School of Medicine—Graduate Programs

The University of Pittsburgh School of Medicine has a long tradition of research excellence and training by world-class faculty committed to mentoring the next generation of scientists. It offers a variety of programs leading to the Doctor of Philosophy, the Master of Science, or a certificate. In addition, it works with other schools of the University through collaborative graduate programs. The School of Medicine offers an MD program, described in the professional section of this bulletin. It also offers a joint MD/PhD program enabling exceptionally able students to earn both degrees simultaneously.

Contact Information

Associate Dean for Graduate Studies

524 Scaife Hall

412-648-8957

Fax: 412-648-1977

www.medschool.pitt.edu/grad/grad.asp

Biomedical Informatics Program

Biomedical informatics is the science and engineering of information handling in health-care delivery and biomedical research. It studies and develops models of the various aspects of health-care delivery and biomedical research in order to better understand how they operate. Those models suggest interventions that my improve health-care delivery and biomedical research, including new methods for capturing, organizing, analyzing, and conveying clinical information to clinicians and researchers. Experiements are performed in which the effect of promising interventions on health-care delivery or biomedical research are observed and compared to existing methods, which serve as controls. The analysis of the results of such experiments can lead to greater understanding of health-care delivery and biomedical research, and thereby to methods with which to improve them.

Example areas of investigations in biomedical informatics at the University of Pittsburgh include the development and evaluation of new computer-based methods for (1) analyzing proteomic data to diagnosis disease, (2) supporting clinical trials, (3) providing clinical information to patients, (4) understanding the mechanism of diseases from genomic data, (5) natural language processing of electronically available medical text to extract important clinical features, (6) alerting clinicians when patient care appears atypical, (7) real-time detection and assessment of outbreaks of infectious disease and (8) teaching clinical trainees.

This program offers both master’s and doctoral degrees. Most students choose to follow a general course of study in biomedical informatics; some, however, elect a specialization in one of the following areas: bioinformatics, dental informatics, health services research, or biosurveillance/infectious disease informatics. The specific curricula for the specializations, which are variations of the general course of study in biomedical informatics, can be found on the Training Program Web site at www.cbmi.pitt.edu.

Individuals who want a less intensive exposure to informatics may seek a 15-credit certificate in lieu of an academic degree. The biomedical informatics certificate can be a means of augmenting professional training in fields related to informatics and/or fulfilling educational needs associated with a professional position. Trainees across all health professions are welcome.

Contact Information

Toni Porterfield

Training Program Coordinator

M-183 VALE

412-647-7113

Fax: 412-647-7190

E-mail: tlp@cbmi.pitt.edu

Admissions

Financial Aid

Curriculum

Course Listing

Degree Requirements

In addition to School of Medicine requirements, all University requirements as detailed in the Regulations Pertaining to Graduate Study at the University of Pittsburgh section of this document apply.

MS Degree

Credits: The Master of Science in Biomedical Informatics requires a minimum of 36 credits consisting of required biomedical informatics core (4–7 credits); required computational competency (6 credits); biomedical informatics distribution (12 credits minimum); electives (6 or more credits); and research methods (8 or more credits including BIOINF 2480: Master’s Thesis/Project Research).

All required courses must be taken for a letter grade, with the exception of the Journal Clubs/Colloquiums and some independent and/or dissertation studies (to be determined by faculty advisors). A minimum “B” grade is required in all graduate courses.

Research Project or Thesis: A key element of the program is a research project with two key deliverables: (1) the writing and submission of a paper of publishable quality based upon the research and (2) the completion of an oral examination on its contents. A master’s project committee will oversee the student’s research progress, including the oral comprehensive examination. Students have the option of developing their projects into a formal master’s thesis.

Successful completion of the oral examination on the research project satisfies the comprehensive examination requirement of the University's Committee on Graduate Studies. Final certification of the completion of the master's degree requires submission of the hard copy of the master's research project to the program coordinator.

PhD Degree

Credits: To earn the PhD degree in biomedical informatics, a student must complete a program of study approved by a committee of biomedical informatics faculty. This program must include a minimum of 72 credits; successful completion of a written preliminary evaluation followed by an oral exam; an MS-level research project involving significant research, design, or development work and a written report; successful completion of a doctoral comprehensive examination composed by a doctoral committee; and 18 or more credits of research work leading to an acceptable dissertation. All required courses must be taken for a letter grade, with the exception of the Journal Clubs/Colloquiums and some independent and/or dissertations studies (to be determined by the faculty advisors). A minimum “B” grade is required in all graduate courses.

Admission to Candidacy/Dissertation: To qualify for admission to candidacy, a student must have completed formal coursework with a 3.3 GPA or higher, successfully completed the master’s level project, passed the comprehensive examination, and received approval of the proposed subject and plan for the dissertations from their dissertation committee following a prospectus meeting. The dissertation committee usually includes the principal dissertation advisor and four additional University graduate faculty (a majority of the committee must be biomedical informatics core faculty).

An appropriate dissertation project involves a substantive piece of original and independent biomedical informatics research, grounded in an appropriate mode of literature and providing a significant contribution to the field. The dissertation must be successfully defended in a public oral defense. The dissertation process will follow the applicable regulations and procedures of the University and the School of Medicine, as described in the Regulations Pertaining to Doctoral Degrees section of this document.

Certificate in Biomedical Informatics

The biomedical informatics certificate is a 15-credit (minimum) experience. The curriculum of all students in this program will have the following general structure:

Research Project: The research project should be summarized in a report commensurate with its scope, one copy of which must be submitted to the training program coordinator after approval by the student’s research advisor.

