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A&S—Computational Biology

Joint Pitt-CMU PhD Program in Computational Biology

David Zuckerman and Russell Schwartz, 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 behavior science.

The Joint CMU-Pitt 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

 

 

 

University of Pittsburgh:

Carnegie Mellon University:

Directors:

Daniel M. Zuckerman, PhD
Associate Professor 
Department of Computational Biology
School of Medicine, University of Pittsburgh
3501 Fifth Avenue, BST3,
Room 3078
Pittsburgh, PA 15260
412-648-3315 (phone)
412-648-3163 (fax)
ddmmzz@pitt.edu

Russell Schwartz, PhD
Associate Professor of Biological Sciences, and Computer Science
Carnegie Mellon University
654B Mellon Institute, 4400 Fifth Ave.
Pittsburgh, PA 15213
412-268-3971 (phone)
412-268-7129 (fax)
russells@cmu.edu

     

Associate Directors:

James Faeder, PhD
Associate Professor
Department of Computational Biology

School of Medicine, University of Pittsburgh

3501 Fifth Avenue BST3

Room 3082

Pittsburgh, PA 15260

412-648-8171 (phone)

412-648-3163 (fax)

faeder@pitt.edu

Carl Kingsford, PhD

Associate Professor

Department of Computational Biology

School of Computer Science, Carnegie Mellon University

Gates Hillman Center,

Room 7705

5000 Forbes Avenue

Pittsburgh, PA 15213

412-268-1769 (phone)

412-268-2977 (fax)

carlk@cs.cmu.edu

     

Program Coordinators:

Kelly M. Gentille
Educational Programs Administrator
Department of Computational Biology
School of Medicine, University of Pittsburgh
3501 Fifth Avenue, BST3,
Room 3052
Pittsburgh, PA 15260
412-648-8107 (phone)
412-648-7819 (fax)
kmg120@pitt.edu

Thom Gulish
Administrative Coordinator
Lane Center for Computational Biology
Carnegie Mellon University
4400 Fifth Avenue
Pittsburgh, PA 15213
412-268-2474 (phone)
412-268-2977 (fax)
tgulish@cmu.edu

     

Program Website:

www.compbio.pitt.edu

www.compbio.cmu.edu

 

 

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 backgrounds does not include these courses may be admitted with the additional requirement to take appropriate compensating classes. For more information on prerequisites, visit http://www.compbio.cmu.edu/?page_id=91

The early application receipt deadline is December 15. Required application materials include:

  • Completed online application
  • Three letters of recommendation
  • 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 $75

Applications are reviewed by the Joint CMU-Pitt PhD Program in Computational Biology. Each admitted student is assigned an initial university of matriculation, and receives an admissions offer letter from that university. Incoming students can be placed directly in a laboratory (if mutual interest exists between a student and an advisor), or go through a period of three rotations, after which the student chooses an advisor. 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.compbio.cmu.edu/?page_id=163

Financial Aid

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

Teaching Assistantships

Although all students are supported as research assistants throughout their time in the program, there are opportunities to assist in the teaching courses of the program. Students are also 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-plus are formal coursework, and the remaining to be completed with full-time research.

All students are required to take five 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

  • Machine Learning
  • Intro to Computational Structural Biology
  • Computational Genomics
  • Cellular and Systems Modeling
  • Laboratory Methods for Computational Biologists

In addition, all students are required to take five graduate elective courses: a life science/physical science course and an advanced interdisciplinary elective specified for the student’s chosen area of specialization; a quantitative elective from a program-wide menu; and two general electives.

Specialization Areas

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

For more information on the curriculum, see

http://www.compbio.cmu.edu/?page_id=87

Other Courses

In addition to core and elective courses, students 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 their second year and ending in the year before their thesis defense, 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 first- and second-year 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 to 75 percent 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 background but not with sufficient background to take all of the core course would take a mix of missing prerequisites and core courses in each of the first two semesters (approximately 90 percent time) and spend 10 percent 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 percent 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 29-credits (core plus elective) 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 second 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 29 credit hours of core plus 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 Master's of Science degree. However, it might become necessary for a PhD student to transfer to an MS 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.

Courses

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.compbio.cmu.edu/?page_id=50

Molecular Biophysics and Structural Biology

The Molecular Biophysics and Structural Biology graduate program at the University of Pittsburgh and Carnegie Mellon University 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 and Carnegie Mellon University
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
E-mail: MBSBinfo@medschool.pitt.edu
www.mbsb.pitt.edu

Program Director: James Conway (UPSOM) and Gordon Rule (CMU)

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.mbsb.pitt.edu/index.php/apply-for-the-mbsb-program

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 and interactions; Principles of protein structure and dynamics; Membrane proteins; Gene regulation and signaling; Cellular biophysics; Chemical structure and 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 PhD 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 and summer semester of the first year.

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

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

Molecular Biophysics II: Bimolecular Interactions & Dynamics (MSMBPH/MOLBPH 2012)—taken during the first spring term of the first year

Molecular Biophysics III: Theory and Simulation (MSMBPH/MOLBPH 2013)—taken during the fall term of the second year

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

Structural Biology and 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—with the permission of his/her advisor, students are permitted to choose from a number of courses offered at Pitt as well as CMU.

