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Interdisciplinary Doctoral Program in Bioinformatics


Office of Graduate Studies
University of California, San Diego, La Jolla, California



Detailed Information

Programs of Study


The University of California, San Diego (UC San Diego) offers a graduate program leading to the Doctor of Philosophy (Ph.D.) in bioinformatics and systems biology. Bioinformatics has been defined as computer-assisted analyses of large data sets pertinent to biological processes. The Bioinformatics and Systems Biology Graduate Program draws upon the expertise of affiliated faculty members from the Division of Biological Sciences; the Departments of Bioengineering, Chemistry and Biochemistry, Computer Science and Engineering, Mathematics, Physics, and the Biomedical Sciences Graduate program.

The program is organized around a formal course requirement. There are four compulsory core courses and four courses to be chosen from a list of electives approved by the Curriculum Committee. One 4-unit course in the winter and spring quarters as well as the summer sessions will be a research rotation in the laboratory of a program faculty member. The electives are intended to maximize the flexibility of the program, but at least one course must be chosen from the biology field and one from the computer science and engineering field. It is general program policy to be as adaptive as possible to the needs of the individual student. Upon completion of formal course requirements, students are required to take a qualifying examination that tests their capabilities and ascertains their potential for independent study and research. The degree requires the completion of a dissertation and defense of the research. The normal time for completion of a Ph.D. in the Bioinformatics and Systems Biology Graduate Program is five years.

There is enormous demand from industry for trained professionals in bioinformatics. The pharmaceutical industry, agribusiness, and biotechnology companies often draw people with the appropriate interdisciplinary skills from academia. A new era in biology is underway; the ability to decipher the genetic code of living organisms is dramatically changing the understanding of the natural world and promises to substantially improve the quality of human life. The accelerated growth of modern biology warrants revolutionary changes in academic curricula and the need for academic faculty members who have broad interdisciplinary training. The Bioinformatics and Systems Biology Graduate Program is designed to prepare students for a career in industry and/or academia.

Research Facilities


UC San Diego is a premier research institution with state-of-the-art research facilities. In addition to all the standard experimental facilities, there are several fully equipped computer laboratories connected by high-speed networks to the San Diego Supercomputer Center, the School of Medicine, and the Division of Natural and Physical Sciences, and the California Institute for Telecommunication and Information Technology (CalIT2). In addition, a Bioinformatics Computer Library is available for students in the program.

Financial Aid


The program supports full-time graduate students at the Ph.D. level. Financial support is available in the form of fellowships, traineeships, teaching assistantships, and research assistantships. Awarding of financial support is competitive, and stipends average $25,000 for the academic year, plus tuition and fees. Sources of funding include University fellowships and traineeships from an NIH training grant. Funds for support of international students are extremely limited, and the selection process is highly competitive.

Cost of Study


In 2009–10, full-time students who are California residents pay $3645 per quarter in registration and incidental fees. Non-California residents pay a total of $8657 per quarter in registration and incidental fees. Fees are subject to change.

Living and Housing Costs


UC San Diego provides Associated Residential Community Housing (ARCH) which offers housing to eligible graduate and professional students in four residential communities. Current monthly rates range from $483 for a single student to $1430 for a family. In fall 2010, UC San Diego ARCH will be opening Arris Verde, with housing for an additional 450 graduate students. See http://hdh.ucsd.edu/arch/gradhousing.html for more information.

There is also a variety of off-campus housing in the surrounding community. Prevailing rents range from $613 per month for a room in a private home to $1361 or more per month for a two-bedroom apartment. Information may be obtained at http://www.ucsd.edu/current-students/student-life/housing/offcampus/search.html.

Student Group


Current campus enrollment is 26,500 students, of whom 22,500 are undergraduates and 4,000 are graduate students. Currently, the Bioinformatics and Systems Biology Graduate Program has an enrollment of 47 graduate students.

Location


The 2,040-acre campus spreads from the coastline, where the Scripps Institution of Oceanography is located, across a large wooded portion of the Torrey Pines Mesa overlooking the Pacific Ocean. To the east and north lie mountains, and to the south are Mexico and the almost uninhabited seacoast of Baja California.

