Principal Investigator/Program Director (Last, First, Middle):
TROPSHA, Alexander
A. BACKGROUND
1. The need for a Research Training Program at UNC-Chapel Hill
According to the working definition used by the National Institutes of Health, bioinformatics is the
"research, development or application of computational tools and approaches for expanding the use of
biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze or
visualize such data" (http://grants2.nih.gov/grants/bistic/CompuBioDef.pdf). The success of the genome
science initiative at the UNC-CH will depend on the presence of a strong bioinformatics program at all levels,
from education and training to support and research. Since the fields of genomics and proteomics also present a
wide variety of important analytical problems that are of great value to basic research in the mathematical,
computational and statistical sciences, there is overwhelming enthusiasm for a new Research Training Program
in Bioinformatics among a wide spectrum of UNC-CH academic and research units (see attached letters of
endorsement from UNC-CH Vice-Chancellor for Research and Graduate Studies Tony Waldrop and Director
of Carolina Center for Genome Science Terry Magnuson as well as letters of support from 18 Chairs of basic
science Departments and Schools).
It is generally recognized that the most effective and productive way to foster synergies among different
disciplines is through shared graduate training. Both within the United States and globally, educational
opportunities in the field of bioinformatics have not kept pace with the burgeoning demand for trained
individuals in both academia and industry. The need for bioinformatics professionals is particularly acute in
North Carolina where biotechnology is a major component of the state economy. Thus, by offering a Research
Training Program in Bioinformatics, UNC-CH serves an institutional need as well as providing a concrete
benefit to the state. This program will also serve students well, as bioinformatics trainees have excellent career
prospects for the foreseeable future. Such prospects are indicated by obvious interest from major local
pharmaceutical and biotech companies (see letters of matching support from GlaxoSmithKline and BD
Biosciences which guarantee two additional graduate positions each year should this proposal be funded).
Developing a rigorous graduate training program in bioinformatics presents special challenges. A
bioinformaticist works at the intersection of multiple different disciplines, including but not limited to
biochemistry, biophysics, computer science, genetics, information science, statistics and structural biology. In
order to produce a competent graduate in a finite amount of time, it is necessary to develop a curriculum that
truly cuts across academic disciplines, rather than being a sum of multiple independent degrees. In addition,
students come to bioinformatics from very different backgrounds (e.g. recent computer science undergraduates
with little exposure to biology and biology undergraduates with little exposure to computer science). Only a
flexible program at an institution with a wide variety of offerings can accommodate such a diversity of student
backgrounds. UNC-CH is well equipped to deal with both of these challenges, and the proposed program is
designed to address them.
2. INSTITUTIONAL BACKGROUND AND COMMITMENT
In order to foster a successful research environment and to expand upon the pre-existing institutional
strength in genomic science, UNC-CH recently established the Carolina Center for Genome Sciences
(CCGS). The proposed Research Training Program in Bioinformatics will be administered by the CCGS. The
following goals of the CCGS have been defined:
to provide leadership in studying biological sciences in the context of whole genomes
to explore the relationship between genomic organization and biological function and malfunctioning of
genes as well as interacting networks of genes
to explore the relationships between the genomic organization and the disease state
to explore the relationship between genomic organization and the evolutionary process
to investigate the interactions between genomes and the environment
to develop training opportunities in genomics at the undergraduate, pre-, postdoctoral and graduate medical
education level
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to support technology-based research into tools for deciphering genome function and for translation into
medical practice
to develop experimental, theoretical, and computational research tools to enhance genomic research
to organize and maintain core facilities that provide the latest technologies essential for genetics/genomicsrelated research
to promote the distribution of novel genomic technologies through technology transfer
UNC-CH has committed substantial resources to establishing the CCGS as a university-wide Center
(Appendix 1). The director of the CCGS reports directly to the Dean, School of Medicine/Vice Chancellor for
Medical Affairs. UNC-CH has recruited Dr. Terry R. Magnuson from Case Western Reserve University to
head both CCGS and the newly created Department of Genetics. The CCGS serves to focus genomics as an
integrated academic discipline on campus through recognition of three umbrella programs: experimental
genomics, analytical genomics, and social genomics program. The latter area is being developed to focus on
policy driven research in the areas of ethical, legal and business ramifications of managing individual genomic
data. The fourth component of the CCGS is education, as experimental, analytical and social genomics are
important subjects for the next generation of students (from the undergraduate to the postgraduate level).
