (1995). Serum antinuclear antibodies in women with silicone
breast implants. Rheumatology 22:236-240.
6)
Chiang, C-F., Tenenbaum, S. A., Verrett, R., Leissinger, C.A. and Garry R.F. (1995).
The activity of granzyme A, a serine protease in the killing granules of cytotoxic T-
lymphocytes, is reduced in cells from HIV-infected hemophiliacs. AIDS Research &
Human Retroviruses 12:235-239.
7)
Jaspan, J. B., Bryer-Ash, M., Sullivan, K., Lopez, M., Wolfe, M., Clejan, S., Cao, Y.,
Tenenbaum, S., Sander, D. M., Ahmed, B., and Garry, R. F. (1996). The interaction of a
type A retroviral particle and class II human leukocyte antigen susceptibility genes in the
pathogenesis of Graves' disease. Journal of Clinical Endocrinology and Metabolism
81:2271-2279.
8)
Scandurro, A. B., Rondon, I. J., Wilson, R. B., Tenenbaum, S. A., Garry, R. F. and
Beckman, B. S. (1997). Interaction of erythropoietin RNA binding protein with
erythropoietin RNA requires an association with heat shock protein 70. Kidney
International 51:579-594.
9)
Tenenbaum, S.A., Rice, J. C., Espinoza L R-, et al. (1997). Use of antipolymer antibody
assay in recipients of silicone breast implants. Lancet 349; 449-454.
10)
Tenenbaum, S.A., Carson C.C., Lager, P.J. and Keene, J.D. (2000). Identifying mRNA
subsets in messenger ribonucleoprotein complexes by using cDNA arrays.
Proceedings of the National Academy of Sciences (U S A) 97(26):14085-90.
11)
Brown, V., Ceman, S., Peng, J., Darnell, J.C., O’Donnell, W.T., Tenenbaum, S. A., Jin,
X., Wilkinson, K.D., Keene, J.D., Darnell, R.B., and Warren, S.T. (2001). Identification of
mRNAs associated with the fragile X mental retardation protein complex in the brain.
Cell 107; 477-487.
12)
Keene, J.D. and Tenenbaum, S.A. (2002). Eukarotic mRNPs May Represent Post-
Transcriptional Operons. Molecular Cell 9; 1161-1167.
13)
Tenenbaum, S.A. and Keene, J.D. (2002). Using messenger RNP autoantibodies to
reveal networks of posttranscriptional operons. In From Proteomics to Molecular
Epidemiology. K. Conrad (Eds.); Pabst Science Publishers. 3; 26-42.
14)
Eystathioy, T., Chan, E.K.L., Tenenbaum, S.A., Keene, J.D., Griffith, K., and Fritzler,
M..J. (2002). A phosphorylated cytoplasmic autoantigen, GW182, associates with a
unique population of human mRNAs within novel cytoplasmic speckles. Molecular
Biology of the Cell 13; 1338-1351.
15)
Tenenbaum, S.A., Lager, P.J., Carson C.C., and Keene, J.D. (2002). Ribonomics:
Identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding
proteins and genomic arrays. Methods 26; 191-198.
16)
Tenenbaum, S.A., Carson C.C., Atasoy, U., and Keene, J.D. (2003). Combining en
masse array analysis of gene regulation using genome-wide approaches to nuclear run-
ons (emRON) and mRNP isolation (ribonomics). Gene 317; 79-87.
17)
Intine, R.V., Tenenbaum, S.A., Sakulich, A.L., Keene, J.D., and Maraia, R.J. (2003).
Differential phosphorylation and subcellular localization of LaRNPs associated with
precursor tRNAs and translation-related mRNAs. Molecular Cell 12: 1301-1307.
18)
Penalva, L.O., Tenenbaum, S. A., and Keene, J.D. (2004). Gene Expression Analysis
of Messenger RNP Complexes. Methods Mol Biol. 257:125-34.
Research Support:
Funding
Funded Grant:
NIH 1R21HG003679-01 (9/01/04-07/31/06)
Role:
PI
Title of Project:
Identifying functional regulatory elements in RNA
Budget:
410,000 Total Direct Costs
Major Goals:
As part of the ENCODE project we will develop new technologies
combining ribonomic profiling with tiling array analysis that will
facilitate the system-wide identification of RNA based regulatory
elements.
Pending Grant: NIH 1R21 HG003625-01 (Pending 4/01/05-03/31/07)
Role: PI
Title of Project:
Using RNA-binding proteins to study the hidden transcriptome
Budget:
300,800 Total Direct Costs
Major Goals:
We are combining ribonomic profiling with tiling array analysis to
facilitate
the system-wide study of the hidden transcriptome.
Pending Grant: NIH 1R21MH074319-01 (Pending 4/01/05-03/31/07)
Role: PI
Title of Project:
Using RBPs to Study Gene Expression in Schizophrenia
Budget:
413,600 Total Direct Costs
Major Goals:
We are combining ribonomic profiling with tiling array analysis to
facilitate
the system-wide study of gene expression in schizophrenia.