The University


The University of California System has ten campuses. UC San Diego comprises the General Campus, the School of Medicine, and the Scripps Institute of Oceanography. Established in La Jolla in 1960, it is one of the newer campuses, but in this short time it has become one of the major universities in the country.

Applying


Admissions criteria are in accordance with the general requirements of the Office of Graduate Studies (OGS). Candidates ought to have an interdisciplinary track record and persuasion to work across biology, medicine, computational sciences, and engineering. The most competitive applicants have an undergraduate degree in any of the disciplines in the biological sciences, the physical sciences, computer science, mathematics, or engineering with a strong background in the complementary disciplines.

Admission review will be on a competitive basis, based on the applicant’s undergraduate track record, Graduate Record Examination (GRE) General Test scores, and other scholastic achievements. Special attention will be given to the quantitative and analytical section scores of the GRE. Attention will also be given to the motivation and career plans of applicants. The applicants will be screened and evaluated by the program’s admissions committee with input from faculty in all participating departments. In addition, applicants must submit a completed UC San Diego Application for Graduate Admission found at https://graduateapp.ucsd.edu (use major code BF76). Official transcripts (English translation must accompany official transcript when written in other languages), TOFEL scores (required only for international applicants whose native language is not English and whose undergraduate education was conducted in a language other than English), and three letters of recommendation from individuals who can attest to the academic competence and to the depth of the applicant’s interest in pursuing graduate study must also be submitted for consideration. The deadline for filing a fall 2010 application for both international and U.S. residents is January 8, 2010. Applications are considered for admission for the fall quarter only.