B. PROGRAM PLAN
1. Program Direction
The director of the Research Training Program in Bioinformatics will be Alexander Tropsha, Ph.D.,
Associate Professor of Medicinal Chemistry and Associate Director of the Carolina Center for Genome
Sciences. Dr. Tropsha’s main expertise is in the area of biological and chemical database analysis
(chemoinformatics and structural bioinfortmatics). He is particularly interested in establishing general
principles of knowledge integration in the area of biomolecular informatics (cf., for instance, his recent
review1). Dr. Tropsha received his M.S. degree in chemical enzymology from Moscow State University,
Moscow, Russia, and Ph.D. in Biochemistry and Pharmacology from the same institution. He is currently the
head of the Laboratory for Molecular Modeling at the School of Pharmacy and the Director of Graduate Studies
in the Division of Medicinal Chemistry and Natural Products.
Dr. Tropsha currently supervises nine Ph.D. students, two postdoctoral fellows, and a Research Assistant
Professor; his research is supported by grants from NIH, NSF, and private and public companies and
foundations. Dr. Tropsha will devote 10% effort to the Training Program. Dr. Tropsha brings to the
directorship background and skills in biomolecular informatics and in developing practical software tools for
biological research as well as his experience in directing a graduate program in the School of Pharmacy. Dr.
Tropsha will be assisted in administrative activities by Ms. Geri Osborn, a recently recruited Manager of
CCGS (see letter of endorsement from Dr. Magnuson). The administrative assistant will be the primary contact
for prospective applicants and for administrative concerns of the trainees.
Three committees will be established at UNC to assist Dr. Tropsha in the operation of the program. The
Executive Committee will include high-level scientific administrators at UNC, including Deans and Senior
Associate Deans of the Schools of Medicine, Public Health, Pharmacy, Information and Library Science, the
College of Arts and Sciences, the Director of the Carolina Center for Genome Sciences, and the Director of the
Health Science Library as well as industrial bioinformatics specialists (see letters of support from
GlaxoSmithKline and Becton Dickinson). The members of the committee have scientific backgrounds in all
relevant disciplines representing major pillars of bioinformatics, i.e. statistics, computing, genetics, informatics,
medicine, public health, and library science. This committee will advise the Program Director on strategic
planning issues and will ensure, via the administrative power of its members, that the Program is supported by
an adequate body of teaching and training faculty.
1
Tropsha, A. Recent Trends in Computer-Aided Drug Discovery. Current Opinion in Drug Discovery & Development ,
2000, 3, 310-313.
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Curriculum and Progression Committee will include representatives from all participating departments.
This committee is crucial for the operation of this training program. It will assume major responsibility for
forming the curriculum, new course development, and monitoring students’ progress through the program. The
members of this committee will ensure that the training program, which in its current form complements
existing degree granting programs, integrates smoothly with the latter programs. This committee will meet in
two capacities: (1) In monthly division meetings, the training program will be discussed with respect to
departmental activities, and (2) monthly educational advisory meetings will cover items specific to the training
program, such as curricula, requirements, student advising, etc. Members of this committee may also serve as
academic advisors to bioinformatics trainees. Finally, a Program Admissions Committee will be formed each
year by representatives of participating departments. All students supported by this Program, will be
concurrently admitted by a participating department. The Program Admissions Committee will review all
incoming applications and recommend students for funding.
2. Program Faculty
When UNC completes its aggressive recruitment efforts in bioinformatics, it will have more than 20 faculty
mentors in the proposed Training Program (see Appendix 1 for information on faculty recruitment). Appendix
2 summarizes the breadth of research interests of the present bioinformatics faculty. They will provide their
guidance to trainees either as course directors or research advisors, or both.
3. Proposed Training
a. General principles.
The proposed training program is intended to provide a sound basis for professional bioinformatics work in
either academia or industry and to produce research of national and global stature. All predoctoral students will
be receiving Ph.D. degrees from their respective degree-granting departments with a concentration in
Bioinformatics. We recognize that the present leaders in the field of bioinformatics were not trained in this
field; rather, they have been trained in basic specialties relevant to informatics, i.e. data management, scientific
computing, and statistical methods. Correspondingly, we emphasize basic training in these core specialties for
all students in the program. Students will be required to take classes in scientific computing (COMP16) and
statistics (STAT101) or have prior equivalent experience. Students coming from a background in the
computational/engineering fields will need to take an introductory molecular biology class for non-biologists
that will be developed by Prof. Marshall Edgell (or have equivalent prior experience). Higher level core
courses will be offered (many newly developed specifically for this Program, see Appendix 3) to address the
specific needs of students in the Bioinformatics Program. Required courses will include:




Biological Information Storage and Retrieval (INLS 110), a new course to be taught by Prof. Brad
Hemminger on databases and data mining.