Additional Requirements for Master’s, Doctoral, and Certificate Students in Biomedical Informatics

Instruction in the Responsible Conduct of Research: This Web-based set of instructions and evaluation modules may be accessed at http://rpf.health.pitt.edu/rpf.

Attendance at and participation in the Center for Biomedical Informatics’ invited lectures, symposia, conferences, etc. (e.g., The Annual Lindberg Lecture, the IAIMS Retreat, and particularly the Annual Training Program Retreat). Such lectures are considered important educational experiences, as well as introducing students to primary researchers and their work in the field of biomedical informatics.

Training Faculty

Course List

Funding

Clinician Educator Training Program (CETP)

This program is designed for a diverse group of individuals whose career focus is medical education and clinical teaching. These include fellows and faculty in general medicine, subspecialty medicine, pediatrics, family medicine, and psychiatry. The CETP offers both a master’s degree and a certificate in medical education.

Contact Information

Tammy Dennis

Coordinator of Student Services

Institute of Clinical Research Education

200 Meyran Ave, Room 302

Pittsburgh, PA 15213

412-692-2686

Fax: 412-586-9672

www.icre.pitt.edu/cetp

Admissions

Admissions Criteria:

• U.S. citizens, non-citizen nationals, or permanent residents.
• Completion of the MD, DDS, DMD, DC, OD, ND, PharmD, PhD, or DNS degree.
• A high level of interest and potential for the pursuit of long-term career focus in teaching and leadership positions in medical education programs.

Financial Assistance

Curriculum

Degree Requirements

In addition to School of Medicine requirements, all University requirements pertaining to the master’s degree apply as detailed in the Regulations Governing Graduate Study at the University of Pittsburgh.

Master of Science

The degree requires completion of a minimum of 30 credits including the core curriculum, required elective courses, and a thesis or substantive research project.

Credits: Required courses include MEDEDU 2100 (2 credits), MEDEDU 2110 (2 credits), MEDEDU 2140 (1 credit), MEDEDU 2080, MEDEDU 2120 (1 credit), MEDEDU 2130 (1 credit), BCHS 3002 (2 credits), MEDEDU 2150 (1 credit), MEDEDU 2005 (1 credit), MEDEDU 2010 (3 credits), MEDEDU 2020 (4 credits) MEDEDU 2040 (1 credit), and MEDEDU 2160 (1 credit).

Thesis or Substantive Research Project: Three credits will be awarded for the project. The project must satisfy the following requirements: (1) be primarily independent work by the trainee, (2) be reported to the respective sponsoring faculty in written form, and (3) form the basis for a comprehensive review of competence by a committee of at least three training faculty recommended by the major advisor and approved by the program director. The four standard mechanisms for the project are:

• Formal curriculum development project: A candidate may submit a formal curriculum development project, including the planning or completion of a needs assessment, implementation of the curriculum, and evaluation and feedback.
• Peer-reviewed manuscript: A candidate may elect to write one first-author manuscript related to the trainee’s research project in medical education or curriculum development, as evidence of independent work. The manuscript must represent original work and meet the submission requirements of peer-reviewed journals.
• A standard thesis: A candidate may elect to write a master’s thesis in his or her field of specialty. A thesis produced under this option must conform to all applicable university policies regarding theses (visit http://www.pitt.edu/~graduate/etd for details on submitting theses electronically).
• A grant proposal for an R01, K-award, or equivalent award: A junior faculty candidate may elect to write an R01 or equivalent research proposal on which he or she is the principal investigator and to submit this proposal as evidence of his or her ability to plan and conduct independent research in the area of medical education.

Certificate in Medical Education

The certificate in medical education requires the completion of 15 credits, including MEDEDU 2100 (2 credits), MEDEDU 2140 (1 credit), MEDEDU 2130 (1 credit), MEDEDU 2220 (1 credit), and MEDEDU 2230 (2 credits).

Training Faculty

Course Listings

Clinical Research Training Program (CRTP)

Funded through the National Institutes of Health (NIH), the Clinical Research Training Program (CRTP) aims to teach trainees the skills necessary to design and conduct high quality clinical research involving human subjects. The CRTP offers a certificate and a Master of Science in Clinical Research. Fundamentals of clinical research methods and biostatics are taught through an eight-week intensive summer program. Didactic and experiential training in grant writing and ethics of human subject research are major components of the training.

Contact Information

Tammy Dennis

Coordinator of Student Services

Institute of Clinical Research Education

200 Meyran Ave, Room 302

Pittsburgh, PA 15213

412-692-2686

Fax: 412-586-9672

www.icre.pitt.edu/cetp

Admissions

Admissions Criteria

• U.S. citizens, non-citizen nationals, or permanent residents.
• Completion of the MD, DDS, DMD, DC, OD, ND, PharmD, PhD, or DNS degree is highly recommended.
• A high level of interest and potential for the pursuit of innovative clinical research as a major career focus.
• Preference will be given to candidates in departments or programs assuring 50–75 percent protected time for at least two years.

Financial Assistance

Curriculum

Degree Requirements

In addition to School of Medicine requirements, all University requirements pertaining to the master’s degree apply as detailed in the Regulations Governing Graduate Study at the University of Pittsburgh.

Master of Science

The degree requires completion of a minimum of 30 credits including the core curriculum, required and elective courses in one of the specialty tracks, and a thesis or substantive research project.

Credit Requirements:

Core Curriculum Courses: CLRES 2005 (1 credit), CLRES 2010 (3 credits), CLRES 2020 (4 credits), CLRES 2040 (1 credit), CLRES 2050 (1 credit), CLRES 2071 (3 credits), and CLRES 2072 (2 credits).

