Computational Biology

University of California, Berkeley

Overview

Computational biology is an academic growth area that binds together multiple areas of biological research with the mathematical and computational sciences. It takes center stage in the new data-oriented biology by facilitating scientific discoveries based on high-throughput methods. The genomic revolution has fundamentally changed the biological sciences, and computational biology provides the means for translation of genomic discoveries into a new understanding of complex biological systems and eventually into improvements of the human condition through the development of solutions to environmental problems, new drug discoveries, and personalized medicine.

The Center for Computational Biology is Berkeley’s hub for research and training in computational biology and bioinformatics. Through courses, seminars, scientific meetings, and innovative training programs for PhD students administered by the Graduate Group in Computational Biology, the center catalyzes biological discoveries at the interface of biology, computation, and mathematics/statistics. As a campus strategic initiative, the center fosters an interactive, innovative, and collegiate environment for faculty, students, and postdoctorates drawn from five colleges and over a dozen academic departments. Faculty research interests are likewise diverse, ranging from computational and statistical genomics to population, comparative, and functional genomics; from bioinformatics and proteomics to evolutionary biology, phylogenomics, and statistical and computational methods development for modeling biological systems.

Undergraduate Programs

There is no undergraduate program in Computational Biology.

Graduate Programs

Computational Biology: Designated Emphasis (DE), PhD

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Courses

Computational Biology

Faculty and Instructors

+ Indicates this faculty member is the recipient of the Distinguished Teaching Award.

Faculty

Adam Arkin, Professor. Systems modeling.
Research Profile

Doris Bachtrog, Associate Professor. Evolution of sex and recombination, Y degeneration, dosage compensation, sexually antagonistic variation.
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Lisa F. Barcellos, Associate Professor. Public health, genetic epidemiology, human genetics, autoimmune diseases, multiple schlerosis, lupus erythematosus, rheumatoid arthritis, epigenetics, genomics, computational biology.
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Carl Boettiger, Assistant Professor. Theoretical ecology, ecoinformatics, modeling, data science, resilience, early warning signals, decision theory.
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Steven Brenner, Professor. Molecular biology, computational biology, evolutionary biology, bioengineering, structural genomics, computational genomics, cellular activity, cellular functions, personal genomics.
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Perry De Valpine, Associate Professor. Population ecology, mathematical modeling and statistics.
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Sandrine Dudoit, Professor. Genomics, classification, statistical computing, biostatistics, cross-validation, density estimation, genetic mapping, high-throughput sequencing, loss-based estimation, microarray, model selection, multiple hypothesis testing, prediction, RNA-Seq.
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Michael B. Eisen, Professor. Genomics, genome sequencing, bioinformatics, animal development.
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Steven N. Evans, Professor. Genetics, random matrices, superprocesses and other measure-valued processes, probability on algebraic structures -particularly local fields, applications of stochastic processes to biodemography, mathematical finance, phylogenetics and historical linguistics.
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+ Phillip Lewis Geissler, Professor. Statistical mechanics, theoretical chemistry, microscopic behavior of complex biological and material systems, biomolecular structure and dynamics, nonlinear vibrational spectroscopy.
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Wayne Marcus Getz, Professor. Africa, disease ecology, wildlife conservation, resource management.
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Oskar Hallatschek, Assistant Professor.

Teresa Head-Gordon, Professor. Computational chemistry, biophysics, bioengineering, biomolecules, materials, computational science.
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Ian Holmes, Assistant Professor. Computational biology.
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Haiyan Huang, Associate Professor. Applied statistics, functional genomics, translational bioinformatics, high dimensional and integrative genomic/genetic data analysis, network modeling, hierarchical multi-lable classification.
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Alan Hubbard, Associate Professor.

John P. Huelsenbeck, Professor. Computational biology, evolutionary biology, phylogenetics.
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Nicholas Ingolia, Assistant Professor. Ribosome Profiling, translation, genomics.
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Nicholas P. Jewell, Professor. AIDS, statistics, epidemiology, infectious diseases, Ebola Virus Disease, SARS, H1N1 influenza, adverse cardiovascular effects of pharmaceuticals, counting civilian casualties during conflicts.
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Michael I. Jordan, Professor. Computer science, artificial intelligence, bioinformatics, statistics, machine learning, electrical engineering, applied statistics, optimization.
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Sona Kang, Assistant Professor. Epigenetics, chromatin remodeling, gene expression, diabetes, metabolic diseases.
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+ Richard Karp, Professor. Computational molecular biology, genomics, DNA molecules, structure of genetic regulatory networks, combinatorial and statsitical methods.
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Sung-Hou Kim, Professor. Computational genomics, Structural Biology, drug discovery, disease genomics.
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Lexin Li, Associate Professor.