Computational Genetics (BIO 162), a new course to be taught by Prof. Todd Vision providing introduction
to the fundamentals of computational molecular biology and sequence analysis
Structural Bioinformatics (BIOC 276), taught by Prof. Alexander Tropsha, covering computational
methods for protein structure analysis and prediction,
Advanced Methods in Bioinformatics (BMME 231), a new course to be taught by Prof. Michael Giddings
covering machine learning approaches in bioinformatics.
Students will also be expected to participate in a Bioinformatics Discussion and Seminar, to be hosted each
semester by a different department. This course is designed to provide an open scholarly forum for the students
and to serve as a community-building exercise for the program. We will encourage attendance by
Bioinformatics faculty and other interested individuals. Electives will include both existing and new
specialized courses available for all trainees; examples include evolutionary biology, statistical genetics, and
stochastic processes in biology.
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We expect that most predoctoral trainees will finish their required course work within two years although
those lacking many pre-requisites might require part of a third year. All students will have two research
rotations in the first two semesters of the program. They will be able to choose their research mentors from all
training faculty irrespective of their departmental association. We expect that by the beginning of the third
semester, all predoctoral trainees will choose their primary research mentor, working in this professor’s
laboratory towards their Ph.D. Importantly, the research mentor will provide the financial support for the
student from this point on. It is expected that the students develop a working relationship with a secondary
mentor in a complementary field, who will actively participate in oversight of the student’s training program
and be on the thesis committee. For example, a student with a research mentor in Computer Science might find
a secondary mentor in Biochemistry. During the entire training period (five years on average), students will
participate in the Bioinformatics discussion group that will be organized and run in rotations by one of the
senior faculty mentors, and we expect that all students will attend PhD defenses of their peers. Students will
also be expected to present a seminar annually. In the initial years this can be a summary of current work in the
field, but beginning the third year it should be a description of the student’s own research. Summer research
internships with local biotech and pharmaceutical industries will provide valuable work experience for students,
and such internships will be encouraged in the early years of the training program. These internships will be
based on existing working relationships between senior faculty in the Bioinformatics Program and local
companies. For instance, four students in Dr. Tropsha’s laboratory participated in industrial rotations at
GlaxoSmithKline, BD Biosciences, Syngenta, and Pfizer last summer. Such internships have an additional
benefit of fostering ties between academia and industry.
b. Guidance and Monitoring
The progress of trainees will be reviewed regularly by the training program faculty. Upon entry to the
program, each trainee will be assigned to a member of the faculty. This faculty member will serve as the
trainee’s advisor until the student has identified a thesis or dissertation committee chair and second
complementary mentor. It is the responsibility of the student to meet regularly with the faculty advisor (or
committee chair) and keep the advisor aware of progress toward degree requirements. As training program
appointments are renewed annually, the faculty reserves the right not to renew the funding of a trainee who fails
to demonstrate satisfactory progress during a 12-month appointment. The training experience of all trainees
includes the Program course requirements, the Departmental PhD requirements, and the research rotation
requirements.
c. Degree Requirements.
Predoctoral Training: All trainees enroll in a degree program within the established degree programs in
participating departments. The predoctoral training typically leads to the Ph.D. degree. A minimum of 49
semester hours is required for the Ph.D. degree, including both the Departmental and the Training Program
requirements. In addition to required core courses, elective and prerequisite classes are selected in consultation
with the student’s advisor. Coursework in the first and second years is complemented by continuous research
assistantship experiences in projects ongoing at UNC-CH.
Teaching: There will be at least a semester-long teaching assistantship requirement for all trainees. The
motivation for this requirement is the observation that established teaching skills are increasingly important
criteria for success in academia. Trainees can fulfill this semester requirement as teaching assistants in core
informatics courses or relevant courses in their home departments.
d. Representative Examples of Curricula
See Appendix 3
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e. Industrial Training and Extramural Support.
