Proposal for a Ph.D. in Bioinformatics/Comp.Bio
Request for Authorization to Plan a New Doctoral Degree Program in Bioinformatics and
Computational Biology (Ph.D.)
Date: November 21, 2005
Constituent Institution: The University of North Carolina at Chapel Hill
CIP Discipline Specialty Title: Biological Sciences/Life Sciences
CIP Discipline Specialty number: 22
Level: D
Exact Title of the Degree: Bioinformatics and Computational Biology
Exact Degree Abbreviation: Ph.D.
Does the program constitute a substantive change as defined by SACS?
No
a) Is it a more advanced level than those previously authorized? Yes
b) Is the program a new discipline division? No
Proposed date to establish degree: Fall, 2007
Do you plan to offer the proposed program away from campus during the first year of
operations? No
This proposal to establish a new degree program, a new Ph.D. in Occupational Science, has been
reviewed and approved by the appropriate campus committees and authorities.
____________________________________________________________________________
Chancellor of the University
Date
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Proposal for a Ph.D. in Bioinformatics/Comp.Bio
CONTENTS
Page
Section 1: Description of the BCB Graduate Degree Program
A. Statement of Educational Objectives
B. Relationship of Proposed BCB Graduate
Degree Program to Institutional Mission
C. Relationship of Proposed Program to Existing Programs
D. Special Features or Conditions that Make
UNC-Chapel Hill an Appropriate and Unique Place to Initiate
the Proposed BCB Graduate Program
Section 2: Other Institutions Offering Similar Programs
Section 3: Enrollment Estimates
Section 4: Current and Projected Demand for Graduates
Section 5. Procedures to Be Used to Plan the Proposed Program.
Section 6: Opportunities for Research Support
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Proposal for a Ph.D. in Bioinformatics/Comp.Bio
SECTION 1. DESCRIPTION OF THE PROGRAM
The major objective of this proposal is to obtain authorization to develop a new PhD
Curriculum in Bioinformatics and Computational Biology (BCB). This is a natural evolution of
the existing non-degree granting BCB Training Program that was established at UNC in 2002
and that has been successfully recruiting and training students in its three years of existence. The
faculty members involved in computational biological research are distributed among more than
a dozen departments at UNC-CH yet they have many common research interests and equally
important, strong commitment to training students in the broadly defined areas of Bioinformatics
and Computational Biology. The majority of these scientists are members of the Carolina Center
for Genome Sciences (CCGS) that houses the BCB Program. With the recent recruitment of a
large group of bioinformatics faculty, a strong need has been identified at UNC to expand the
BCB Program to support the computational and experimental genomics research enterprise and
produce the next generation of leading specialists in this highly interdisciplinary research area.
A. A brief description of the program and a statement of educational objectives
The landscape of computational biomedical research at the University of North Carolina
at Chapel Hill (UNC) has changed drastically in the last several years concurrent with rapid
growth of genomics and bioinformatics and computational biology research nationwide. The
Carolina Center for Genome Sciences (CCGS) was established in 2001 with a mission to support
collaborative research projects in experimental and computational genomics and promote
training of new specialists in these disciplines. To meet this goal, ten faculty positions were
allocated by the Deans of the School of Medicine and the College of Arts and Sciences to recruit
specialists in Bioinformatics and Computational Biology, with several additional positions made
available by individual departments. These efforts have brought to UNC just in the last five
years a new cohort of young, motivated scientists in experimental and computational genomics
and proteomics. As the fields of bioinformatics and computational biology continue to grow and
become integral parts of genomics and molecular biology research, the need for graduate training
programs that bridge the biological and mathematical and computational sciences will also
increase. Computational biologists and bioinformaticians most be sufficiently trained in genetics
and molecular biology in order to identify important biological problems that require quantitative
methods of analysis, while at the same time posses the computational and mathematical skills
needed to solve these problems. To address these requirements, The Graduate Training Program
in Bioinformatics and Computational Biology (BCB) was established at UNC in 2002. The
program was started with a competitive intramural grant, and last year was awarded an NIH
training grant. In its current form the BCB graduate program does not grant a degree, rather
students receive a Certificate of Training in Bioinformatics and Computational Biology. To
obtain this certificate, students must fulfill all the requirements of their home department, while
at the same time completing the work required by the program. This consists of laboratory
rotations, participating in the BCB colloquium, and completion of a year long modular course.
