Ph.D. in Computational and Systems Biology

Program Overview		Computational and Systems Biology are developing fields of endeavor that aim to understand biological systems through mathematical analysis, numerical simulation, data collection, refinement and improvement of models based on comparison with experimental data and the development of theories to enhance our understanding of biological systems. Fields of modern genetics (including genomics and proteomics) and molecular and cell biology are the current focus of research in systems biology.Myriad computational tools including deterministic and stochastic modeling, Monte Carlo simulations, data mining and data analysis are needed in approaching these problems. Applied mathematical topics including nonlinear dynamical systems (discrete and continuous), partial differential equations, probability and statistics, linear algebra, network theory, numerical analysis, control theory, asymptotic and perturbation methods provide some of the fundamental tools needed to carry out the requisite modeling and analysis.
Aims and Objectives		The doctoral program in Computational and Systems Biology will train scientists, mathematicians, engineers, and/or quantitative biologists via a combination of coursework, independent study, optional laboratory rotations and individual mentoring so as to provide them with a strong grounding in modern biology and genomics as well as in mathematical methods needed for modeling and computational work. This training is applied to an original dissertation that may be characterized by the following: An outstanding original biological problem that motivates the need for the development of mathematical models or computational approaches; A significant component of original, advanced mathematical modeling or computational investigation; The presence of conceptual and/or computational challenges in the implementation of the mathematical models and/or computational methods.
CGU Faculty		please refer to our PEOPLE page
KGI Faculty		Brian Aufderheide, Assistant Professor Physiological Control, Optimization of Fermenters, Systems Analysis of Genetic and Metabolic Networks Deb Chakravarti, Director of Proteomics, Beckman Professor of Applied Life Sciences Experimental and Computational Proteomics, Protein Chemistry, Immunology, Vaccine Discovery and Development James Cregg, Director of Research, Professor Molecular and Cellular Biology, Expression Systems, Bioprocessing, Cell Biology T. Gregory Dewey, Dean of Faculty, Robert E. Finnigan Professor of Applied Life Sciences Computational Biology, Molecular Biophysics, Theoretical Biology David J. Galas, Chancellor, Chief Scientific Officer, Norris Professor of Applied Life Sciences Molecular Biology, Computational Biology, Genomics Technology Chen-Chen Kan, Professor Recombinant Protein Expression, Proteomics, Structure-based Drug Discovery Brenda Mann, Fletcher Jones Foundation Assistant Professor Biomaterials, Tissue Engineering Ali Nadim, Professor (joint with CGU) Bioengineering, Microfluidics, Computational and Applied Mathematics Angelika Niemz, Fletcher Jones Foundation Assistant Professor Biomaterials, Biomimetics Alpan Raval, Assistant Professor (joint with CGU) Computational Biology, Bioinformatics Animesh Ray, Associate Professor Molecular Computation Herbert Sauro, Assistant Professor Biochemical Control Systems, Systems Biology Software Tools, Network Analysis Sheldon M. Schuster, President, Professor Biochemistry, Enzyme Structure and Function James D. Sterling, Associate Professor Bioengineering, Fluid Mechanics and Microfluidics, Heat Transfer, Systems Modeling David Wild, Director of Computing, Associate Professor Computational Biology and Bioinformatics
Program Organization		The program will be administered jointly by Keck Graduate Institute and the School of Mathematical Sciences at Claremont Graduate University.A Program Coordinator from among the faculty members will be appointed at each campus; the Program Coordinators will oversee the operation of the Program, advise students, appoint preliminary advisors and recommend appointments to doctoral committees. Major policy changes will be recommended by a Steering Committee and may only become effective after approval by each campus following its own procedures. The Steering Committee will be co-chaired by the two Program Coordinators. In addition, the Provost at CGU and the Dean of Faculty at KGI will appoint two additional members to the Steering Committee after consultation with each campus Program Coordinator. The KGI faculty will be responsible for responding to inquiries about the program and for acting upon applications for admission and financial aid.The appointment of the CGU Coordinator to the PhD Program will be made through recommendation of the mathematics faculty to the Provost. The CGU doctoral faculty will also respond to inquiries about the program and act (in cooperation with the KGI faculty) upon applications for admission and financial aid.