Principal Investigator/Program Director (Last, First, Middle):
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Loghin, Evelina
POSITION TITLE
Biochemist
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
Clemson University
MS
2000
Biochemistry
University of Medicine and Pharmacy Carol Davila
BS
1997
Pharmacy
Positions and Honors:
Professional Experience
Research Technologist, Department of Biological Sciences, University at Albany State University
of New York (SUNY), September 2001-present
Research Technologist III, Department of Bioengineering, Clemson University, December 2000-
2001
Graduate Student, Department of Biological Sciences, Biochemistry Program, Clemson
University & GHS Biomedical Cooperation May 1998 - December 2000.
Pharmacist, Salviafarm, Ploiesti, Romania, 1997.
Honors and Awards
GHS/CU Biomedical Graduate fellowship
Research Skills
Maintain cell culture (mammalian and yeast, Saccharomyces cerevisiae).
Assays for analysis of DNA recombination: Transfection/Transformation of plasmid DNA into the
mammalian and yeast cells respectively; Reporter gene assays such as -galactosidase and
Luciferase/Renilla.
Nucleic Acid techniques: DNA purification (plasmid preparation), sub-cloning, PCR (cold and
radioactive), RNA isolation and analysis (Northern), agarose and polyacrylamide gel
electrophoresis.
Protein techniques: Protein separation by SDS-PAGE, detection by Coomassie Brilliant Blue R-
250, and Ponceau S, Immunoblotting (Western), and protein identification by enhanced
chemiluminescence (ECL).
Protein purification using MBP, GST, TAP, and His tags.
In vivo Protein-Protein interaction by Co-immunoprecipitation.
Protein-DNA interaction by Chromatin Immunoprecipitation (ChIP).
In vitro kinase assays using -P32 and different purified proteins.
Enzyme kinetics techniques – Bicinchoninic Acid Assay (BCA) and Quantigold assays for protein
concentration estimation, and colorimetric assays for Alkaline Phosphatase, Horseradish
Peroxidase enzymes.
Prepare silicon surfaces for adsorption of different proteins/enzymes.
Research experience
Research Technologist, Dep. of Biology SUNY at Albany, Sept. 2001-present
My work at SUNY involves the general stress response (the most common type of stress in
yeast) in Saccharomyces cerevisiae.
General stress in yeast consists of heat shock, osmotic shock, glucose starvation, low pH,
irradiation and each tress triggers the transcription of about 200 genes (known as stress
response element, STRE-containing genes) that protect and adapt cells.
o
Analyzed the kinetics of Cyc7 (a gene whose expression is activated under stress) mRNA
by heat shock.
o
Performed the Co-immunoprecipitation to identify the physical interaction between
proteins involved in the general stress response such as Srb10 and Srb11 (two members
of the mediator complex), Srb11 and Msn2 (a transcriptional factor that activates the
STRE genes upon stress), Srb11 and Rox3 (an essential member of the mediator
complex).
o
Analyzed the interaction between different proteins and genes involved in the general
stress response by performing Chromatin Immunoprecipitation (ChIP), a powerful in vivo
technique that looks at the DNA-Protein interaction. The ChIP method was used to verify
the interaction between proteins such as Msn2, Srb11, and Srb10 and genes whose
expression is altered under stress (Cyc7).
o
Performed kinase experiments to check the enzymatic activity of Srb10 protein using
substrates like CTD and Rsk1 (a protein that is been suggested to regulate the specificity
of Srb10 activity).
Research Technologist, Dept. of Bioengineering, Clemson University, Dec. 2000-Sept. 2001
My work was part of a project whose goal was to make MEMS devices compatible with biological
fluids.
Several proteins/enzymes were used to study their adsorption to the different organic surfaces.
Biochemical and specific surface methods were used to determine how much protein is bound to
the surface and the state (native/denatured) of the protein after adsorption to the surface.
o
Performed protein assays, such as Bicinchoninic Acid assay (BCA) and Quantigold.
o
Performed enzyme kinetic assays for alkaline phosphatase and horseradish peroxidase
enzymes.
o
Analyzed protein/enzymes adsorption to different chemical surfaces (silicon, glass).
Research Associate, Dep. of Biology, Clemson University, May 1998-Dec. 2000
Verified that PPAR is endogenously expressed and functionally active in MCF-7 and MDA-MB-
231breast cancer cells.
Identified PPAR 1 as the major isoform present in breast cancer cells at least at the level of
transcription.