These additional expectations coupled with the already high course load of disciplines such as
mathematics, statistics, and computer science places an undue burden on the students and
minimizes the amount of research training they receive in the first two years of their graduate
careers. Therefore, it has become clear that while the BCB program has been very successful at
attracting high quality students and enjoys growing enthusiasm among UNC faculty, to
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Proposal for a Ph.D. in Bioinformatics/Comp.Bio
adequately train the next generation of computational biologists and bioinformaticians requires a
Ph. D. dedicated to these fields.
The BCB program defines its mission broadly as training new generations of researchers
who specialize in the development and application of innovative mathematical, computational,
statistical, and software tools to important biological and biomedical problems. The Ph.D.
program would provide students with the in depth training in mathematics, statistics and
computer science needed to conduct research in bioinformatics and computational biology, while
at the same time providing them with a solid background in genetics and cell and molecular
biology. The proposed curriculum also contains sufficient flexibility so that it can be tailored to
meet the individual needs of students with diverse research interests.
The new program offering a Ph.D. in Bioinformatics and Computational Biology will
accept academically qualified applicants who have completed undergraduate degrees in
biochemical, computational, mathematical, or statistical disciplines. This program will require 54
credits and include content in four domains: (a) computational, statistical, mathematical, and
information science, (b) molecular and structural biology, (c) research design and methodology,
and (d) competencies for an academic career. The course of study will culminate in a doctoral
dissertation that generates new knowledge in Bioinformatics and Computational Biology.
Graduates with this academic degree will be prepared to: (a) conduct active original research in
the area of PhD specialization, (b) engage in the interdisciplinary collaborative research with
experimental scientists specializing in genetics, genomics, and proteomics (c) teach professional
courses in the area of their expertise.
B. Relationship of Proposed BCB Graduate Degree Program to Institutional Mission
UNC-Chapel Hill generates premier scholarship in biological and biomedical sciences.
The Ph.D. in Bioinformatics and Computational Biology is consistent with the University’s
mission of advancing academic excellence and public service. The BCB program has had and
will continue to have several positive effects on the quality of graduate education and research at
UNC. It will help bring highly qualified and motivated students to UNC who are interested in
working at the interface between computational and experimental biomedical disciplines. It will
expand formal course offerings at UNC to include most current and advanced topics in
computational biomedical research and therefore will enrich current departmental PhD programs.
It will foster the collaboration between computational and experimental BCB mentors distributed
between participating UNC departments via joint supervision of students’ rotation and PhD
projects. At the current stage, the program offers the Certificate of Training in Bioinformatics
and Computational Biology which complements traditional PhD degrees received via
participating graduate programs. We believe that since both the program and the fields of
bioinformatics and computational biology have matured at UNC over the past three years (as
indicated by the recognition of the BCB Program by the NIH, which recently awarded a 5-year
grant to UNC) there is an immediate need to transition into a stand-alone PhD granting
curriculum.
C. Relationship of Proposed Program to Existing Programs at UNC.
Student training is naturally an important component of all research programs at UNCCH. There are sixteen PhD programs and curricula hosting BCB faculty, which are currently
associated with the BCB training program as follows:
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Proposal for a Ph.D. in Bioinformatics/Comp.Bio

Eight programs in the School of Medicine: Biochemistry and Biophysics, Cell and
Developmental Biology, Cell and Molecular Physiology, Pathology and Laboratory
Medicine, Pharmacology, Biomedical Engineering, Microbiology and Immunology, and
Curriculum in Genetics & Molecular Biology;
 Five programs in the College of Arts and Sciences: Biology, Chemistry, Computer Science,
Mathematics, Statistics & Operations Research;
 One in each of the Schools of Public Health (Biostatistics), Pharmacy (Medicinal Chemistry),
and Information and Library Science.
There has also been a dramatic expansion of organized interdisciplinary training efforts at
UNC-CH in the past five years. The examples of institutional training programs include: Cell
and Molecular Biology Training Program supported by NIGMS; Cellular and Molecular
Biophysics program (funded by NIH), Cancer Biology (funded by an NCI training grant),
Vascular Biology (funded by NIH), Functional genomics of model organisms (funded by
Novartis to the Department of Biology in 2000). All of these programs offer interdisciplinary
training with the students receiving their degrees in one of the existing PhD programs. In
addition, there are several interdisciplinary PhD granting curricular which provide more
comprehensive graduate training in areas where typically there are no comparable departmentbased PhD programs (e.g., Cirricular in Toxicology, Materials Science, Genetics). The
experience accumulated at UNC-CH in establishing and managing interdisciplinary training
programs provides an extremely favorable and nurturing environment for the BCB program. The
BCB Program has the broadest appeal to UNC departments in both basic biomedical as well as
mathematical, statistical, and computational sciences (see support letters from Department
Chairs). This is the only computationally oriented biomedical training program at UNC Chapel
Hill that provides a unique contribution to the graduate training offering at UNC-CH.