The Faculty and Their Research


  • Department of Bioengineering
  • Gaurav Arya, Ph.D., Assistant Professor. Gene regulation ranging from chromatin structure regulation to protein-DNA recognition; optimization of the design of short peptides and siRNAs that can bind to genes and mRNAs with maximum efficiency; development of new, computationally efficient multi-scale simulation methods to allow the systematic study of such complex biological systems.
  • Jeff Hasty, Ph.D., Associate Professor. Computational genomics and the dynamics of gene regulatory networks.
  • Xiaohua Huang, Ph.D., Assistant Professor. Genomics, molecular biotechnology, and bioinformatics including chemistry and biophysics of protein and DNA molecules and technologies to uncover greater information regarding the human genome and genetics.
  • Trey Ideker, Ph.D., Associate Professor. Developing large-scale, computer-aided models of biological signaling and regulatory pathways.
  • Andrew D. McCulloch, Ph.D., Professor. In-vivo, in vitro, and computational models to investigate the relationships between the cellular and extracellular structure of cardiac and electrical and mechanical function of the normal and diseased heart; tissue engineering for cardiac regeneration; systems biology approaches to cardiac genotype-phenotype relationships.
  • Bernhard Palsson, Ph.D., Professor. Reconstruction of genome scale networks (metabolic, regulatory, and signaling); mathematical assessment of their properties and experimental determination of their functions; systems biology.
  • Shankar Subramaniam, Ph.D., Professor and Chair. Bioinformatics and systems biology; networks and phenotypes for mammalian biology.
  • Kun Zhang, Ph.D., Assistant Professor. Development and application of new genome technologies, with emphasis on stem cell research and personalized medicine.
  • Division of Biological Sciences
  • Steven Briggs, Ph.D., Professor. Molecular mechanisms by which mechanical forces induce a signal transduction and modulate gene expression results in cellular function, such as proliferation functions, such as proliferation migration and apoptosis.
  • Joseph R. Ecker, Ph.D., Professor. Molecular biology and genetics of plants.
  • Steve Kay, Ph.D., Professor and Dean. Construction and evolution of complex genetic networks that underlie circadian rhythms in animals and plants; development and use of cutting-edge technologies for measuring transcription in live cells, tissues and intact organisms.
  • Amy Kiger, Ph.D., Assistant Professor. Functional genomics of cellular morphogenesis.
  • William F. Loomis, Ph.D., Professor. Cell differentiation in Dictyostelium discoideum where a complete physical map is available; application of high-resolution genetic techniques to analyze temporal and spatial patters of gene expression.
  • Eduardo Macagno, Ph.D., Professor. Neurobiological research: molecular pathways underlying the regulation of neuronal growth cone dynamics and interactions leading to neuronal arbor formation, studies of the roles of gap junctions in the early differentiation of the central nervous system, application of imaging mass spectrometry to the mapping of peptides and proteins in leech embryos and adult nervous system sections.
  • James Posakony, Ph.D., Professor. Computational and biological approaches to elucidate the structure and operation of gene regulatory networks that direct animal development.
  • Milton H. Saier Jr., Ph.D., Professor. Transcriptional and metabolic regulation in bacteria, transport-protein evolution.
  • Julian I. Schroeder, Ph.D., Professor. Molecular and cell biological elucidation of signal-transduction cascades in higher plant cells.
  • Inder Verma, Ph.D., Adjunct Professor. Understanding the molecular mechanism of the function of proto-oncogenes and suppressor genes, gene therapy.
  • Biomedical Sciences Program
  • Ruben Abagyan, Ph.D., Professor. Protein-protein docking and interface prediction interaction, ligand docking and drug discovery, molecular modeling and bioinformatics, force field development.
  • Philip E. Bourne, Ph.D., Professor. Structural bioinformatics, structural genomics, protein structure classification, protein structure prediction, protein-protein interactions, protein evolution, cell signaling, apoptosis.
  • Pieter Dorrestein, Ph.D., Assistant Professor. Biosynthesis and functional roles of post-translational modifications that may be involved in antibiotic resistance.
  • Christopher Glass, M.D., Ph.D., Professor. Molecular mechanisms by which sequence-specific transcription factors regulate the development and function of macrophages.
  • Lawrence S. B. Goldstein, Ph.D., Professor. Understanding the molecular mechanisms of organelle and vesicle movement and the role of transport dysfunction in neurodegenerative diseases.
  • Vivian Hook, Ph.D., Professor. Protease mechanisms in peptide neurotransmitters and in neurodegenerative diseases.
  • Richard Kolodner, Ph.D. Professor. Genetic and biochemical mechanisms of genetic recombination, DNA repair and suppression of spontaneous mutations using Saccharomyces cerevisiae, mouse and human systems.
  • Sanjay Nigam, M.D., Professor. Molecular and cellular mechanisms of branching morphogenesis as they relate to organ development.
  • Lucila Ohno-Machado, M.D., Ph.D., Professor. Biomedical informatics, prognostic modeling using parsimonious machine learning algorithms.
  • Jerrold Olefsky, M.D., Professor. Cellular and molecular studies of transmembrane signaling events mediated by insulin, IGF-1 and growth factors.