The regulation of PPAR1 is totally relying in 1 kb fragment of 5’ flanking region and it involves
phosphorylation.
o
Handled two types of breast cancer cell lines (MCF-7 and MDA-MB-231) and mouse
fibroblast cells (CHO K1).
o
Handled E.Coli bacterial cells (maintaining the cell culture, and transforming the bacterial
cells into competent cells).
o
Developed an antisense expression vector for peroxisome proliferator activated receptor
gamma 1 gene (PPAR1) and tested on MCF-7 and MDA-MB 231 human breast cancer
cells.
o
Tested a human 3Kb fragment of PPAR 1 5' flanking region for promoter activity in two
types of breast cancer cells, MCF-7 and MDA-MB 231.
o
Performed deletion analysis to find the regions of PPAR 1 promoter important in
regulation of PPAR 1 gene transcription.
o
Tested the new constructs generated by deletion analysis in human breast cancer cells.
o
Sequenced PPAR 1 promoter.
Publications:
Abstracts and Presentations
Evelina Loghin
and Michael W. Kilgore - Regulation of Peroxisome Proliferator Activated
Receptor gene expression in MCF-7 and MDA-MB 231 human breast cancer cells. 9th Annual
South Carolina Statewide Research Conference on Molecular Approaches to Biological
Problems, Wild Dunes, SC, January 2000.
X Wang, PL Tate, SR Thoennes, E Loghin, TM Price and MW Kilgore. Signal Cross Talk between
Estrogen Receptor Alpha and Beta and the Peroxisome Proliferator-Activated Receptor gamma1
in MDA-MB-231 Breast Cancer Cells. Era of Hope, Department of Defense Breast Cancer
Research Program Meeting. Atlanta, GA, June 2000.
MW Kilgore, X Wang, SR, Thoennes, E Loghin and TM Price. Estrogen Receptor Alpha and Beta
Mediate Transcriptional Activation of the Peroxisome Proliferator-Activated Receptor Gamma1 in
MDA-MB-231 Breast Cancer Cells. 82nd Annual meeting of the Endocrine Society, Toronto,
Canada, June 2000.
Xin Wang, Evelina Loghin and Michael W. Kilgore. Peroxisome proliferator-activated receptor
gamma: Novel promoters and transcriptional regulation in human breast cancer cells. 83nd
Annual meeting of the Endocrine Society, June 2001.
Publications
Keith Lenghaus, Jeff W. Dale, J.Caroline Henderson, David C. Henry, Evelina R. Loghin, and
James J. Hickman. Enzymes as Ultrasensitive Probes for Protein Adsorption in Flow Systems.
Langnuir 2003, 19, 5971-5974
Principal Investigator/Program Director (Last, First, Middle):
Tenenbaum, Scott A.
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Shablovsky, Georgi Georgievich
POSITION TITLE
Research Assistant
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
Pavlov Medical Institute, St. Petersburg, Russia
M.D.
1992
Internal Medicine
McGill University, Montréal, Canada
Ms.Sc.
1999
Molecular Biology
A. Positions and Honors.
Positions and Employment
1988
Assistant Programmer, Center of Prophylaxis of Pulmonary Diseases, St.
Petersburg, Russia
1992-1994
Fellow in Hematology/Oncology and Molecular Biology, Petrov Research Institute
of Oncology, St. Petersburg, Russia
2000-2002
Programming Analyst, Mid-Hudson Media, Hudson, NY
2002-2004
Research Associate, Bioinformatics, Department of Biology, Rensselaer
Polytechnic Institute, Troy, NY
2004-
Research Associate, Center for Functional Genomics, University at
Albany, NY
Other Experience and Professional Memberships
2002-2004
Web Developer, Bioinformatics Center at RPI and Wadsworth, Rensselaer
Polytechnic Institute, Troy, NY
2004 -
Web-Based Database Application Programmer for Sloan Science Master's
Outreach Project
B. Selected publications (in chronological order).
1.
N. Dainiak, L. Karkanitsa, O.A. Aleinikova, J. Albanese, G. Shablovsky, S. Sorba, Q. Hamid,
[1996] “Plasma membranes and cytokine gene expression: utility in assessing biological
effects of exposure to ionizing radiation from the Chernobyl accident in healthy individuals
and myelodysplastic syndrome” (abstract). Presented at the Annual Meeting of the
American Society of Hematology, (December 6, 1996).
2.
G. Shablovsky, N. Dainiak, L. Karkanitsa, N.G. Kruchinsky, V.A.Ostapenko, O.Ghaffar,
Q.Hamid. [1997] “IL-4 and IL-5 in patients exposed to ionizing radiation in Chernobyl”
(abstract). Presented at the Annual Meeting of the American Thoracic Society (May 5,
1997).
3.
R. Taha, G. Kovalev, G. Shablovsky, N. Dainiak, O. Ghaffar, and Q. Hamid, “Expression of
Th2-type cytokines in the bronchial mucosa of children with asthma compared to adult
atopic asthmatics” (abstract). Presented at the Annual Meeting of the American Thoracic
Society (May 5, 1997).
4.
G. Shablovsky, O. Ghaffar, R. Taha, A. Soussi-Gounni, R. Olivenstein, P. Ray, A. Ray, Q.
Hamid. [1998] “Expression of Stem Cell Factor and c-kit in Allergic Asthma” (abstract).