D. Special Features or Conditions that Make UNC-Chapel Hill an Appropriate and
Unique Place to Initiate the Proposed BCB Graduate Program
There is strong enthusiasm and support for the Training Program in Bioinformatics and
Computational Biology among a wide spectrum of UNC-CH academic and research units. Both
administrators and faculty recognize the importance of this interdisciplinary training program to
enhance education of UNC students interested in biological computing as well as to foster
collaboration between experimental and computational scientists.
There is a strong need to sustain and expand this unique interdisciplinary training
program at UNC. Continuing aggressive recruitment of faculty in Bioinformatics and
Computational Biology, dedication of the CCGS to these areas of research, and an obvious
interest in this program among current and prospective trainees indicate that the need for the
BCB program at UNC will continue to grow. The expanded program will better serve the
educational needs of both current and prospective UNC students as well as faculty interested in
computational biomedical research. It will continue to foster the collaboration between
computational and experimental faculty. Many innovative research projects are conducted by
graduate students, and the expansion of the BCB training program will enhance the number and
quality of collaborative projects between faculty who in many cases jointly supervise students’
rotations or research projects.
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Proposal for a Ph.D. in Bioinformatics/Comp.Bio
Section 2. Other Institutions Offering Similar Programs
It is important to consider the BCB program at UNC in the context of similar efforts
elsewhere. There is an intense demand for bioinformaticists and computational biologists in the
academic and industrial marketplace. It is anticipated that this need will grow in the coming
decades (Pool and Esnayra, 2000;1 Zatz, 20032). Although many programs have been established
in recent years (a recent survey by Bioinform.com lists 74 programs nationwide3 including the
UNC program), the demand for specialized training programs in bioinformatics remains very
strong.2 This is also indicated by the interest expressed by major local pharmaceutical and
biotechnology companies in the BCB program.
The deficit of appropriately trained scientists in bioinformatics and computational
biology can be attributed, in large part, to its highly interdisciplinary nature. Trainees need to
gain fluency in multiple, and very different, disciplines (e.g. biochemistry, biophysics and
genetics, but also computer science and statistics). It is a serious challenge for traditional
academic departments to produce well-trained bioinformatics and computational biology
graduates and do it in a finite amount of time. Thus, we feel it is necessary to view
bioinformatics and computational biology as fields unto their own, with unique training
requirements that are best met in an independent graduate training program. The development of
such a program at UNC-CH has been and will continue to be a collaborative effort among all the
relevant faculty and departments.
Section 3: Enrollment Estimates
Our projections are based on the trends observed in three years of the BCB program operation as
a non degree-granting curriculum and expected level of financial support for the Program. For
instance, in 2005 we received 46 applications, made 13 offers of admission, and matriculated 6
students. Four of the students are eligible for the support from the NIH (American citizens), and
three of them are currently supported by the NIH training grant using all three available slots.
We expect that the combination of the NIH and UNC funding will allow us to recruit 7-8 new
students every year and support them for 18 months.
Section 4: Current and Projected Demand for Graduates
#
The Labor Department's Bureau of Labor Statistics recently reported 4 that “when
scientists began decoding the human genome in 1990, they collected staggering amounts of
biochemical data. To organize these data, employers turned to computer experts or to biologists
who had some computer knowledge. But as demand increased, the field of bioinformatics grew
from a small sideline to an established career. Bioinformatics specialist is now a common job
title…” The North Carolina Biotechnology Center publication “North Carolina's Biotechnology
Community, 2002,” lists 156 biotechnology-related companies, 77 contract research and testing
companies, and 223 supporting companies and nonprofit organizations. Many of these
companies and organizations employ bioinformatics and computational biology specialists in
their workforce. The number of biotechnology related companies in North Carolina is increasing
1
Pool, R. and J. Esnayra (2000) Bioinformatics: Converting Data to Knowledge. National Academy
Press. Washington, D.C.
2
Zatz, M. (2002). Bioinformatics Training in the USA. Briefings in Bioinformatics, 3, 353-360.