Additional information on the core curriculum can be found at http://www.mbsb.pitt.edu/index.php/training/curriculum

Training Faculty

The Molecular Biophysics and Structural Biology training faculty can be found at the following Web site:

http://www.mbsb.pitt.edu/index.php/people/faculty

 

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.mbsb.pitt.edu/index.php/training/curriculum

Center for Neuroscience Training Program (CNUP)

The Center for Neuroscience (CNUP) Training Program is an inter-school PhD degree-granting program offered cooperatively by the School of Medicine and the Kenneth P. Dietrich School of Arts and Sciences.  The 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 training faculty focus on several prominent themes, including behavioral/systems/cognitive, cell and molecular, development/plasticity/repair, and the neurobiology of disease.

This large research-based training program offers outstanding opportunities for students to pursue research in laboratories within more than 30 different departments and University centers. Major features of the program include extensive collaborative interactions among its faculty members and its affiliation with the Auditory Research Group, the Brain Institute, the Center for the Neural Basis of Cognition, (a joint program with Carnegie Carnegie Mellon University), Conte Center for the Neurosciences of Mental Disorders, Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh Center For Pain Research, and other campus research centers.

Contact Information

Center for Neuroscience
A210 Langley Hall
Pittsburgh, PA 15260
412-624-5043 (phone)
412-624-9198 (fax)
jblaney@pitt.edu

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 (160 verbal, 155 quantitative) and a 4.5 in analytical writing.

Additional information and a link to our online application can be found at: cnup.neurobio.pitt.edu/training/phd/admissions.aspx

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 23-credit course requirement covering fundamental material in cellular and molecular neurobiology, systems neurobiology and several elective courses. 

Specifically, the following core courses are required:

 

BIOST 2041 Intro to Statistical Methods 1 3 cr.
MSNBIO/NROSCI 2010 Scientific Ethics 1 cr.
MSNBIO/NROSCI 2100 Cell and Molecular Neurobiology 1 5 cr.
MSNBIO/NROSCI 2101 Cell and Molecular Neurobiology 2 3 cr.
MSNBIO/NROSCI 2102 Systems Neurobiology 6 cr.
MSNBIO 2624 Grant Writing 3 cr.

 

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: cnup.neurobio.pitt.edu/people/faculty.aspx?by=x1

Neuroscience Courses:

Our complete list of courses may be viewed at: cnup.neurobio.pitt.edu/training/phd/courses.aspx#cc

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 inter-school PhD program offered cooperatively by the School of Medicine and the Dietrich 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  Web site: www.pimb.pitt.edu

Admission Requirements and Procedures

Students most likely to gain admittance will have 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, and three letters of recommendation. Scores from a GRE subject test are strongly encouraged. 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 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: 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: 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: www.pimb.pitt.edu/FacultyIndex.php

Course List

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

PhD in Clinical and Translational Science

The University requires the successful fulfillment of a minimum of 74 credits for awarding a PhD in Clinical and Translational Science.  To receive the PhD in Clinical and Translational Science, trainees must complete the Core Curriculum, Advanced “Selectives,” Research Specialization, completion and successful defense of a Comprehensive Examination, completion of the Doctoral Prospectus and defense of the Doctoral. A minimum “B” grade is required in all graduate courses.

Credit Requirements:

Core Curriculum Courses: Required courses include 19 credits of coursework, including: CLRES 2005 Computer methods for Clinical Research, CLRES 2010 Clinical Research Methods, CLRES 2020 Biostatistics, CLRES 2040 Measurement in Clinical Research, CLRES 2050 Ethics and Regulation of Clinical Research, CLRES 2071 and CLRES 2072 Research Design and Development Seminar (Parts I and II), 2 credits of coursework in Laboratory Methods and 2 credits of coursework in Translational Research.

Advanced “Selective” Courses: Advanced “Selective” courses focus on advancing methodological or analytic tops that will be most useful to the student’s chosen area of research. At least 6 credits must be in advanced analytic methods (i.e. statistics or epidemiology) and at least 4 credits must be in research methods (i.e. clinical trial design, imaging methodology, or pharmacogenomics)

Research Specialization Courses: Research Specialization courses focus on making the student flexible in selecting training experiences in areas specific to their research area. Research Specialization courses should total 24 credits, and may either be directed research credits or coursework selected by the student and mentor.

Comprehensive Examination: Individuals pursuing the PhD in Clinical and Translational Science are required to complete a Comprehensive exam. This exam consists of a written examination in the form of an NIH R01-style proposal (including, at a minimum, specific research aims, background and significance, and research methods) and an oral defense of the written portion.

Doctoral Prospectus and Dissertation: Individuals pursuing the PhD in Clinical and Translational Science must complete both a Doctoral Prospectus and successfully complete and defend a Doctoral Dissertation.

  • Dissertation Prospectus Meeting – Individuals must prepare a dissertation proposal for presentation to a doctoral dissertation committee at a formal dissertation overview meeting. At this meeting, the dissertation committee members will provide guidance in shaping the conceptualization and methodology for the individual’s Doctoral Dissertation.

  • Doctoral Dissertation – The proposal, writing, and defense of a culminating research project. The written work must conform to the University of Pittsburgh style manual (www.pitt.edu/~graduate/etd/formatguidelineshtml.html) The Final Oral Defense is a public defense of the Doctoral Dissertation. The entirety of the dissertation committee must be in attendance at the Final Oral Defense.







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