Presented at the Annual Meeting of the American Academy of Allergy, Asthma and
Immunology (March 13, 1998).
Principal Investigator/Program Director (Last, First, Middle):
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Zaleski, Christopher
POSITION TITLE
Bioinformatics
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
Rockland Community College
AAS
1996
Business Administration
Western Connecticut State University
BA
1999
Computer Science
University at Albany
BA
2005
Biology
(1)Positions and Honors:
Technical Summary:
Languages: High level of proficiency and recent focus in Java 2, with solid experience in Visual Basic,
SQL, HTML, JavaScript and C++.
Operating Systems: High level of proficiency with all flavors of Microsoft Windows. Also some limited
experience with RedHat Linux and Macintosh OS.
Development Environments: Borland JBuilder, Sun Forte, Microsoft Visual Studio
Database Management Systems: Microsoft SQL Server 6.5/2000
Communications protocols: TCP/IP, JDBC, JMS
Employment:
Initia Inc. New City, NY
Software Systems Engineer 1/01 – 9/02
Software based videoconferencing system solutions.
One of three lead engineers responsible for project design concepts and
system architecture. Decisions included Design Patterns, Inter-process
communication and DBMS.
Directly managed a team of four developers with design and implementation
of client and server-side modules. Assisted with design pattern choices, code
implementation and integration.
Assisted in creation of project timelines and assured the completion of
functionality requirements were fullfilled in a timely manner.
Designed and coded server-side modules including Session Management,
Scheduling, and Asynchronous Communications protocols. Technologies
used included many standard J2SE/J2EE APIs, JMS, JDBC, extensive Multi-
Threading, Reflection, and Socket IO.
Assisted in distribution and support of beta systems on customer sites.
VideoBureau Inc. New City, NY
Software Development Engineer 3/99 – 1/01
Videoconferencing software development, hardware control, and installation.
Design and implementation of a web-based client interface for
videoconferencing control system. Created using HTML, Java, JavaScript,
VBScript, and Active Server Pages. The interface was Drag-and-Drop
controllable, and reflected current state of system sessions and controlled
devices using real-time data.
Created web-based interface for videoconferencing system database. Used
HTML, JavaScript and ADO to implement sets of forms and wizards for
database I/O.
Implemented Multimedia control station interface using VisualBasic. Used to
directly control and schedule content for up to fifty audio/video devices,
including conferences, security cameras and television.
Boehringer Ingelheim Inc. Ridgefield, CT
Lead Support/Systems Analyst 5/97 – 3/99
Top 20 international pharmaceutical company.
Lead support of international remote access services, consisting of
connectivity from Windows 95 clients to Netware servers and Windows NT
domains. Responsible for all remote access related support that could not be
handled by tier 1 support staff.
Managed software and hardware rollouts for the company sales force,
including shipping & receiving of laptops, modem installations, and software
installations/upgrades.
Taught training classes on the use of remote access & telecommuting to
classes of ten to fifty clients.
Traveled nationally for on-site support of software and hardware, as well as
installation of Cisco ISDN routers.
(2)Publications:
(3)Ongoing Research:
Discovery of common structural motifs in unaligned RNA sequences that have been precipitated using
Ribonomic techniques.
Role: Bioinformatics
Timothy Edward Baroni
Wadsworth Center (NYSDOH)
David Axelrod Institute for Public Health
PO Box 22002 - CMS 5228 100 Heritage Rd., Apt. 7
Albany, NY 12201-2002 Guilderland, NY 12084
(518) 402-2536 (518) 577-7089
tbaroni@wadsworth.org tbaroni@bigfoot.com
Education
Ph.D. - Chemistry (August 1992 - May 1997; University of Kansas, Lawrence, KS)
Research
director - Professor Joseph A. Heppert, Ph. D. Dissertation: “High Oxidation State
Complexes of Tungsten with Ortho-Chelating Phenols”
B.S. - Chemistry (August 1988 - May 1992; Rockhurst College, Kansas City, MO)
Research Experience
Wadsworth Center (NYSDOH)
Division of Genetic Disorders
Postdoctoral research affiliate Marlene Belfort, Ph.D. Oct 2003–present
Project: “Mechanism of cleavage in natually-occurring and engineered inteins”
Washington University School of Medicine
Department of Medicine, Division of Oncology
Postdoctoral research associate Professor K. Weilbaecher, M.D. Aug 2002–Sep
2003
Project: “3-integrin mediation of bone metastases in mice”
Department of Medicine, Division of Molecular Oncology
Postdoctoral research associate Professor R. K. Brachmann, M.D. June 2000–July
2002
Project: “Suppressor mutations to bestow transcriptional activity to common p53
mutants”
Washington University (Department of Chemistry)
Postdoctoral research associate Professor K. L. Wooley, Ph.D. June 1999–May 2000
Project: “Inorganic-polymeric core-shell nanoparticles”
University of Kansas (Department of Chemistry)
Postdoctoral research associate Professor A. S. Borovik, Ph.D. June 1997–July 1998
Project: “2,6-Carbamidoylpyridine ligands in supramolecular assemblies”
Graduate research assistant Professor J. A. Heppert, Ph.D. Oct. 1992–May 1997
Dissertation: “High Oxidation State Tungsten Phenoxides with Ortho-Chelating
Groups”
Rockhurst College (now Rockhurst University, Department of Chemistry)
Undergraduate research assistant Professor D. Gibbs, Ph.D. June 1990-May 1991
Project: “Stereoselective production of -hydroxyketones via fermentation by S.