Specialty Track Required Courses: This requirement includes 7 credits in clinical trials research, 10 credits in effectiveness, outcomes, and quality research, 9 credits in epidemiology and 8 credits in translational research.

Thesis or Substantive Research Project: The substantive project must satisfy the following requirements: (1) be primarily independent, (2) be reported to a specialty track faculty member in written form, and (3) form the basis for a comprehensive review of competence by a committee of a specialty track. Three mechanisms for the substantive project are:

• A standard thesis: A candidate may elect to write a master’s thesis in his or her field of specialty. A thesis produced under this option must conform to all applicable university policies regarding theses (visit http://www.pitt.edu/~graduate/etd for details on submitting theses electronically) and must be defended before a CRTP review committee (described below). 
• A grant proposal for an R01, K-award, or equivalent award: A junior faculty candidate may elect to write an R01 or equivalent research proposal on which he or she is the principal investigator and to submit this proposal as evidence of his or her ability to plan and conduct independent research in the area of medical education. To serve as the substanative project for the master’s degree, such a proposal must be reviewed and approved by an appropriate scientific review committee from the candidate’s department. It must also be reviewed and approved by a CRTP review committee (described below).
• Two manuscripts for publication in peer-reviewed journals: A candidate may elect to write two first-author manuscripts related to his or her research project and to submit these manuscripts as evidence of independent work. The manuscripts must be original research papers of the type submitted to peer-reviewed journals. Both manuscripts must be reviewed and approved by a CRTP review committee.

Comprehensive Examination: The product of one of the three research project options above must be reviewed and defended before a committee of the training faculty. This committee shall consist of the trainee’s mentor, a member of the program-training faculty and an ad hoc member of the faculty.

Certificate in Clinical Research

The certificate requires the completion of 15 credits including the summer core curriculum, CLRES 2050 (1 credit) and 5 additional credits of elective coursework. The summer core curriculum consists of CLRES 2005 (1 credit), CLRES 2010 (3 credits), CLRES 2020 (4 credits), and CLRES 2040 (1 credit). Certificate students who wish to enroll in the CLRES 2017 (3 credits) and CLRES 2072 (2 credits) Research Design and Development Seminar course must submit a one-page statement to the Leadership Committee outlining (1) why they want to take the grant-writing course, and (2) how the grant-writing course will help their career development.

Training Faculty

Course Listings

Interdisciplinary Biomedical Science Graduate Program

Students may be admitted into 7 PhD degree-granting programs in the School of Medicine or the School of Arts and Sciences through the Interdisciplinary Biomedical Science Graduate Program. These programs include:

• Biochemistry and Molecular Genetics
• Cell Biology and Molecular Physiology
• Cellular and Molecular Pathology
• Immunology
• Molecular Pharmacology
• Molecular Virology and Microbiology
• Neuroscience (Neurobiology)

Students will not be admitted to pursue the master’s degree. However, master’s degree programs are available in each of the programs leading to the doctoral degree. Students who cannot complete the PhD program for personal, financial, academic, or medical reasons may be awarded the master’s degree.

These programs are described in more detail below. Students who are primarily interested in studying neuroscience also have the option of applying through the Center for Neuroscience Training Program, an interschool program that is described below.

The Interdisciplinary Biomedical Science Graduate Program is flexible and accommodates students whose research interests are still evolving by introducing them to a variety of fields through interdisciplinary courses and laboratory experiences. For those students who have a clearly defined research interest, the program offers the opportunity to move quickly into the laboratory and accelerate their study.

Contact Information

Associate Dean for Graduate Studies

524 Scaife Hall

412-648-8957

Fax: 412-648-1077

E-mail: gradstudies@medschool.pitt.edu

www.gradbiomed.pitt.edu

Admissions

Financial Assistance

Academic Standards

Students must maintain a minimum cumulative GPA of 3.00 in courses. In addition, a minimum of a B grade must be earned in each of the required courses and in each of the degree-granting program core courses.

General Degree Requirements—All Interdisciplinary Biomedical Science Students

The first term core course, Foundations of Biomedical Science, is required of all students and is followed by increasingly specialized course work in the program the student has chosen. A course in statistics and a course in research ethics are also required of all students. The first year includes three laboratory research rotations. (See listing of Required Courses below.) Students are guided through their first year of graduate study by a faculty mentor assigned by the program.

The mentor helps to identify rotation laboratories, provides advice on classes, and ensures that students reach appropriate milestones in the first year of the program. At the end of the first year, a preliminary student performance evaluation is conducted by the Program Steering Committee. When a student has successfully completed the preliminary evaluation and chosen a dissertation advisor, the student transfers into one of the degree-granting programs.

Evaluation following the first year is undertaken by the degree-granting program and includes course performance and a comprehensive exam at the end of the second year of study. The comprehensive exam is in the form of an original research proposal followed by an oral examination before a faculty committee composed of three program training faculty members with one appointed as chair. Upon successful completion of the comprehensive exam, the student presents a dissertation proposal to a dissertation advisory committee and is admitted to candidacy. The training program is completed by execution of an original and independent research project and defending a dissertation. Please see Regulations Pertaining to Doctoral Degrees.

Required Courses—All Students

The following courses are required of all students in the Interdisciplinary Biomedical Science Program:

INTBP 2000 Foundations of Biomedical Sciences Lecture, INTBP 2005 Foundations of Biomedical Sciences Conference, INTBP 2020 Introduction to Statistical Methods, INTBP 2290 Scientific Ethics, and INTBP 2010 Laboratory Research Rotation.  A minimum of 72 credits beyond the baccalaureate degree is required for the PhD degree.