3
Bioinform.com, August 2, 2004
4
Crosby, O. New and emerging occupations. http://www.bls.gov/opub/ooq/2002/fall/art02.pdf
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Proposal for a Ph.D. in Bioinformatics/Comp.Bio
every year, and specifically in Research Triangle Park. This growth provides a positive outlook
for graduates of our new BCB graduate program.
Section 5. Procedures to Be Used to Plan the Proposed Program.
In its three years of existence the BCB program has established a working infrastructure
that will provide necessary scientific leadership and administrative support during the planning
process. The BCB Program is directed by Dr. Alexander Tropsha, 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 bioinformatics). Administration of the BCB Program is through the CCGS office,
which provides partial funds for the Program administrative staff (additional funds have been
allocated from the UNC-GA grant awarded to the BCB program last year). The Center has
recently established an administrative support infrastructure, which includes a staff of three
people in support of three training programs supported by the Center. Ms. Cara Marlow directs
this support group and serves as the Student Administrative Assistant. This support group also
includes Ms. Sausyty Hemreck (technical support including meeting and core course scheduling,
budget management, travel reimbursement etc.) and Mr. C. Hawkins (computer and web
support). The program offices are currently located in room 4309 in the Biomolecular Research
Building.
Three committees have been established to assist Dr. Tropsha in the operation of the
program. The Senior Advisory and Executive committee counsels the Director on strategic
planning issues related to the general direction and progress of the program. In currently includes
Jeffrey L Dangl (Biology), M. Gregory Forest (Math), Pat Sullivan (Genetics), and Jan Prins
(Comp. Sci.). The Admissions Committee is involved in reviewing all incoming applications and
in making decisions concerning students’ funding by the BCB Program. In consists of J. Scott
Provan (chair) (OR/Stat), Brad Hemminger (SILS), Ethan Lange (Genetics), Todd Vision
(Biology), and Wei Wang (CS). Curriculum and Progression Committee is responsible for
developing and maintaining the rigorous program of education for each BCB student, taking into
account both individual student’s background and experience and the uniform goals of the BCB
program. In includes Tim Elston (Math), Morgan Giddings (Micro. & Immunol), Jack Snoeyink
(Comp. Sci), Fred Wright (Biostat), Perry Haaland (BD Biosciences, industry rep), and Vic
Weigman (Student Representative). Initially, members of the above committees will be involved
in the development of the PhD Curriculum. They are expected to generate the advanced draft that
will be distributed for comments to all faculty in the BCB program. The final proposal approved
by all members of the BCB Program will be submitted to the Graduate School for the approval.
Section 6: Opportunities for Research Support
Bioinformatics and computational biology are extremely interdisciplinary in nature
having their roots both in computational, mathematical, and statistical sciences as well as in all
basic biochemical and biomedical areas. The majority if not all UNC scientists who are heavily
involved in computational biomedical research have strong ongoing collaborations with
experimental scientists. Correspondingly, it was natural for us to recognize two highly related
groups of BCB members, i.e. core faculty (who mostly conduct computational research aimed at
hypothesis generation) and resource faculty (who mostly conduct experimental biomedical
research and generate experimental data used for developing and testing computational and
mathematical/statistical models or pose important biological problems that can be addressed by
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Proposal for a Ph.D. in Bioinformatics/Comp.Bio
computational means). These two groups complement each other by providing an outstanding
research environment for collaborative training of young specialists in BCB areas.
The BCB training program currently includes 25 core and 24 resource members.
Members of the BCB faculty have appointments in departmental-based graduate programs at
UNC; many also have appointments in the interdepartmental curricula that grant PhD degrees.
In addition, the majority of BCB faculty are active members of the CCGS, which helps promote
collaboration between experimental and computational scientists.
Collectively these
investigators hold over # federal grants and participate in over # different Program Project or
Center grants (Table 3). There is a mix of junior and senior faculty with # assistant, # associate
and # full professors who can serve as mentors for our BCB students.
UNC mentors are well funded to provide research support to BCB students after they
have completed their first year of training when they are supported by the training program.
Currently, two sources provide financial support for the BCB trainees in their first year: a grant
from the UNC General Administration ($100K/year) and a recently awarded grant from the NIH
that currently funds three students, with anticipated increase in funding to support eight students
starting next (2006-2007) academic year. It is critical for the continuing competitive support
from NIH to have ongoing matching support from UNC.
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