cerevisiae”
Research Interests
Developing methods to solve problems simply and practically: a“back-to-basics”
approach to
assess artificial, contrived, or natural systems what does my experiment tell me?
Molecular bases of disease: By what mechanism do mutations alter signaling?
Genetic and/or biochemical screening to identify proteins and/or small molecules to
modulate signaling pathways/cellular processes
Expression profiling (by chip, ELISA, etc.), molecular modeling, computational
chemistry,
and bioinformatics: virtual experiments to direct research
Timothy E. Baroni (2 of 4)
Professional Experience
RGB Laboratories, Inc. (Kansas City, MO – now owned by Roots, Inc.) May 1991–
August 1992
Quality assurance analysis of liquid and solid fertilizers (AA, pH, gravimetry, TDS,
etc.)
Performed product and process research and development
Awards and Honors
1991 ACS Undergraduate Award in Analytical Chemistry
Phi Lambda Upsilon (chemistry honor society, inducted Spring 1996)
University of Kansas Graduate Teaching Fellowship (Fall 1992 and Spring 1994)
University of Kansas Graduate Research Fellowship (Spring 1993–Fall 1993 and
Summer
1994– Spring 1997)
Professional Organizations
American Chemical Society (1991–2000)
American Association for Cancer Research (2002-present)
Teaching Experience
Assistant Professor – Kansas City Kansas Community College (August 1998–
August 1999)
General Chemistry for allied health professional programs: Instructed and
prepared
material for both laboratory and lecture sections.
Organic Chemistry I & II: Instructed and prepared materials for both
laboratory and
lecture sections for these traditional undergraduate chemistry track classes.
Developmental Math: a chemistry-oriented, problem solving mathematics
class
Teaching Assistant and Research Assistant – University of Kansas (1992–1998)
Molecular modeling, computational chemistry, and bioinformatics: virtual
experiments to
direct research
Instructed undergraduate laboratories in General Chemistry I & Organic
Chemistry II.
Substitute lecturer in Professor Heppert’s graduate level inorganic classes
Mentor and instructor to graduate & undergraduate students in experimental
design,
preparation and analyses and projects
Abstracts
1. “Restoring fuction to p53 mutants” T. E. Baroni, T. Wang, H. Qian, L. N. Truong, J.
Zeng, A.
E. Denes, S. W.-Y. Chen, and R. K. Brachmann (AACR Meeting, San Fancisco , CA,
2002)
2. “Supramolecular assemblies of 2,6-bis(carbamoylpyridines)” Q. Yu, T. E. Baroni, A.
S.
Borovik (KANSYN Meeting, Lawrence, KS, 1998)
3. “Supramolecular assemblies of tungsten complexes with unusual chelating
groups” T. E.
Baroni, V. L. Kolesnichenko, J. A. Heppert (KANSYN Meeting, Manhattan, KS, 1997)
4. “Organometallic free acids of high-valent tungsten.” T. E. Baroni, R. R. Hodel, R. P.
Kingsborough, M. D. Morton, A. L. Rheingold, G. P. A. Yap, J. A. Heppert (National ACS
Meeting, Anaheim, CA, 1994)
Timothy E. Baroni (3 of 4)
Publications
1. Baroni, T. E., Wang, T., Qian, H., Truong, L. N., Zeng, J., Denes, A. E., Chen, S. W.-Y.,
and
Brachmann, R. K. "A global suppressor motif for p53 cancer mutants" Proceedings of
the
National Academy of Sciences 2004, 101, 4930-4935.
2. Qian, H., Chen, S.W.-Y., Baroni, T. E., Wang, T., and Brachmann, R. K. "Wide
spectrum of
residual wild-type and dominant-negative activities of p53 cancer mutants"
(submtted).
3. Kolesnichenko, V., Mason M. H., Botts J. B., Botts A. M., Baroni T. E., Heppert J. A.,
Rheingold A. L., Liable-Sands L., Yap G.P. “Tungsten oxo salicylate complexes from
tungsten
hexachloride reactions systems” Inorganic Chemistry 2001, 40, 5010-5016
4. Yu, Q.; Baroni, T. E.; Borovik, A. S.; Liable-Sands, L.; Rheingold, A. L. “Hydrogen
bonded
antiparallel -strand motifs promoted by 2,6-bis(carbamoylpeptide)pyridine”
Journal of the
Chemical Society, Chemical Communications (Cambridge) 1999, 16, 1467-
1468.