Admission		The Deans from both institutions, in consultation with the Program Coordinators, will appoint an Admissions Committee consisting of four faculty members, two from KGI and two from CGU. The Admissions Committee will review the files and recommend admission into the Program. Other faculty may review files and make recommendations to the committee. The review process maywill ordinarily include personal interviews of applicants whenever possible. Students must fulfill the general requirements for admission with graduate standing to each institution. Students must also meet the special requirements of this program. These include: A baccalaureate degree in mathematics or a scientific or engineering discipline from an accredited institution. Applications from outstanding candidates with degrees in other areas may be accepted conditionally; normally, these students will be expected to take, during their first year of enrollment, the necessary coursework to eliminate deficiencies in their backgrounds. A Grade Point Average of at least 3.0 at the undergraduate level, and of at least 3.5 in any previous graduate work (in order for the application to be competitive). Suitable scores on the Graduate Record Examinations, with acceptable performance in the Verbal and Quantitative sections. Written and spoken proficiency in English. Applicants must submit: the appropriate application forms; transcripts of all their post-secondary coursework; three letters of recommendation from current or former professors, supervisors, or other appropriate persons; a statement of purpose, explaining their interest in the program; results of the Graduate Record Examination.
Faculty Advisors and Doctoral Committees		Upon admittance, each student will be assigned a Faculty Mentor from either institution. The Program Coordinators, who may themselves serve as Faculty Mentors, will make this appointment. After completing the first year of study and receiving a favorable evaluation of progress (based,for instance,on course grades, seminar participation, etc.), the student will select a Doctoral Advisor and at least two other persons, one from each campus, to serve on a three-person Doctoral Committee. The selection of the Doctoral Advisors and members of the Doctoral Committee will depend upon their availability and willingness to serve and must be approved by the two Program Coordinators and by the CGU Provost and KGI Dean of Faculty. The Faculty Mentor may serve as the Doctoral Advisor to the student. Additional Committee members may be scientists from an outside institution, such as a national laboratory, industry, or another accredited university. The Doctoral Committee, being the student¡¯s official advising unit, will develop a suitable course of study; administer the Qualifying Exam; monitor the progress of the research work, and administer the student's Final Exam (Doctoral Dissertation Defense). A member of the Doctoral Committee, including the Faculty Mentor and Doctoral Advisor may be replaced if requested by either the student or the member, and with the agreement of the appropriate Program Coordinator and Deans.
Coursework		The program shall consist of a minimum of 72 units of coursework, 24 to be completed at CGU, and 24 to be completed at KGI.At least 24 additional units of Research, Practicum, Dissertation and/or Graduate Seminar can be taken at either institution. Alternatively, up to 24 units of graduate coursework towards the degree program may be transferred upon approval by the program coordinators. (Note: The credit accounting system is somewhat different at the two institutions. In particular, graduate math courses at CGU are typically 4 credits each, whereas KGI¡¯s full-semester courses are 3 credits each, with the typical contact hours being the same. Therefore, an easier accounting of the requirement would be: the equivalent of six 4-credit courses at CGU, the equivalent of six full courses at KGI, and an additional six semester-long graduate courses transferred into the program, or taken at either KGI or CGI). It is envisioned (though not required) that the students will follow one of three major tracks that would determine their course selection:Computational Molecular Biology (e.g., bioinformatics, biosequence analysis, data mining), Computational Systems Biology (e.g., modeling of metabolic and signal transduction networks), and Bioengineering Modeling (e.g., biotransport phenomena, biofluid dynamics, Control). Preparatory coursework could include: Molecular Biology, Genetics, Biochemistry, Thermodynamics, Biophysics, Nonlinear Dynamics, Numerical Analysis, Differential Equations, Statistics, Probability, Linear Algebra, Algorithms, Stochastic Systems and Equations, Simulation, Programming (Fortran, C, Matlab), Computational Molecular Biology, Computational Systems Biology, Control, and Information Theory.
Qualifying Examination		The Qualifying Exam shall consist of a term research project supervised by a Faculty Mentor. The research topic will be approved by the Program Coordinators jointly, in consultation with the Faculty Mentor. The student will be required to prepare a written account of the research work performed and its results, and offer an oral presentation before the members of the Doctoral Committee. If the student fails all or part of the Qualifying Exam, he/she may request to address the Committee¡¯s concerns a second time.The student is normally terminated if he/she fails the Qualifying Exam a second time.
Dissertation Proposal		The Dissertation Proposal shall be submitted by the student to the Doctoral Committee before completion of the student's third academic year in the program. It will be similar in format to a scientific grant proposal to a major funding agency. It will describe the research project that the student intends to carry out, on which his/her Doctoral Dissertation will be based. The student will also be required to offer an oral presentation before the Doctoral Committee. Upon successful completion of this presentation, the student will be recommended for Advancement to Candidacy for the Doctoral Degree.
Doctoral Dissertation		After completion of the dissertation research work, the candidate will submit and present a public oral defense of his/her Dissertation to the Doctoral Committee. An account of the work performed by the student will be submitted for publication to a peer-reviewed, international research journal, before the above presentation can take place. Following the presentation, the student's Doctoral Committee will make a recommendation to the Deans to pass or fail the student.