The development of this expanded training program has already generated substantial interest among
industrial organizations throughout the Research Triangle Park. We have negotiated agreements with two
major local pharmaceutical companies, GlaxoSmithKline and BD Biosciences, which committed to support one
trainee each contingent upon funding for this training program from the UNC Office of the President. All
trainees will be encouraged to participate in industrial rotations after their first year. An example of an
agreement under development with GSK is shown in the Appendix 4. We will continue to seek additional
resources from local profit and non-for-profit organizations to increase the number of trainees and be able to
attract the most outstanding foreign applicants. The requested support from the Office of the President will
allow us to attract future extramural funding for the program from major Federal foundations such as NIH and
NSF as well as private institutions and foundations.
4. Trainee Candidates
a. Recruitment Plans and Selection Criteria
The availability of this training program will be indicated on the home pages of all participating
departments. A sample recruitment flyer has been drafted and is attached to this proposal as Appendix 5. Both
predoctoral and postdoctoral applicants apply directly to the Graduate Schools of UNC using the standard
admission forms. GRE scores are required. Applicants indicate the department and area of interest on their
application. Applications are forwarded by the Graduate School to the appropriate department. The Training
Program faculty work closely with the department to identify which applicants may be interested in
Bioinformatics.
In reviewing each application, the Admissions Committee will consider the qualifications of the individual
student including such criteria as grade point average, GRE scores, letters of recommendation, the statement of
the student’s interests, the institution granting the undergraduate degree and professional experience.
Additionally, minorities and women have priorities in the review process. Typical criteria for most departments
include average undergraduate GPA greater than 3.3 and average GRE score of 1300 for admitted students.
Careful consideration will be given to the candidate’s ability to successfully integrate into the Bioinformatics
Program.
C. RECRUITMENT OF UNDERREPRESENTED ETHNIC AND RACIAL GROUPS
Using UNC minority recruitment resources, we will participate in recruitment fairs at institutions such as
Gauladet, NC Central, NC A&T, Norfolk State and Prairie View. We will also develop and mail recruiting
posters to a number of predominantly minority institutions and post on our home page an invitation to
undergraduate students at these institutions to contact Program faculty.
D. RESPONSIBLE CONDUCT OF RESEARCH
Responsible conduct of research is taught formally in a course for all graduate trainees in the medical center.
The course covers human subjects, scientific misconduct, responsible authorship, and other topics. Attendance
in this course is required of all trainees.
E. HUMAN SUBJECTS –
Each research study carried out at UNC that involves the participation of human subjects is reviewed by the
Committee for the Protection of the rights of Human Subjects (IRB) prior to its initiation. As mandated by NIH
guidelines, al clinical research studies carried out at UNC must include appropriate representation of women
and minorities.
F. VERTEBRATE ANIMALS –
UNC projects involving the participation of vertebrate animals must be reviewed by the Institutional Animal
Care and Use Committee (IACUC) prior to its initiation.
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APPENDIX 1. RESOURCES COMMITTED BY UNC-CHAPEL HILL TO THE CAROLINA
CENTER FOR GENOME SCIENCES.
RECURRING: (in 2000-2001 dollars)
EPA: $1.8 million (18 faculty positions funded at $100,000 per faculty, split equally between the Center and
the participating Department)
-New Faculty Appointments: The Chancellor committed 18 new faculty positions for the CCGS. The
positions are distributed amongst the Center’s founding academic partners:
-College of Arts and Sciences: 6.5 positions
-School of Dentistry: 1 position
-School of Information and Library Sciences: 1 position
-School of Medicine: 4.5 positions
-School of Nursing: 1 position
-School of Pharmacy: 1 position
-School of Public Health: 3 positions
SPA: $100,000 for technical support for core facilities
Support for Genetics and Molecular Biology Curriculum (from SOM): $153,375 per year
Medical genetics resident (from SOM): $42,000 per year
Recurring overhead (future):
Average grants dollars per faculty $500,000 X 18 = $ 9 million
45% overhead recovery: $225,000 X 18 = $4.05 million
NON-RECURRING:
Provost funds 2000-2001: $2 million, used for equipment purchases for microarray, sequencing and
proteomics facility
Start-up funds from Provost: $275K/position x 18 = $4.05 million (split equally between the Center and the
participating department
EXTERNAL:
Howard Hughes Medical Institute: $2.6 million to develop mammalian genetics
Federal allocation: $2.25 million ($850,000 earmarked for programmatic development and $1.4 million for
one time infrastructure development to update animal facilities with new ventilated caging systems).