5. Yu, Q.; Baroni, T. E.; Borovik, A. S.; Liable-Sands, L.; Rheingold, A. L. “Synthesis
and
structure of chiral 2,6-bis(2-carbamoyl)carbamoylpyridine ligands” Tetrahedron
Letters
1998, 39, 6831-6834.
6. Baroni, T. E.; Bembenek, S.; Heppert, J. A.; Hodel, R. R.; Laird, B. B.; Morton, M. D.;
Barnes, D. L.; Takusagawa, F. “Hydrogen bonding in tungsten(VI) salicylate free
acids”
Coordination Chemistry Reviews 1998, 174, 255-282.
7. Baroni, T. E.; Kolesnichenko, V. L.; Seib, L.; Liable-Sands, L. M.; Yap, G. P. A.;
Rheingold, A.
L.; Heppert, J. A. “Supramolecular assemblies of tungsten complexes with unusual
chelating
groups.” Polyhedron 1998, 17, 759-768.
8. Baroni, T. E.; Heppert, J. A.; Hodel, R. R.; Kingsborough, R. P. “Supramolecular
assemblies
involving organometallic free acids.” Organometallics 1996, 15, 22, 4872-4879.
Laboratory Skills & Research Specialties
Vigorous verbal and well-written communication skills on a variety of topics,
especially
relating to chemistry, biology and physical sciences.
Chemical background ideal for understanding technologies and strategy for
molecular
processes, since most molecular biology techniques are biochemical in nature.
Design and construction of targeting vectors for conditional knockout mice using
Cre-loxP
technology.
Organizing and performing general lab tasks (equipment operation and
troubleshooting, oil
changes, repairs, ordering materials, cleanups, freezer and incubator maintenance).
Strong background in molecular biological techniques: restriction digests, gel
electrophoresis, PCR, cloning, sub-cloning, vector construction for genomic and
plasmid
constructs, including plasmid library generation and screening in yeast.
Experience in tissue culture techniques: preparation of media, manipulation,
freezing, and
transfection of adherent and suspended cell lines as well as harvesting of murine
tissues for
primary culture.
Conversant in Western blotting and immunochemical detection practices.
Mouse manipulation techniques in barrier facility: caging, sacrificing, anesthesia,
injections
(subcutaneous, peritoneal, intratibial, left ventricle), dissections, tissue harvesting
and
fixation.
Adept at computer operation, configuration, software and hardware installation,
troubleshooting, modest programming. Familiarity with MS-DOS, Windows
3.11/95/98, Mac
OS X, and many flavors of UNIX (including building of source code).
Timothy E. Baroni (4 of 4)
Skilled in use of DNA Strider, BLAST, MS Office X, Filemaker Pro (track sample origin,
storage and bioinformatic data in a variety of templates ). CS ChemOffice, Jandel
Scientific’s
Sigma Plot, and Internet resources (http, FTP, telnet, e-mail protocols, newsgroups,
etc.)
Proficient with several molecular modeling programs: Alchemy and Sybyl (PC or
UNIX,
Tripos), Chem3D (PC/Mac), QUANTA/CHARMM (UNIX), CAChe (Mac), ISISDraw (PC).
Training in manipulation of air and/or water sensitive chemicals via Schlenk line and
glove
box techniques to perform inorganic and organic synthesis: solid state
(ampoule/bomb) and
homogeneous reactions, ligand synthesis, organometallic & coordination
compounds.
Post-synthetic compound purification via chromatography, distillation, sublimation,
or
recrystallization
NMR spectroscopy -- 1H, 13C, NOE, and simple 2D experiments (COSY, ROSY, etc.).
Familiarity with Varian XL300, Bruker AM500 & DRX400, and GE QE300
spectrometers, IR,
UV-Visible and mass spectral data interpretation
Conversant in X-ray diffraction: single crystal (data collection and refinement) &
powder
diffraction spectra.
Simple glassblowing (sealing ampoules, repairing star fractures/cracks, simple
modifications)
Minor electrical and mechanical repair experience (glove boxes, rotory evaporators,
stirring/hot plates, pH meters, balances, and other common laboratory equipment)
References
Marlene Belfort, Ph.D., Division Chair, Division of Genetic Disorders, Wadsworth
Center, New York
State Department of Health, 120 New Scotland Ave, Albany, NY 12208 — (518) 473-
3345 —
belfort@wadsworth.org
Katherine N. Weilbaecher, M.D., Assistant Professor, Washington University School
of Medicine,
Depatment of Medicine, 660 S. Euclid, Box 8069, Saint Louis, MO 63110-1026 —
(314) 454-
8858 — kweilbae@im.wustl.edu
Rainer K. Brachmann, M.D., Assistant Professor, University of California at Irvine,
Departments of
Medicine and Biological Chemistry, Med Sci I, C202, Zot 4075, Irvine, CA 92697-
4075 — (949)
824-8778 — rbrachma@uci.edu
Joseph A. Heppert, Ph.D., Professor, Director of Center for Science Education,
University of
Kansas, Department of Chemistry, Rm 1023 Malott Hall, Lawrence, KS 66045 —
(785) 864-
4150 — jheppert@ku.edu
Principal Investigator/Program Director (Tenenbaum, Scott, A.):
BIOGRAPHICAL SKETCH
Provide the following information for the key personnel in the order listed on Form Page 2.