Biochemistry and Molecular Genetics Program

The Biochemistry and Molecular Genetics (BMG) Graduate Program brings together faculty in both basic and appliced sciences, including researchers from the School of Medicine, the University of Pittsburgh Cancer Institute, and the Pittsburgh Center for Human Gene Therapy. BMG research is at the cutting edge of many emerging technologies, including stem cell biology, proteomics, computational biology and genomics. Our work has direct relevance to many diseases including cancer, diabetes, muscular dystrophy, and other genetic disorders. Faculty research interests encompass a wide variety of fields, and can be broadly divided into five major areas: molecular mechanisms of gene expression and signal transduction; gene therapy; oncogenes and tumor suppressor genes; cell cycle control and DNA replication; and protein structure-function analysis.

Biochemistry and Molecular Genetics Core Courses

The following are core courses in the biochemistry and molecular genetics program: MSBMG 2520 Eukaryotic Molecular Genetics, MSBMG 2510 Biochemistry of Macromolecules, and MSBMG 2550 Research in Progress Seminar.

Cell Biology and Molecular Physiology Program

The program in cell biology and physiology has a rich tradition of scientific training and discovery. For example, members of this program were first to identify the hormonal mechanisms that regulate the female menstrual cycle. Graduates of the PhD program are now chairs of departments at six major U.S. medical schools. Today, the program brings together basic and clinical research faculty who are dedicated to their research programs and to the training of students. Among the medical school departments, this faculty is uniquely focused on integrative biology: using the tools of genetics and molecular biology to understand the integrated functions of cells and organisms in the era following description of the human genome. The program is home to the Center for Biological Imaging, a world-class, state-of-the-art imaging center. Through this unique facility, advances in laser confocal microscopy, live cell multicolor fluorescence microscopy, electron microscopy, and computer-assisted image processing have facilitated University-wide research efforts and collaborations. Areas of research interests in the program include genetic disorders of ion channels, regulation of gene expression during development, membrane traffic of proteins and lipids, signal transduction in diabetes, and neuroendocrine control of reproduction.

Cell Biology and Physiology Core Courses

The following are the core courses for the cell biology and physiology program: MSCBMP 2830 Cell and Molecular Physiology, MSCBMP 2880 Cell Biology of Normal and Disease States, and MSCBMP 2840 Regulations of Membrane Traffic.

Cellular and Molecular Pathology Program

The cellular and molecular pathology program offers exciting and unique opportunities within the biomedical sciences. The program combines both basic science and clinical research to explore fundamental questions related to the biology of normal tissue growth and development, tissue engineering, as well as the cellular and molecular pathways leading to disease in human and animal models. Active research programs investigate diverse topics such as liver development, disease and transplantation, developmental neuroscience and neurological diseases, mechanisms of gene regulation, cancer biology, angiogenesis, pulmonary disease, inflammation and autoimmunity, genetics, bioinformatics, and molecular diagnostics. Research laboratories are located throughout the medical center campus and research studies involve both basic research scientists (PhD's) and clinican scientists (MD/PhD's).

Cellular and Molecular Pathology Core Courses (MD/PhD's)

Immunology Program

The immunology program focuses on six areas of research: cancer immunology, transplantation immunology, infectious disease immunology, autoimmunity, immunology of lung diseases, and basic immunologic mechanisms. Cancer immunology studies include tumor antigen discovery and presentation, in vivo vaccination strategies to develop safe and effective treatments for cancer, and the search for underlying genetic or biochemical defects that lead to cell transformation and tumorigenesis that may also influence tumor immunogenicity. These studies emphasize intracellular signal transduction, programmed cell death, and oncogene function. Transplantation immunology concentrates on weakening the immune response to allow foreign organ and tissue transplants. Program members focus on the basic biology of immune cell non-reactivity (tolerance) to foreign organs and tissues, as well as on the use of new immunomodulatory drugs to promote transplant acceptance without endangering patients' abilities to resist infections.

Studies of the immune response to infectious disease focus on mechanisms the immune system uses to eliminate viral, bacterial, or parasitic infections as well as the immune evasion mechanisms employed by pathogens. Investigation of autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosis, and type-1 diabetes involve detailed analysis of the molecular mechanisms underlying the autoimmune response and of the development of novel therapeutic and preventive measures for these often-fatal diseases.

Immunology of lung diseases studies both basic mechanisms of dendritic cell maturation and their influence on T-cell differentiation and the relevance of these interactions in disease second in tolerance. Some foci of basic immunologic mechanisms include cell and organ development and homeostasis, cellular activation and inactivation signaling cascades, and the use of gene therapy to modulate immune responses.

Immunology Core Courses

The following are core courses in immunology: MSIMM 2210 Comprehensive Immunology, MSIMM 2230 Experimental Basis of Immunology, MSIMM 3220 Contemporary Topics in Immunology, and MSIMM 3230 Immunology and Human Disease.

Molecular Pharmacology Program

The program is focused on molecular and cellular mechanisms of intracellular signaling using a combination of biochemical, molecular biological, biophysical, ultra structural, and imaging approaches. Basic information on cellular communication in health and disease provides the basis for the development and testing of novel therapeutic agents. Applications of this common theme are directed toward research in drug discovery, cancer, pharmacology, signal transduction, neurodegenerative diseases, and cell and organ system pharmacology. Formal interactions with the Pittsburgh Cancer Institute, the Center for Neuroscience, the Pittsburgh Institute for Neurodegenerative Diseases (PIND), the Division of Clinical Pharmacology, the Drug Discovery Program, and the Center for Biological Imaging provide a broad multidisciplinary approach to training in modern molecular pharmacology.