Hooker Proteomics Gift: $25 million for proteomics ($5 million per year for five years. To be used for
faculty recruitment, equipment purchases and program development)
Whitaker Foundation Award: $ 1 million to create a graduate training tract entitled “Functional Genomics
for the Biomedical Engineers”
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NIH Genetics Training Grant: $210,392 current year direct costs. This award includes stipend support for 8
predoctoral students per year.
SPACE.
Administrative space will be housed in the new Human Biomolecular Research Building. Participating
academic departments will provide research laboratories for faculty from their current allotted space. The seven
academic partners will be required to assist the CCGS by providing funds for upgrading existing physical space
to meet the changing scientific needs and requirements associated with genomics research. Although some of
the computational needs will be housed in the new Bioinformatics building, it is also understood that
experimental and computation projects are inherently linked and must interact. The design of adjacent “wet”
and “dry” space such as that in the new Human Biomolecular Research Building achieves this goal.
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FACULTY RECRUITMENT
UNC is aggressively recruiting leading specialists in experimental and computational genomics and
proteomics. The following advertisement appeared in one of the September 2001 issues of the Science
magazine.
Genomics at UNC-Chapel Hill
The Carolina Center for Genome Sciences
Providing context, meaning and utility to the immense catalogs of sequence data is a challenge orders-ofmagnitude more complex than previously faced. Yet, with these data, the potential for producing exciting bench-tobedside-to-population based paradigms is limitless. To fuel discovery and to capitalize on these extraordinary
opportunities during the post-genome functional biology era, the University of North Carolina at Chapel Hill has
established the newly integrated, multi-disciplinary Carolina Center for Genome Sciences. Through the efforts of the
Center and its member academic departments, 16 outstanding faculty were recruited last year:
Shawn Ahmed: The Department of Genetics, School of Medicine and the Department of Biology. Research
Area: Telomere replication, DNA damage, and germline immortality
Dennis Cheek: School of Nursing
Research Area: Cardiovascular
Frank Conlon: The Department of Genetics, School of Medicine
Research Area: Heart development, Mesodermal patterning, T box genes
Greg Copenhaver: Department of Biology, College of Arts and Sciences
Research Area: Centromere structure, tetrad analysis, Arabiposis
Brad Hemminger: The School of Information and Library Sciences
Research area: Medical and bio-informatics, Computer-human interfaces, Computer-supported collaborative
work Information visualization
Jason Leib: The Department of Biology, College of Arts and Sciences
Research Area: Transcriptional networking, microarray analyses
Rihe Liu: The Division of Medicinal Chemistry, School of Pharmacy
Research Area: RNA: protein fusion arrays
Fernando Pardo-Manuel: Department of Genetics, School of Medicine
Research Area: Female meiosos, Chromosome segregation, Non-mendelian genetics
Charles Perou: Department of Genetics, School of Medicine
Research Area: Breast cancer, Genomics, Microarrays, Tumor classification, Drug resistance
Larysa Pevny: Department of Genetics, School of Medicine
Research Area: Neural induction, Neurogenesis, SOX proteins
David Threadgill: Department of Genetics, School of Medicine
Research Area: Disease susceptibility, Mutagenesis, Colon cancer, Genetic engineering, Microarrays
Debbie Threadgill: Department of Genetics, School of Medicine
Research Area: C. jejuni, Glycobiology, Genetics of blycosylation, Peripheral neuropathy, Host-pathogen /
symbiont interations
Marcia Van Riper: School of Nursing
Research Area: Social genomics
Todd Vision: Department of Biology, College of Arts and Sciences
Research Area: Computational genetics, genome evolution and the architecture of complex traits
Fred Wright: Department of Biostatistics, School of Public Health
Research Area: Statistical Genetics
Fei Zou: Department of Biostatistics, School of Public Health
Research Area: Statistical Genetics
The Center continues to expand its faculty recruitment in genomics in association with The College of Arts and Sciences,
The School of Medicine and The School of Public Health. The following positions are available:
Bioinformatics: preference will be given to specialists in mathematical, statistical, and computer sciences. We
are looking for scientists who bring modern tools of theory, modeling and computation to bear on critical aspects of
biological information. We encourage applicants working at any level of biological organization, from biochemistry and
genomics to systematics and evolution; and using any appropriate quantitative approach, including combinatorial
analysis, data mining, and stochastic and geometric modeling. Depending on the topic, the primary appointment for this
position will be in the Departments of Computer Science, Mathematics, Operations Research or Statistics and/or an
appropriate Department in the School of Medicine.