Susan Marqusee, Professor. Amino acids, determinants of protein structure and folding, biophysical, structural and computational techniques, translocation, protein synthesis.
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John Marshall, Assistant Professor. Utilize mathematical models to predict the utility of genetic control strategies for a variety of mosquito-borne diseases.

Elchanan Mossel, Professor. Applied probability, statistics, mathematics, finite markov chains, markov random fields, phlylogeny.
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Michael Nachman, Professor. Population genetics, evolution, genomics, mammalian evolution.
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Rasmus Nielsen, Professor. Statistical and computational aspects of evolutionary theory and genetics.
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George Oster, Professor. Computational biology, developmental biology, mathematical modeling of molecular and cellular systems, protein motors, cell motility, spatial pattern formation in eukaryotic and prokaryotic cells, neural pattern formation.
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Lior Pachter, Professor. Mathematics, applications of statistics, combinatorics to problems in biology.
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Elizabeth Purdom, Assistant Professor. Computational biology, bioinformatics, statistics, data analysis, sequencing, cancer genomics.
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+ Jasper D. Rine, Professor. Biology, cell biology, DNA replication, gene regulation, saccharomyces cerevisiae, genetic analysis, genome, cholesterol biosynthetic pathway, modification of proteins, prenylated proteins.
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Daniel S. Rokhsar, Professor. Biology, collective phenomena and ordering in condensed matter and biological systems, theoretical modeling, computational modeling, behavior of quantum fluids, cold atomic gases, high temperature superconductors, Fermi and Bose systems.
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Kimmen Sjolander, Professor. Computational biology, algorithms, phylogenetic tree reconstruction, protein structure prediction, multiple sequence alignment, evolution, bioinformatics, hidden Markov models, metagenomics, statistical modeling, phylogenomics, emerging and neglected diseases, machine-learning, genome annotation, metagenome annotation, systems biology, functional site prediction, ortholog identification.
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Yun Song, Associate Professor. Computational biology, population genomics, applied probability and statistics.
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John Taylor, Professor. Evolution, fungi, phylogenomics, mycology, population genomics.
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Mark J. Van Der Laan, Professor. Statistics, computational biology and genomics, censored data and survival analysis, medical research, inference in longitudinal studies.
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Nir Yosef, Assistant Professor. Computational biology.
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Emeritus Faculty

Peter J. Bickel, Professor Emeritus. Statistics, machine learning, semiparametric models, asymptotic theory, hidden Markov models, applications to molecular biology.
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David A. Patterson, Professor Emeritus. Computer Architecture & Engineering (ARC), Computer Architecture and Systems: Parallel Computing performance, correctness, productivity,Biosystems & Computational Biology (BIO), Cancer tumor genomics, Operating Systems & Networking (OSNT).
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Montgomery Slatkin, Professor Emeritus. Evolutionary theory, genetic evolution, natural populations of plants and animals populations, human populations, natural selection structure genomes.
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Terence P. Speed, Professor Emeritus. Genomics, statistics, genetics and molecular biology, protein sequences.
Research Profile

Contact Information

Computational Biology Graduate Group

574 Stanley Hall

Phone: 510-642-0379

Fax: 510-666-3399

compbiograd@berkeley.edu

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PhD Program Chair & Head Graduate Advisor

Haiyan Huang

Phone: 510-642-6433

http://www.stat.berkeley.edu/~hhuang/

hhuang@stat.berkeley.edu

Graduate Program Coordinator

Kate Chase

574 Stanley Hall, MC #3220

Phone: 510-642-0379

katechase@berkeley.edu

Director, Center for Computational Biology

Lisa F. Barcellos PhD, MPH

324 Stanley Hall

Phone: 510-642-7814

Fax: 510-643-5163

lbarcellos@genepi.berkeley.edu

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