Molecular Pharmacology Core Courses

The following are core courses in the molecular pharmacology program: MSPHL 2310 Principles of Pharmacology, MSPHL 3360 Molecular Pharmacology, MSMPHL 2360 Biology of Signal Transduction and either MSPHL 3310 Cancer Biology and Therapeutics, or MSPHL 3370 Neuropharmacology.

Molecular Virology and Microbiology Program

The molecular virology and microbiology program faculty address a diverse array of contemporary issues ranging from elucidation of the molecular mechanisms governing pathogen-host interactions to the epidemiology underlying infectious diseases. Research topics include the study of gene expression, mechanisms of persistence and pathogenesis, the host immune response, and molecular-based strategies to combat infectious disease. As a result, students in the program gain a comprehensive interdisciplinary background in modern molecular virology and microbiology with a strong underpinning in molecular biology, immunology, and biochemistry. This program acts as a network to coordinate and promote collaborative basic and clinical advancement of microbiology and virology, enabling transfer of new ideas and technologies among faculty laboratories to the clinical arena.

Molecular Virology and Microbiology Core Courses

The following are core courses in molecular virology and microbiology: MSMVM 2410 Molecular Virology, MSMVM 3410 Microbial Pathogenesis, MSMVM 2470 Contemporary Topics, and MSMVM 2450 Research Seminar.

Neuroscience Program

Graduate training in neuroscience is a University of Pittsburgh campus-wide program coordinated through the Center for Neruoscience (CNUP), an organization that promotes research and related academic activities in the neuroscience community. As such, the CNUP Graduate Training Program maintains a seperate admissions process. For application procedures and program and training faculty description, visit the CNUP Web site at http://cnup.neurobio.pitt.edu.

The CNUP is a campus-wide organization that promotes research and related academic activities in the large neuroscience community, and it is important to note that a major feature of the program is the extensive collaborative interactions among its faculty.

For additional information on CNUP, contact the program coordinator at E1448 Biomedical Science Tower, Phone: 412-648-9537, Fax: 412-648-1441, E-mail: blaney@brain.bns.pitt.edu, or visit the Web site: http://cnup.neurobio.pitt.edu/graduate.cfm.

Degree Requirements

The minimal requirements established by the Graduate Faculty of the University, as described under General Academic Regulations, should be read in conjunction with program-specific degree requirements described in the following sections.

The requirements for the PhD degree in neuroscience include the following required course work:

In addition to University requirements for graduate degrees, students are also required to pass a reprint exam following their first year of study, to obtain research experience in at least two separate laboratories (either done initially as research rotations or later as a research apprenticeship) and to serve as a teaching assistant for at least one term (or course).

Interdisciplinary Biomedical Science Graduate Program Faculty

• Biochemistry and Molecular Genetics Program Training Faculty
• Cell Biology and Physiology Training Faculty
• Cellular and Molecular Pathology Training Faculty
• Immunology Training Faculty
• Molecular Pharmacology Training Faculty
• Molecular Virology and Microbiology Training Faculty
• Neuroscience Training Faculty

Joint Pitt-CMU PhD Program in Computational Biology

Ivet Bahar and Robert F. Murphy, Directors

Computational biology is defined as the development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques to the study of biological, behavioral, and social systems.* It is an interdisciplinary approach that draws from specific disciplines such as mathematics, physics, computer science and engineering, biology, and behavioral science.

The Joint Pitt-CMU PhD Program in Computational Biology is an intensive, interdisciplinary training program that provides students with a deep understanding of the current state of the art in computational biology. Students in this program acquire the quantitative background and research skills needed to advance the field of computational biology. In addition, they develop the critical thinking skills needed to appreciate the potential, strength, and limitations of computational, mathematical, and engineering tools for tackling biological problems.

*NIH Working Definition, July 17, 2000.

Contact Information

Admissions

The interdisciplinary character of the program is unique and distinct from many other programs that are focused toward a specific discipline. The program seeks outstanding students from the biological, physical and computational sciences, and engineering. For example, computational biology majors, or double majors in biology and quantitative sciences are ideal candidates.

Recommended Prerequisites

For students planning their undergraduate course schedules in anticipation of applying for the PhD in computational biology, prerequisites in life sciences, computer science, physical sciences, mathematics, statistics, and computational biology are recommended. Students whose background does not include these courses may be admitted with the additional requirement to take appropriate compensating classes. For more information on prerequisites, see http://www.ccbb.pitt.edu/compbio/Admissions/prerequisites.html.

Application

The application receipt deadline is January 15. Required application materials include:

• Completed online application
• Three letters of recommendation
• Official transcripts from all colleges and universities attended
• Official report of GRE scores (general, required; subject, recommended)
• Official report of TOEFL score (required for foreign applicants from countries other than Canada, Australia, the United Kingdom, or New Zealand)
• Application fee of $50

Applications are reviewed by the Joint CMU-Pitt PhD Program in Computational Biology. Each admitted student is assigned an initial research advisor and receives an admissions offer letter from the university at which that advisor holds his/her primary appointment. Students have the ability to change advisors (subject to agreement of the new advisor and availability of support) and to transfer between the two universities to reflect advisor changes.

For more information on application process, see http://www.ccbb.pitt.edu/compbio/Admissions/.

Financial Aid

All students are provided with a stipend and full tuition remission. Assistance is also provided for health insurance.

Teaching Assistantships

There is no formal teaching requirement in the program. However, if the resources are available, interested students may participate in currently available courses that utilize graduate student teaching assistants. Students are encouraged to develop teaching skills by mentoring other students and passing on their knowledge to lab mates and fellow students.