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Biomacromolecules: preference will be given to those candidates that possess a broad base research focus in
bioinformatics and to those that desire an appointment in an excellent Chemistry department with active research
programs that include combinatorial chemistry, capillary electrophoresis, structural (X-ray, AFM, NMR) studies of
biomacromolecules, neurochemistry, realistic molecular dynamics of biomacromolecules, theory of enzyme reactivity or
RNA/DNA catalysis.
Biological Chemistry: Priority will be given to candidates with interests, broadly defined, in the areas of proteomics,
gene expression arrays, structural biology and the development and application of new chemical methods to the
investigation of problems in genomics. Primary appointment will be in the Division of Biological Chemistry of the
Department of Chemistry. Applications are strongly encouraged from candidates whose expertise will bridge the
interface between chemistry and biology.
Behavioral Phenotyping: Preference will be given to candidates with expertise in mouse behavioral phenotyping. We
are particularly interested in individuals with active research programs in neuroscience that focus on gene-behavior
interactions. The appointment for this position will be in the Department of Psychology, and the successful candidate
will also assume responsibility for the directorship of the Mouse Behavior Phenotyping Core of the interdisciplinary
Neurodevelopmental Disabilities Research Center.
Cellular Imaging: Priority will be given to applicants whose research involves the use and development of sophisticated
light microscopy techniques to study how protein complexes work as molecular machines in living cells and developing
organisms. Primary appointment will be in the Department of Biology.
Human Genetics: We are specifically targeting candidates interested in common diseases, cancer genetics,
structure/function and genomic organization. Physician scientists are encouraged to apply. UNC-Chapel Hill has
exceptionally strong programs in medical genetics, mouse genetics, and invertebrate genetics. The primary academic
appointment will be in the Department of Genetics, with the possibility of joint appointments in relevant Clinical
Departments.
Nutrition: We are seeking an individual with a doctorate in an appropriately related discipline and a track record in an
area of research focused on the use of genomics to study questions pertinent to the field of nutrition (e.g., genomics and
metabolism, genomics and nutrition epidemiology) to fill a tenure-track or tenured appointment in the Dept. of Nutrition
beginning on or after July 1, 2002. Rank will be determined by the applicant's qualifications.
Statistical Genetics: We are seeking candidates with a strong background in both statistics and genetics. We
are interested in persons who can develop and evaluate new statistical techniques, as well as assist in the
analysis complex genetics data bases. The primary appointment will be in the Department of Biostatistics
with the possibility of a joint appointment in the Department of Genetics or the reverse if appropriate.
Successful candidates will be expected to contribute to undergraduate, graduate or postgraduate teaching
and to establish an externally funded research program. Review of applications will begin on October 15, 2001.
Send curriculum vitae, a description of research interests, and four letters of reference to: Dr. Terry
Magnuson, Director of The Carolina Center for Genome Sciences, CB 7000, Room 43 MacNider,
University of North Carolina, Chapel Hill, NC 27599-7000. Please indicate the position of interest.
UNC is an equal opportunity/ADA employer. Women and minorities are encouraged to apply.
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APPENDIX 2. PARTICIPATING FACULTY MENTORS.
Max Berkowitz
Marshall Edgell
Michael
Giddings
Brad Hemminger
Jan Hermans
Clyde Hutchison
Andrew Nobel
Lars Nyland
Chemistry
We are interested in the elucidation of the intricate nature of
processes occurring in condensed phases. Thus we study the structure
and dynamics of water next to metallic surfaces, structural and
dynamical properties of surfactant monolayers on the water/air and
on water/oil interfaces and structural and dynamical properties of
phospholipid membranes. Our research is performed using molecular
dynamics computer simulation technique
Microbiology &
Dr. Edgell is exploring the use of the mathematical formalism of
Immunology
regression analysis to enhance the use of mutagenesis to test
hypotheses concerning protein folding and stability. This research is
bringing high throughput biophysics and computer modeling to bear
on hypothesis testing. The research is a collaboration drawing on
expertise from molecular genetics, computer modeling, biophysics
and statistics.
Microbiology/
Development of bioinformatics methods within the purview of
Immunology and proteomics (the comprehensive study of proteins expressed in a cell).
Biomedical
Particular focus upon methods by which multiple isoforms of
Engineering
proteins are expressed by single genes.
School
of Development of bioinformatics methods within the purview of
Information
and proteomics (the comprehensive study of proteins expressed in a cell).
Library Science
Particular focus upon methods by which multiple isoforms of
proteins are expressed by single genes.
