Curriculum in Bioinformatics & Computational Biology - UNC Chapel Hill

Training

 

Degree Requirements

The BCB PhD program combines didactic training with research and teaching experience to prepare students for a growing number of careers in bioinformatics and computational biology.  There are six required elements described below that together ensure a high standard of scholarship and scientific proficiency.  It is expected that all students will complete these requirements within five years. 

PhD requirements at a glance:

Year 1

Year 2

Years 3-5

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PhD requirements in detail:

1. Coursework

The required coursework is designed with three tiers of formal training: foundational (introductory) courses, core modules, and electives. Since incoming students come from a broad range of disciplines (e.g., math, computer science, biology, genetics, statistics), it is important to ensure that all students have a common foundation on which to build their BCB training.  The first year is dedicated to establishing this foundation and training all students with a common set of core BCB courses.  Incoming students will consult with their first-year advisors in the BBSP first year group as well as the BCB Student Progression Director to select one or two introductory-level courses that address any specific deficiencies in their backgrounds. For students who do not require any foundational classes, these credit hours can be taken as additional electives to provide more in-depth training.  During their first year, most BCB students will also take six core modules, two in the first semester and four in the second semester.  Students will be expected to demonstrate competence in all six subject areas covered by the modules for the written qualifying exam.  Each module is a short course designed to address a specific topic in bioinformatics and computational biology.  Names and brief descriptions of each module are listed below.  Since bioinformatics and computational biology encompass diverse fields of study, students are required to take two electives to receive specialized, in-depth training in mathematical, computational, physical, or biological sciences to enhance their specific research interests. All electives must be approved by the student’s thesis advisor and the BCB Student Progression Director.

CCore BCB modules (1 credit each)

BCB 712 Databases, metadata, ontologies, and digital libraries for biological sciences

Course Description:
This module introduces the basic information-science methods for storage and retrieval of biological information.  Instructors review standard database types and their applicability to bioinformatics data generated in research laboratories.  Students learn the role of metadata and ontologies as standardization mechanisms for providing interoperability between different information resource types such as genetic sequences, microarray maps, and journal articles.

BCB 715 Mathematical and computational approaches to modeling signaling and regulatory pathways

Course Description:
This module provides an introduction to the basic mathematical techniques used to develop and analyze models of biochemical networks.  Both deterministic and stochastic models are discussed.

BCB 716 Sequence analysis

Course Description:
This module is designed to introduce students to concepts and methods in the comparative analysis of nucleic acid and protein sequences, including sequence alignment, homology search, phylogenetics and genome assembly.

BCB 717 Structural bioinformatics

Course Description:
This module introduces methods and techniques for protein modeling including structure determination, protein architecture, approaches to folding simulations, structure prediction, and structure based drug design.

BCB 720 Introduction to Statistical Modeling

Course Description:
The module will introduce foundational statistical concepts and models that motivate a wide range of analytic methods in bioinformatics, statistical genetics, statistical genomics, and related fields.

BCB 722 Foundations of Population Genomics
Course Description:
This course will cover the fundamental principles of population genomics. We will address such questions as: What are the evolutionary forces that have shaped the genetic diversity we see today? Can we distinguish one such force from another? Can we estimate their relative strengths? Is any of this relevant for studying the role of genetics in complex disease? The goal of the course is to equip students with foundational knowledge in the theory of evolution, which serves as the bedrock of modern biology, and to demonstrate its relevance to modern-­-day genetic applications in biomedicine.

Current Course Schedule

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2. Colloquium

The Colloquium meets once per week for one hour during the academic year.  Students receive one credit hour per semester for the Colloquium (BCB 710) and are required to participate for the first 2 years of graduate school.  The main goals are to expose students to the research interests of BCB faculty, and provide an opportunity for students to present their own work and receive input from their peers and faculty.  During the fall semester, the Colloquium agenda alternates between a “journal club” discussion and a faculty research seminar. During the spring semester, the Colloquium agenda alternates between journal club presentations by first and second-year students on research articles of their choice and research seminars presented by senior BCB students.  Such presentations provide students with valuable feedback on their research projects as well as opportunities to hone their oral presentation skills.  The Colloquium also hosts guest speakers throughout the year to present seminars that focus on relevant research outside UNC and on career opportunities in bioinformatics and computational biology.