Curriculum

The curriculum is designed to train students who will shape the next generation of discovery in computational biology in academia and industry. Students are required to complete 72 credit hours of academic work toward partial fulfillment of the requirements for completion of dissertation study. Of these, 30+ are formal coursework, and the remaining to be completed with full-time research.

All students are required to take five of six core graduate courses. The core courses aim at providing a strong common background in computational biology before they specialize in particular research areas.

Core Courses

• Algorithms
• Machine Learning
• Computational Genomics
• Computational Structural Biology
• Cellular and Systems Modeling
• Computational Biology Wet Lab

All students are required to take five graduate elective courses. The first elective should be a life science/physical science course, specified  for a student’s chosen area of specialization.  Three additional elective courses must be drawn from that area of specialization and one may be from any area.

Specialization Areas

• Computational Genomics
• Computational Structural Biology
• Cellular and Systems Modeling
• Bioimage Informatics
• Computational Neurobiology

For more information on the curriculum, see http://www.ccbb.pitt.edu/compbio/Curriculum/.

Other Courses

In addition to core and elective courses, student take complementing courses, if needed, and participate in program seminar, journal clubs, ethics courses and directed studies toward their dissertation projects.

Program Seminar Series

Students enrolled in the program are expected to attend scientific seminars during all years of training. Beginning in the third year, students present their research progress to fellow students and the faculty on at least an annual basis.

Journal Club

Effective presentation of scientific data is an invaluable aspect of graduate training. Therefore, all students must present a scientific article on a topic (selected by a faculty member) that introduces students to the methodology and applications of computational biology. The talk is made in a format that allows the student to develop basic presentation skills. Students subsequently receive feedback on their talks, thereby improving their presentations skills as their graduate training advances.

Training in Ethics

Ethical conduct and scientific integrity is an essential aspect of research. This is especially important given the competitive nature of funding processes and the high demand for productivity. Hence, the program instructs students on the significance and practice of ethical conduct.

Directed Study

Credits are given for laboratory projects (wet or computer labs) under the direction of the dissertation advisor prior to admission to candidacy for the doctorate.

Scheduling

We anticipate two types of course schedules for students in the program. The default for students who have taken the prerequisites will be to take three courses in each of the first two semesters (50-75% time) and spend the remaining time on research. Such students would normally take the core courses in the first year along with one additional course. The third and fourth semesters would be split between taking electives and doing research.

Students who enter with some biology or computer science or physical science background but not with sufficient background to take all of the core courses would take a mix of missing prerequisites and core courses in each of the first two semesters (approx. 90% time) and spend 10% time on research. These students would then take a mix of remaining core courses and electives in the third and fourth semesters (along with 30% research) and finish electives in the fifth and/or sixth semesters.

Comprehensive Examination

Students are required to pass a comprehensive examination after completion of their 27-credits (core + elective) courses requirement, prior to being officially admitted to candidacy to the PhD degree. Students are expected to complete this examination no later than the spring semester of their third year, and can take it as early as the end of the fall semester of the 2nd year. The comprehensive examination consists of two parts: a 15-page “grant-style” written proposal of the proposed research, followed by an oral defense of the proposed research.

Post-Comprehensive Qualifying Examination

Students who have been accepted to PhD candidacy conduct research on a full time basis, and are required to complete a minimum of 40 credit hours (9 credits per semester) of full-time dissertation study in order to meet the criteria for dissertation defense. Hence, all students will have completed at least 72 credit hours of study prior to graduation, including 27 credit hours of core + elective courses, and at least 40 credit hours of dissertation research.

Completion of Degree

The program is structured in such a way that students can finish their degree within four years of entering their dissertation laboratory. However, it is recognized that the actual time required to attain the degree depends on the specific type of research undertaken and how quickly progress is made in completing the experimental program.

Terminal Masters Degree

The Program does not admit students whose goal is to attain a M.S. degree. However, it might become necessary for a PhD student to transfer to an M.S. track for academic reasons or reasons beyond the student’s control, e.g., medical circumstances or a change in family circumstances necessitating a long-distance move.

Training Faculty

The program provides students with cross-disciplinary training in established as well as newly emerging fields of computational biology. Students have access to a community of faculty mentors from the University of Pittsburgh and Carnegie Mellon University, which not only provides a breadth of research areas for investigation, but also offers the technical and intellectual resources to make rapid progress toward their doctoral degree.

For a list of training faculty, see http://www.ccbb.pitt.edu/compbio/Faculty/.

Molecular Biophysics and Structural Biology

The Molecular Biophysics and Structural Biology graduate program at the University of Pittsburgh trains students to conduct research at the interface between biology, chemistry and physics.  The disciplines of Molecular Biophysics and Structural Biology aim to unravel and explain biological phenomena and processes in atomic and molecular detail.  Research conducted by program faculty covers a diverse range of topics in Molecular Biophysics and Structural Biology.  Areas of study focus on understanding fundamental principles involved in reactions and regulatory interactions in biological systems.  Our research projects attempt to answer the following key questions.  How do proteins fold and can we prevent misfolding?  Can we design proteins with novel functions?  How does the coordinated interaction between proteins and nucleic acids lead to cellular differentiation and the formation of an organism?  How do macromolecules assemble into molecular machines and viruses? How do these assemblies operate? How do signals traverse membranes?