Biochemistry and
Methods and techniques for molecular dynamics simulations of
Biophysics
proteins. Solvation models. Computational structural biology.
Microbiology &
Research interests: the minimal cellular genome, structural genomics,
Immunology
mutational analysis of protein stability and dimerization, transposable
elements and the evolution of the mammalian genome. This
laboratory has carried out investigations on biological systems
ranging from bacteriophage to mice. The unifying theme has been a
continuing search for improved methods to learn about gene function
from DNA sequence information. Current projects fall under three
main topics: Genomics, the L1 retroposon in mammals and directed
Mutagenesis.
My research interests that overlap the training grant are multivariate
Statistics
clustering and classification, pattern recognition, and complexity
regularization. To date my work has focussed on the asymptotic
properties of greedy growing algorithms and histogram estimation
schemes using data dependent partitions.
Computer Science
Self-Scheduling N-body Algorithms—a project to explore a family of
algorithms that rapidly compute N-body interactions. Efficient,
complex parallel algorithms for N-body calculations and constructive
solid geometry have been developed as part of the project.
Computational Structural Biology Research Resource-- research
resource providing biochemists, biophysicists and chemists with
high-performance software and hardware. My role is to design and
implement parallel methods of computation, for applications such as
molecular dynamics simulators. I also evaluate and recommend
computing hardware.
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Chemistry
Jan Prins
Computer Science
Scott Provan
Operations
Research
Jack Snoeyink
Computer Science
Alexander
Tropsha
School of
Pharmacy
Todd Vision
Biology
Fred Wright
Biostatistics
TROPSHA, Alexander
We attempt to accurately develop all-atom models for proteins for
which we have partial structural data. We work also to develop
quantum mechanical models for enzymatic active sites. We are
interested in coagulation proteins (serine proteases), HIV-1 RT,
P450's, p21-H-ras and sulfotransferases.
Interests: High-level programming languages; formal techniques in
program development; parallel algorithms and parallel computation;
compilation of programs for parallel execution.
Projects: Software and development for the DeltaSphere 3D Scene
Digitizer with Lars Nyland at 3rdTech, Inc. Irregular Parallel
Algorithms; algorithmic, language, compilation, and hardware
techniques for high performance execution of unstructured Parallel
Computing Resource for Structural Biology: parallel algorithms and
implementations for Molecular Dynamics simulations
Computational methods in networks and network reliability,
geometric and discrete optimization and polyhedral combinatorics.
Current problem areas: (1) designing networks with specified
performance capabilities such as sufficient throughput volume, small
communications delay, specified connectivity, or
enclosure/separation properties, (2) determining shortest paths in
stochastic networks with limited information about network
congestions, (3) characterizing and predicting geometric structure for
protein folding, (4) ongoing development of IDEAS, the
Instructional Database for Educational and Academic Software, a
teaching software platform.
Discrete and computational geometry; Analysis of algorithms;
Geographic Information Systems (GIS); Theory of computer science.
Applications of Computational geometry to protein structure analysis
and prediction.
The major area of our research is Biomolecular Informatics, which
implies understanding relationships between structures (organic or
macromolecular) and their properties (activity or function). We have
developed several methodologies and software tools for Computer
Assisted Drug Design (http://mmlin1.pha.unc.edu/~jin/QSAR.) We
have developed a new approach to protein 3D structure analysis and
prediction based on the principles of statistical geometry (Delaunay
tessellation). This approach affords determination of key structural
and sequence motifs responsible for protein function. Some of our
methodologies have been implemented on the Protein Structure
Workbench at http://mmlsun4.pha.unc.edu/3dworkbench.html.
Genome duplication and chromosomal rearrangement, map-based
analysis of complex phenotypes
Genetic linkage mapping, association studies, microarray analysis
and genomics. Interests also include robust methods for quantitative
trait mapping in humans and model organisms, and in haplotype
reconstruction approaches that do not require strong assumptions of
population history. Recent work includes draft annotations of the
human genome and methods for improving the estimation of gene
expression using oligonucleotide arrays.
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Principal Investigator/Program Director (Last, First, Middle):
Fei Zou
Biostatistics
TROPSHA, Alexander
Statistical genetics, Empirical likelihood, Bioinformatics
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Principal Investigator/Program Director (Last, First, Middle):
TROPSHA, Alexander
APPENDIX 3. TYPICAL PROGRAMS OF STUDY
The following is a typical academic program leading to the Ph.D. in Biochemistry with concentration in Bio-Medical
Informatics for a student with a biochemical background. This program assumes that the student has knowledge of
advanced calculus and a strong background in biochemistry and molecular biology. Elective experiences will be selected
in consultation with the student's advisor. Course credit hours appear after courses. Courses specific to this core appear
in bold.