  • Sergei Kosakovsky Pond, Ph.D., Assistant Adjunct Professor. Algorithms and software for statistical analysis, inference and hypothesis testing on molecular sequence data, particularly in challenges posed by studying the evolution of HIV, with its extreme mutation and recombination rates, multiple adaptive mechanisms, and computational challenges involved in the analysis of very large molecular datasets.
  • Bing Ren, Ph.D., Associate Professor. Understanding how the complex gene regulatory networks in mammalian cells control cellular proliferation and differentiation.
  • Douglas Richman, M.D., Professor In Residence. Natural history and molecular pathogenesis of HIV in a cohort of actually infected patients; studies include cell-mediated and neutralizing antibody immune responses to HIV and the viral escape and evolution in response to these.
  • Michael Rosenfeld, M.D., Professor. Molecular mechanisms by which diverse signaling pathways regulate gene expression to control development and homeostasis.
  • Palmer W. Taylor, Ph.D., Professor. Structure and function of receptors, enzymes, and adhesion molecules involved in neurotransmission.
  • Christopher Woelk, Ph.D., Assistant Adjunct Professor. Cellular modulation of protein coding and non-coding gene expression resulting from HIV-1 infection, infectious diseases, pathogen evolution, evolution and regulation of immunomodulatory gene families, disease diagnosis, and predicting outcomes with gene expression classifiers, identification of interferon-induced antiviral host factors, identification of putative vaccine candidates in the Coccidioides posadadii genome using reverse vaccinology approaches.
  • Ronghui (Lily) Xu, Ph.D., Associate Professor. Statistical methods applicable to the study of cancer.
  • Gene Yeo, Ph.D., Assistant Professor. Understand the impact of RNA processing and regulation in human normal and cancer stem cell biology and neural differentiation.
  • Department of Chemistry and Biochemistry
  • Alexander Hoffmann, Ph.D., Associate Professor and Program Associate Director. Signaling, computational network, transcription stress and immune and inflammatory responses, apoptosis, proliferation.
  • Patricia A. Jennings, Ph.D., Professor. Biophysical chemistry: Protein structure, dynamics and folding: 2, 3, and 4D NMR spectroscopy; PCR; equilibrium and kinetic-fluorescence, absorbance and circular dichroism spectroscopies.
  • Simpson Joseph, Ph.D., Professor. Mechanism of translation, process of initiation in eukaryotes.
  • J. Andrew McCammon, Ph.D., Professor. Computer simulation studies of proteins and subcellular structures, computer-aided drug discovery.
  • Susan S. Taylor, Ph.D., Professor. Relation of structure to function in cAMP-dependent protein kinase.
  • Roger Tsien, Ph.D., Professor. Engineering and use of new molecules to measure and perturb these messengers; cellular mechanisms of synaptic plasticity, especially in the cerebellum; stimulus–transcription coupling via cAMP-dependent protein kinase.
  • Wei Wang, Ph.D., Associate Professor. Inference of gene regulatory networks and determination of protein specificity.
  • Leor Weinberger, Ph.D., Assistant Professor. Dynamical systems biology; stochastic noise and feedback in gene circuits, single-cell biology, computational modeling and experiment.
  • Peter Wolynes, Ph.D., Professor. Theoretical chemistry/biochemistry, statistical mechanics of biomolecules and condensed matter, protein folding and function.
  • John C. Wooley, Ph.D., Adjunct Professor and Associate Vice Chair of Research. Bioinformatics, pharmacogenomics, structural genomics, computational biology.
  • Department of Computer Science and Engineering
  • Scott B. Baden, Ph.D., Professor. New models of execution that would allow one to express self-optimizing programs.
  • Vineet Bafna, Ph.D., Assistant Professor. Computational proteomics.
  • Richard K. Belew, Ph.D., Professor. Study of adaptive knowledge representations as used in biological systems and as can be applied as part of computer systems.
  • Sanjoy Dasgupta, Ph.D., Associate Professor. Development of algorithms for the statistical analysis of high-dimensional data.
  • Charles P. Elkan, Ph.D., Professor. Artificial intelligence with applications to biological problems.
  • Pavel Pevzner, Ph.D., Professor, Ronald R. Taylor Chair, and Program Director. Computational molecular biology and bioinformatics.
  • Yoav Freund, Ph.D., Professor. Computational learning theory and the related areas in probability theory, information theory, statistics, and pattern recognition; applications of machine learning algorithms in bioinformatics, computer vision, network routing and high-performance computing.
  • Marine Biology Research Division
  • Terry Gaasterland, Ph.D., Professor and Director of Scripps Genome Center. Computation and analysis to interpret each microbial genome in its environmental, ecological ,and evolutionary context.
  • Department of Mathematics
  • Michael J. Holst, Ph.D., Professor. Numerical analysis, scientific computation, protein electrostatics.
  • Glenn Tesler, Ph.D., Assistant Professor. Genome analysis and combinatorial mathematics.
  • Ruth J. Williams, Ph.D., Professor. Probability theory, stochastic processes.
  • Department of Physics
  • Terence Hwa, Ph.D., Professor. Structure and function of receptors and enzymes involved in neurotransmission, biological sequence analysis.
  • Jose N. Onuchic, Ph.D., Professor. Theoretical and computational methods for molecular biophysics and chemical reactions in condensed matter.

Correspondence and Information


University of California, San Diego
Bioinformatics and Systems Biology Graduate Program
Powell Focht Bioengineering Hall, Room 228
La Jolla, California 92093-0419
Telephone: 858-822-4948
Email: bioinfo@ucsd.edu