Contact Information

University of Pittsburgh
Molecular Biophysics and Structural Biology Graduate Program
Graduate Studies Office
3550 Terrace Street
524 Scaife Hall
Pittsburgh, PA 15261
Tel: 412-648-8957; Fax: 412-648-1077
Email: MBSBinfo@medschool.pitt.edu
http://www.biophysics.pitt.edu

Admission Requirements and Procedures

Students with at least a baccalaureate degree in physics, chemistry and mathematics as well as cellular and molecular biology are encouraged to apply.  Admissions are based upon the student’s academic record, GRE scores, letters of recommendation, previous research experience, written statement of interest, and a personal interview.  Applicants who are citizens of countries where English is not the official language (and the Province of Quebec in Canada) are required to submit evidence of English Language proficiency by submitting the official results of the Test of English as a Foreign Language (TOEFL) or the International English Language Testing System (IELTS). A minimum TOEFL score of 600 (paper) or 250 (computer) or 100 (iBT), or IELTS score of at least 7.00 is required for admission to the Program.

Additional information and a link to the online application can be a found at http://www.biophysics.pitt.edu/admissions.html.

Financial Assistance

All students receive complete financial support in the form of stipend, tuition and health insurance.

Degree Requirements

All students enter the Program in the fall session and after performing three rotations identify an advisor and area of research. Areas of research focus include: Macromolecular recognition; Virus, lipid and protein structure & interactions; Principles of protein structure & dynamics; Membrane proteins; Gene regulation & signaling; Cellular biophysics; Chemical structure & dynamics. Methodologies employed comprise NMR spectroscopy, X-ray crystallography, cryo electron microscopy, atomic force microscopy, mass spectrometry, infrared spectroscopy and computational molecular biology. Required coursework is completed during the first year. Students are required to complete the Comprehensive Exam by August 31 of their second year in the graduate program.

A minimum of 72 credits beyond the baccalaureate degree is required for the Ph.D degree. The 72 credits are completed by taking required and elective course work as well as dissertation research credits upon being admitted to candidacy.

Laboratory Research Rotation (MSMBPH/MOLBPH 2000)—taken during the first fall, spring & summer semester of the first year.

Macromolecular Structure & Function (BIOSC 2810)—taken during the first fall semester of the first year

Molecular Biophysics I: Structure (MSMBPH/MOLBPH 2001)—taken during the first fall semester of the first year

Molecular Biophysics II: Interactions (MSMBPH/MOLBPH 2002)—taken during the first spring semester of the first year

Molecular Biophysics III: Dynamics & Kinetics (MSMBPH/MOLBPH 2003)—taken during the first spring semester of the first year

Scientific Ethics (INTBP 2290)—taken during the first summer semester of the first year

Structural Biology & Molecular Biophysics Research Seminar (MSMBPH/MOLBPH 2020)—taken every fall and spring semester through graduation

Data and Literature Club (MSMBPH/MOLBPH 2030)—taken every fall and spring semester through graduation

Advanced Elective Courses—6 credits total—a number of courses are available and are listed on the following website: http://www.biophysics.pitt.edu/electives.html

Additional information on the core curriculum can be found at http://www.biophysics.pitt.edu/curriculum.html

Training Faculty

The Molecular Biophysics and Structural Biology training faculty can be found at the following Web site: http://www.biophysics.pitt.edu

Course list

The curriculum stresses an interdisciplinary approach to learning and research in modern Molecular Biophysics and Structural Biology. Upon entering the program, each student is advised by a mentoring committee, explores research options through laboratory rotations and then chooses a thesis advisor in the first year.

A list of available courses can be found at the following Web site: http://www.biophysics.pitt.edu/curriculum.html

Center for Neuroscience Training Program (CNUP)

The Center for Neuroscience (CNUP) Graduate Training Program is an interschool PhD degree-granting program offered cooperatively by the School of Medicine and the School of Arts and Sciences. Neuroscience is the study of the structure and function of the nervous system. The field has emerged during the past two decades as a separate discipline, much as biochemistry and endocrinology became separate disciplines within the biomedical sciences in earlier decades. Rapid growth of this multidisciplinary field has made the study of mind and brain one of the most exciting scientific enterprises of our time.

Understanding the nervous system provides key insights into human nature as well as treatments for a host of devastating neurological and psychiatric disorders. Our program introduces students to the fundamental issues and experimental approaches in neuroscience and trains them in the theory and practice of laboratory research.

Research interests of the CNUP training faculty focus on several prominent themes:

(a) Behavioral/systems/cognitive
(b) Cell and molecular
(c) Development/plasticity/repair
(d) Neurobiology of disease

The field of neuroscience attracts people from many different disciplines in the natural sciences.  The CNUP is a campus-wide organization that promotes research and related academic activities in our large neuroscience community, and one of the center’s defining characteristics is the strong interaction among its members. Many CNUP scientists work on interdisciplinary projects that span two or more thematic areas and often entail formal or informal collaboration among center members.  Please visit the CNUP web site for our list of research concentration areas involving groups of CNUP scientists.

Contact Information

Graduate Program Coordinator
E1440 Biomedical Science Tower
200 Lothrop Street
Pittsburgh, PA 15261
E-mail:argenzio@pitt.edu
http://cnup.neurobio.pitt.edu/graduate.cfm

Admission Requirements and Procedures

Students are admitted into the CNUP training program on the assumption that they will be able to meet all requirements for the PhD degree. Those that are selected show evidence of a high level of intellectual talent, a strong interest in neuroscience, and a commitment to scholarship and research.