Follow this format for each person. DO NOT EXCEED FOUR PAGES.
NAME
Doyle, Francis J.
POSITION TITLE
Bioinformatics
EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)
INSTITUTION AND LOCATION
DEGREE
(if applicable)
YEAR(s)
FIELD OF STUDY
SUNY Geneseo, Geneseo, NY
BA
1996
Communication
Pace University, New York, NY
MS
2000
Computer Science
SUNY Albany, Albany, NY
2003
Nanotechnology
(4)Positions and Honors:
Technical Summary:
Languages: High level of proficiency and recent focus in Java 2 (I am a Sun certified Java Programmer),
with solid experience in IBM Mainframe Assembly, Visual Basic, SQL, and C++.
Operating Systems: High level of current proficiency with all versions of Microsoft Windows, and with a
number of UNIX variants including Redhat Linux. Previous professional experience with IBM Mainframe
OS/390, and Apple Macintosh systems.
Development Environments: Sun Forte, Microsoft Visual Studio, Emacs, ISPF
Database Management Systems: Microsoft SQL Server 2000, MySQL
Communications protocols: TCP/IP (TCP & UDP), HTTP, Telnet, JMS, JDBC, ODBC, H.320/H.323,
SNA, X.25
Employment:
Doyle Systems Analysis, Inc. Albany, NY
Software Systems Consultant 9/02 – 11/04
Various, ranging from VBA MS Office customization, Linux support and
MySQL query analysis, to Java programming and network installation.
Initia Inc./ VideoBureau Inc.
New City, NY
Software Systems Engineer 3/01 – 9/02
Software based videoconferencing system solutions.
Designed and implemented distributed device management framework for
video communications server utilizing JMS. Managed other programmer’s
integration of devices into this framework.
Designed and implemented device drivers for real-time control of Tandberg
and Polycom video codecs,
including XML parsers for state retrieval, and Telnet and HTTP client modules
for high-level device communications.
Designed and implemented the alarm management system for the server,
including an SNMP agent which allowed integration with third party network
monitoring tools. Tested and demonstrated this ability with HP Openview.
Managed project source code control server (StarTeam) and weekly build
(ANT utility)/ archival process.
Represented company by presenting product technology to prospective
(technical and non-technical) investors.
Donovan Data Systems, Inc. New York, NY
Programmer Analyst 8/99 – 3/01
Primary supplier of data systems and software to the advertising industry.
Responsible for maintaining and updating mainframe assembly language
programs for demographic research and analysis.
Programmed client side, PC based user interfaces (in Visual Basic) in
tandem with their corresponding mainframe server applications.
MBIA Insurance Corporation New York, NY
Production Support Intern 7/98 – 2/99
Financial services company, member of both Fortune 500 and the S&P 500 index.
Provided end user support for Windows NT 4.0/Windows 95, MS-Office, and
PC hardware.
Performed large rollouts and configuration of new software.
Lead and assisted in the analysis and resolution of various IT problems
ranging from application troubles to network failure.
Verizon (NYNEX/Bell Atlantic) White Plains/New York, NY
Operations Support Specialist (Contractor) 6/96 – 9/97
.
Provided operational support for the NYNEX NCMS computer telephony
integration system distributed across Windows, AIX, and AS400 platforms.
Created “component failure impact analysis matrix” enabling accurate
determination of impact of component outages on overall system availability.
Performed operational support tasks and user support for CTI applications
running on various systems.
Assisted in analysis and resolution of host/network problems.
(5)Publications:
(6)Ongoing Research:
Discovery of common structural motifs in unaligned RNA sequences that have been precipitated using
Ribonomic techniques.
Role: Bioinformatics
Michael Malak
1 Kimberly Circle
Troy, NY 12180
(518) 283–5611
mmalak@alum.mit.edu
Education Rensselaer Polytechnic Institute, Troy, NY
Doctor of Philosophy in Physics, August 1998
California Institute of Technology, Pasadena, CA
Master of Science in Physics, June 1991
Massachusetts Institute of Technology, Cambridge, MA
Bachelor of Science in Physics, June 1989
Experience CommerceHub, Albany, NY 2001–present
Developer.
Responsible for designing and writing LATEX and Java code to produce packing slips and
other documents for online retailers and their suppliers. Retailers include QVC, Target,
Sears, K-B Toys, Costco, Walgreen’s, Circuit City, Macy’s, Kmart, ShopNBC, and Staples.