First Year
FALL
COMP16
STAT 101
BIOL 162
Intro to Scientific
Programming
3
Statistical Methods I
Computational
Genetics
3
3
3
3
3
1
BIOC 205
BIOC 104, or
BIOC 110/111,
or
BIOC 117/118,
or
BIOC 134, or
BIOC 150-157
1-3 Research
rotation
Research
rotation
Summer
BIOC 212
Second Year
FALL
BMME 231
PHCO 211I
BIOC 1xx
Scientific writing
Industrial Rotation
Advanced topics in
Bioinformatics
Discovery Biology &
Pharmacogenomics
Experimental
Genomics and
Proteomics
SPRING
INLS 110
Biological
Information Storage
and Retrieval
3
Seminar
Enzyme properties
Adv. Mol. Biol.
Cell structure
Studies in str. mol.
biol; Phys. Biochem.
modules
2
3
3
3
3
1
1-3
2
1
3
SPRING
BIOC276
Structural
Bioinformatics
2
1
3
2
Dissertation research
1-3
Research
rotation
Later Years – Dissertation research as directed by individual advisors.
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Principal Investigator/Program Director (Last, First, Middle):
TROPSHA, Alexander
The following is a typical academic program leading to the Ph.D. in Computer Science with concentration in
Bioinformatics for a student with a computational background. This program assumes that the student has some
undergraduate biology and/or chemistry, and a strong background in computer science, which would include
probability/statistics and advanced calculus. Elective experiences will be selected in consultation with the student's
advisor to satisfy distribution requirements in Computer Science (12 hours: 3 theory, 3 systems, 3 applications) and to
prepare for comprehensive and qualifying exams. Course credit hours appear after courses. Courses specific to this core
appear in bold.
First Year
FALL
BIOL 162
COMP 202 or
COMP 204 or
COMP 235
MICR1xx
Computational
Genetics
Analysis of Algorithms
Software Design
Images,
Graphics&Vision
Introductory
Molecular Biology
Lab Research
rotation
SPRING
MATH 192
(COMP 205)
INLS 110
3
COMP 29069 or
COMP 203 or
COMP 254
COMP 291
Exam
2
Scientific Computation
3
Biological Information
Storage and Retrieval
3
Scientific visualization
Parallel and Distrib. C.
Image Processing and
Analysis
Prof. Writing in Comp
Sci.
Comprehensive,
Integrative Paper
3
3
3
Structural
Bioinformatics elective
Scientific visualization
Parallel and Distrib. C.
Image Processing and
Analysis
Physically Based
Modeling
3
3
Summer
Industrial Rotation
Second Year
FALL
BMME 231
COMP 202 or
COMP 204 or
COMP 235 or
COMP 29079
Advanced topics in
Bioinformatics
Analysis of Algorithms
Software Design
Images,
Graphics&Vision
Computational
Geometry
1
3
3
3
3
3
SPRING
MEDC276
COMP 29069 or
COMP 203
or
COMP 254
or
COMP 259
Exam
Qualifying Oral
Lab Research rotation
Later Years – Dissertation research as directed by individual advisors.
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3
3
3
3
Principal Investigator/Program Director (Last, First, Middle):
TROPSHA, Alexander
APPENDIX 4. TYPICAL INDUSTRIAL TRAINEESHIP AGREEMENT.
University of North Carolina at Chapel Hill
_________________Graduate Program
Graduate Industrial Traineeship (GIT)
in cooperation with
Glaxo Wellcome Inc.
Research Triangle Park, NC
Faculty Advisor: ______________
Total Funding: $ ______________
Period of Support: _________________
One graduate student from the Graduate Program in ____________will be placed as a graduate industrial
trainee with Glaxo Wellcome, Inc., Research Triangle Park, NC. Under the supervision of Dr. ____________
of Glaxo Welcome, Inc., and the faculty advisor, the trainee will engage in consulting, collaboration, research
and training related to the ___________ program at the company. The trainee will work ___hours per week for
the period ______________through _________. The trainee selected for this position is __________________.
_________________________
Faculty Advisor
__________
Date
_________________________
UNC Department Head
__________
Date
_________________________
University of North Carolina
__________
Date
_________________________
GlaxoWellcome, Inc.
__________
Date
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