Current Colloquium Schedule

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3. Rotations and Dissertation Research

All BCB students are required to complete three laboratory rotations before selecting a thesis advisor. These rotations will take place within the administrative structure of the joint first-year program (BBSP) such that all three rotations will be completed by the end of the second semester. The rotation selection process must be done in consultation with the assigned first-year advisor and the Student Progression Director. Students are advised to conduct at least five interviews with potential rotation advisors among BCB core and resource faculty. At the end of the third rotation, each student must identify a thesis advisor and home department/curriculum from which they will receive a degree. For a complete list of BCB faculty and descriptions of their research interests, go to the faculty directory.

Students who commit to joining BCB will then select a thesis committee in consultation with their advisors and the Student Progression Director. The committee consists of at least five members, three of whom must be BCB faculty. For more details, click here. The thesis committee chair must be a BCB faculty member, but cannot be the thesis advisor/mentor in order to prevent possible conflicts of interest. Annual committee meetings are to be held starting in the fall semester of the third year to ensure that sufficient progress is being made to complete the dissertation within five years. Students are required to present an oral progress report at each meeting, followed by a discussion of goals for the following year.

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4. Qualifying Exams

Students are required to take a qualifying exam to demonstrate proficiency in the fundamentals of bioinformatics and computational biology, as well as competence in synthesizing these fundamentals into original scientific hypotheses or approaches. The exam consists of both written and oral components.

The written component is taken at the end of the first year, typically in late May. The exam can be postponed until the end of the second year if necessary. Students are assigned a reading list of about 10-15 research papers and a list of key analytical skills that should have been acquired from core coursework. These lists are released two weeks prior to the exam date. The exam itself is administered over the course of four days. Exams are graded as either pass or fail. Students who do not pass have the option to take the exam again the next year. Students who fail a second time are dismissed from the program.

The oral component of the exam must be taken before the end of the third academic year. Students are expected to submit a 12-page proposal to their respective thesis committees based on their dissertation research project. Details regarding the content of these proposals should be discussed at the annual thesis committee meetings at the beginning of the third year. Detailed guidelines for conducting the exam can be found here. Once the proposals are submitted to the thesis committees, students are required to defend their proposals during an oral exam given by their respective committees. Students are expected to demonstrate sufficient knowledge in their chosen research area as well as feasibility in completing their research plan by the end of the fifth year. The specific content of these oral exams is dictated by the thesis committees and moderated by committee chairs. Students who fail have the option to take the exam again at a later date under terms and conditions set by their committees. Students who fail a second time will be dismissed from the program.

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5. Teaching and Professional Development

Students are required to serve as teaching assistants for one course anytime during their second or third years. Students are encouraged to TA for a BCB module to fulfill this requirement but opportunities exist to TA other courses. In addition to attending classes and assisting with grading exams, teaching assistants must also participate by preparing and delivering at least one complete lecture.  Teaching experience provides students with an opportunity to develop their pedagogical skills, in addition to reinforcing scientific concepts that they have learned in the program.  Students are also encouraged to participate in summer internships and other training opportunities at local companies and research institutes.  All BCB students are strongly encouraged to present their work at scientific meetings, either as poster or oral presentations.  The BCB program provides students with some travel support to subsidize the cost of attending such meetings.

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6. Dissertation, Oral Defense, and Publication(s)

Students are required to submit a dissertation by the end of the fifth year unless the program director and respective thesis committees approve an extension.  Specific terms and conditions must be set prior to approval of an extension.  Dissertation projects are presented by each student in a formal seminar that is open to the public.  The seminar is followed by a closed oral defense with the student and his/her thesis committee.  The committee will use this time to ask in-depth questions about the thesis research and to ensure the student’s overall scientific proficiency in the field.  Although it is unlikely for students to fail at this point, thesis committees have the option to pass students conditionally if an unequivocal decision is not made.  In such cases, students will only receive their degrees after successful completion of additional requirements determined by the committees.  All students are required to publish at least one primary-author, peer-reviewed journal article or conference proceeding.  Only under rare circumstances will this requirement be excused via unanimous agreement by the thesis committee.

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