Responsible for tools for maintenance and migration of XML control data.
Wolfram Research, Inc., Champaign, IL 2000–2001
Strategic Applications Developer/Consultant.
Developed examples and applications of J/Link (integration of Mathematica and Java) and
webMathematica. Projects included 12 notebooks with interactive Java controls, multimedia
extensions using the Java Media Framework, and Mathematica Server Pages. Developed
a quantum-mechanics website with applets that display results computed by serverside
Mathematica Server Pages.
Rensselaer Polytechnic Institute, Troy, NY 1994–2000
Assistant Professor (Clinical) of Physics. (2000)
Taught four sections of Studio Physics I (Mechanics). Lectured, led discussions, performed
demonstrations, and assisted students in the highly interactive studio environment.
Developed
hypermedia modules for instruction.
Adjunct Assistant Professor of Physics. (1999)
Taught three sections of Studio Physics II (Electricity and Magnetism, Waves and Vibrations,
and Modern Physics). Lectured, performed demonstrations, assisted students, and
developed hypermedia materials.
Postdoctoral Research Assistant for Project Links, Department of Mathematical Sciences.
(1998–1999)
Developed World-Wide-Web-based hypermedia modules for use in studio classrooms as
part of an NSF-sponsored multi-university collaboration. Wrote HTML and TEX pages, created
Java applets, supervised other HTML and Java programmers, and developed JavaScript
functions for intramodule navigation, mathematical expressions, and multimedia. Module
topics include electromagnetism and Fourier series. Researched the use of TEX as a
hypermedia
language and acted as contact with IBM’s Advanced Internet Publishing group.
Graduate Research Assistant, Anderson Center for Innovation in Undergraduate Education.
(1994–1998)
As part of Project Links, developed Web-based modules for Studio Physics II (Electricity
and Magnetism) and vector calculus. Components include hypertext, graphics, animations,
Java-based interactive illustrations, symbolic math assignments, spreadsheet exercises, and
analysis of videotaped experiments.
Experience
(cont.)
Teaching Assistant (1994–1997) for Studio Physics I (Mechanics) and II (Electricity and
Magnetism).
Lectured, performed demonstrations, assisted students, wrote hypermedia modules and
in-class worksheets, and graded for studio classes.
California Institute of Technology, Pasadena, CA 1990–1993
Teaching Assistant for Undergraduate Computational Physics.
Lectured and assisted students in computer laboratory, wrote problem sets, and graded
students’
programs. Topics included Mathematica, quadrature and integration, Runge-Kutta
methods, simulation of interplanetary probes, simulated neural nets and annealing (the
traveling salesman problem), parallel computation, and computer control of instruments
and experiments.
California Institute of Technology, Pasadena, CA 1989–1990
Teaching Assistant for Graduate Computational Physics.
Topics included basic numerical methods, Hartree-Fock calculation, Metropolis simulated
annealing, white dwarf stars, and fluid dynamics.
Publications
and
Presentations
“JavaScript for Embedding Mathematics in Web Pages”, Michael Malak, invited poster,
MathML International Conference 2000, October 2000.
“Adding Video to Your Web Pages”, Michael Malak, Computing in Science and Engineering,
March 2000.
“Project Links: Hypermedia Modules for Introductory Electricity and Magnetism”,
Michael J. Malak, AAPT Announcer 29, 2. Invited Paper for AAPT Summer Meeting,
August 5, 1999.
“Multimedia Applications in Studio Physics Courses”, K. Min, M. Malak, P. Casabella, J.
Haus, and J. Wilson, in Current Practice in Multimedia Education, R. Bradbeer, ed. Hong
Kong: City University of Hong Kong Press, 1999.
“Hypermedia Modules for Electricity and Magnetism”, Michael J. Malak, Ph. D. thesis,
Rensselaer Polytechnic Institute, June 1998.
“Hypermedia Modules for Electricity and Magnetism”, Michael J. Malak, Joseph W. Haus,
and Jack M. Wilson, AAPT Announcer 27, 4. Contributed Talk at AAPT Winter Meeting,
January 8, 1998.
“Java-based Interactive Illustrations for Studio Physics”, Michael J. Malak and Jack M.Wilson,
AAPT Announcer 27, 12. Contributed Talk at APS/AAPT Joint Meeting, April 19,
1997.
Activities California Institute of Technology, Pasadena, CA 1989–1993
• Chair, Graduate Review Board: Investigated alleged violations of the Honor Code by
graduate students.
• Graduate Student Council: Physics representative, Computer Coordinator,
Publications Committee member.
• Theater Arts at Caltech: Acted and stage-managed.
Massachusetts Institute of Technology, Cambridge, MA 1985–1989
• MIT Dramashop: Acted, directed, built sets, and wrote plays.
• Sigma Pi Sigma (Physics honor society)
Professional
Organizations
American Physical Society
American Association of Physics Teachers