Admission decisions are based on many factors including the candidate's statement of interest and goals in the field of neuroscience, evidence of research experience and accomplishment, letters of recommendation, test scores, grades, and personal interviews. An outstanding record in one of these areas may compensate for poorer performance in another area. In general, successful applicants have a BS degree in biology, chemistry, computer science, mathematics, neuroscience, or psychology with a cumulative grade point average of at least 3.40 (on a 4.00 scale) and a cumulative Graduate Record Exam (GRE) score greater than 1200 (verbal and quantitative) and a 4.5 in analytical writing.

Additional information and a link to our on-line application can be found at: http://cnup.neurobio.pitt.edu/admissions.cfm

Financial Assistance

All students receive full stipend support and individual health benefits. This support is derived from University fellowships and numerous grants funded by the federal government and private agencies. Students in the program also have access to sponsorship on NIH training grants.

PhD Degree Requirements

Credits: A minimum of 72 credit hours including a 24-credit course requirement covering fundamental material in cellular and molecular neurobiology, systems neurobiology and several elective courses. 

Specifically, the following core courses are required:

In addition to University requirements for graduate degrees, students are also required to obtain research experience in at least two separate laboratories; attend journal clubs and research seminars; pass a reprint exam following their first year of study, a comprehensive exam, and a doctoral dissertation and defense; and, to serve as a teaching assistant for at least one term (or course).

Training Faculty

A list of CNUP Training Faculty may be viewed at: http://cnup.neurobio.pitt.edu/Tfac.cfm?id2=t

Neuroscience Courses:

Our complete list of courses may be viewed at: http://cnup.neurobio.pitt.edu/gradcourses.cfm

Program in Integrative Molecular Biology

PIMB is an innovative program in graduate training that rapidly immerses students into a research environment, then mentors them to become independent scientific practitioners, skilled not only in the art of technical execution but in the creative thinking required to address important questions in molecular biology. PIMB is an interschool PhD program offered cooperatively by the School of Medicine and the School of Arts and Sciences. Students receive a PhD in Integrative Molecular Biology.

Molecular Biology is a field of study that has emerged during the last two decades as a separate discipline that focuses on the study of the molecules that comprise living systems. The goal of PIMB is to utilize all of our available resources to create a training and research environment to answer challenging questions of fundamental importance in the life and biomedical sciences. The PIMB faculty are drawn from cellular, developmental, and molecular biologists across the University of Pittsburgh campus and are distributed between two research foci:

• Genomics, Proteomics, and Gene Function
• Cellular and Developmental Biology

Contact Information

Program in Integrative Molecular Biology

Graduate Studies Office

524 Scaife Hall

University of Pittsburgh

Pittsburgh, PA 15261-0001

Telephone: 412-648-8957

Fax: 412-648-1077

E-mail: PIMBinfo@medschool.pitt.edu

http://www.pimb.pitt.edu

Admission Requirements and Procedures

Requirements for admission include a baccalaureate degree from a natural science, physical science, or engineering program, a grade point average of 3.7 (on a scale of 4), combined average GRE scores (Quantitative and Verbal sections) greater than the 80th percentile, scores from a GRE subject test, and three letters of recommendation. Applicants who are citizens of countries where English is not the official language (and the Province of Quebec in Canada) are required to submit evidence of English language proficiency by submitting the official results of the Test of English as a Foreign Language (TOEFL) or the International English Language Testing System (IELTS). A minimum TOEFL score of 650 (paper) or 280 (computer), IELTS score of at least 7.50 or iBT score of at least 114 is required for admission to the Program.

Additional information and a link to the online application can be found at http://www.pimb.pitt.edu/admissions.php

Financial Assistance

All full-time students receive a stipend, educational enrichment fund, computing and network service, and individual health insurance (with option to purchase additional family coverage) during their graduate training.

Degree Requirements

PhD Degree

This is an accelerated program that provides the opportunity for students to complete their degrees in approximately 4 years. Students enter the Program in the summer session, and after performing three rotations identify an advisor and area of research. Areas of research focus include Genomics, Proteomics, and Gene Function and Cellular and Developmental Dynamics. Required course work is completed during the first year. At the end of the first year students take a comprehensive examination that includes the submission of a research proposal to national fellowship programs. Students receive career mentoring during the third and fourth years to ensure a seamless transition to the postdoctoral level. Additional information can be found at the following Web site: http://www.pimb.pitt.edu/curriculum.php.

A minimum of 72 credits beyond the baccalaureate degree is required for the PhD degree. 32 of these credits are completed taking required and elective course work, and 40 of these credits are taken as dissertation research credits upon completing the comprehensive examination and advancing to candidacy. Required course work includes the following:

Laboratory Research Rotation (MSIMB/IMB 2000 – 9 credits) – taken in the summer prior to the first year.

Approaches in Molecular Biology (MSIMB/IMB 2010 – 5 credits) – taken during the fall Semester of the first year.

Scientific Ethics (INTBP 2290 – 1 credit ) – taken during the summer of the second year.

Intro to Statistical Methods  (BIOST 2041– 3 credits) – taken during the summer of the second year.

Departmental/Program Seminar Series (MSIMB/IMB 2050 – 1 credit) and Journal Club/Conference (MSIMB/IMB 2060 – 1 credit) - the Department/Program Seminar and Journal Club/Conference are taken each fall and spring term until graduation.

Advanced Elective Courses – 6 credits total – a large number of courses are available and are listed on the following Web site: http://www.pimb.pitt.edu/curriculum.php - Students are required to select courses in more than one of the following disciplines: molecular genetics, biochemistry, cell biology, and developmental biology.

Training Faculty

The PIMB training faculty can be found at the following Web site:http://www.pimb.pitt.edu/FacultyIndex.php

Course List

A list of available courses can be found at the following Web site:http://www.pimb.pitt.edu/CourseIndex.php