CCB faculty investigators direct, are affiliates of, or have created a number of research centers and institutes related to computational biology and genomics. A non-exhaustive list is provided below. Please email Center of Computational Biology for additions, changes or deletions.
Advanced Light Source
The Advanced Light Source (ALS), a division of Berkeley Lab, is a national user facility that generates intense light for scientific and technological research. As one of the world’s brightest sources of ultraviolet and soft x-ray beams–and the world’s first third-generation synchrotron light source in its energy range–the ALS makes previously impossible studies possible.
Berkeley Phylogenomics Group
The Berkeley Phylogenomics Group develops methods that improve the accuracy of predicted protein function by using a phylogenomic approach integrating evolutionary tree construction and analysis in the annotation pipeline.
Berkeley Structural Genomics Center
The Berkeley Structural Genomics Center pursues an integrated structural genomics program designed to obtain a near-complete structural complement of two minimal genomes, Mycoplasma genitalium and Mycoplasma pneumoniae, two related human and animal pathogens.
California Institute for Quantitative Biosciences
The California Institute for Quantitative Biosciences (QB3) is a consortium of three University of California campuses—UC Berkeley, UC Santa Cruz, and UCSF—that fosters collaborations among scientific faculty that enhance innovation and discovery, and catalyzes the conversion of discoveries into products and services that address society’s critical needs by emphasizing quantitative approaches to the biosciences. Several CCB faculty investigators are affiliates of QB3, including Dr. Susan Marqusee, who directs the UC Berkeley branch.
Center for Bioinformatics and Molecular Biostatistics
The Center for Bioinformatics and Molecular Biostatistics is a center at the University of California San Francisco campus which provides data analytic and statistical support to investigators who are engaged in molecular biologic, genomic, and genetics research projects.
Center for Emerging and Neglected Diseases
The Henry Wheeler Center for Emerging and Neglected Diseases (CEND) at the University of California, Berkeley is a cross-campus, multidisciplinary partnership which seeks to accelerate the innovation of new drugs, vaccines, and diagnostics for diseases that primarily or disproportionately afflict people in developing countries.
Center for Information Technology Research in the Interest of Society
The Center for Information Technology Research in the Interest of Society (CITRIS) creates information technology solutions for many of our most pressing social, environmental and healthcare problems.
Center for Integrative Genomics
The Center for Integrative Genomics is a research center bringing together researchers from several traditionally isolated fields of study to analyze and compare the genome sequences of a broad spectrum of organisms to determine the mechanisms responsible for evolutionary diversity among animals, plants and microbes.
Center for Intelligent Systems
The aim of the Center for Intelligent Systems is to relaunch the field of intelligent systems as an integrated scientific discipline with solid foundations and ambitious, interdisciplinary applications. The Center brings together researchers from artificial intelligence, computer vision, speech recognition, robotics, control theory, operations research, neuroscience, adaptive systems, information retrieval, data mining, computational statistics, and game theory.
Center for Theoretical Evolutionary Genomics
Research at the Center for Theoretical Evolutionary Genomics focuses on the analysis of genomic data through the development of phylogenetic and population genetic theory that are appropriate for the analysis of genomic data.
Computational Phylogenetics in Historical Linguistics
The Computational Phylogenetics in Historical Linguistics (CPHL) project, funded in part by the National Science Foundation, is a collaborative effort involving linguistics, computer science, and statistics aimed at 1) producing and maintaining real linguistic datasets, in particular of Indo-European languages, 2) formulating statistical models that capture the evolution of historical linguistic data, 3) designing stimulation tools and accuracy measures for generating synthetic data for studying the performance of reconstruction methods, and 4) developing and implementing statistically-based as well as combinatorial methods for reconstructing language phylogenies, including phylogenetic networks.
Cyberinfrastructure for Phylogenetic Research
Cyberinfrastructure for Phylogenetic Research (CIPRES) project is an open collaboration funded by the National Science Foundation that involves researchers (biologists, computer scientists, statisticians, and mathematicians) at sixteen institutions to enable large-scale phylogenetic reconstructions on a scale that will enable analyses of huge data sets containing hundreds of thousands of bio molecular sequences.
Joint Genome Institute
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories—Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest—along with the HudsonAlpha Institute for Biotechnology to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup.
Laboratory for Mathematical and Computational Biology
The Pachter Lab develops computational and experimental methods for genomics. We are currently focused on the development of single-cell genomics technologies and their application to RNA biology. The computational challenges we are addressing involve the analysis of high-dimensional data. Theorems are sometimes proven, experiments are occasionally successful, and software is distributed on GitHub. Our group includes students and postdocs with backgrounds in biochemistry, computer science, genetics, mathematics, molecular biology, physics and statistics.
Lawrence Berkeley National Laboratory
Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines.
Reliable Adaptive Distributed Systems Laboratory
The Reliable Adaptive Distributed Systems Laboratory (RAD Lab) is a collaborative space in Soda Hall for researchers in the AMP and LoCal research groups. The RAD Lab is available for use by those in AMP, LoCal and affiliated research groups 24 hours a day, 7 days a week with occasional announced exceptions. All members of the research groups hosted by the RAD Lab should have cardkey access. The RAD lab provides the following amenities: desk space, meeting rooms, kitchenette, printers, fax machines and scanners, bike racks, and various sundry supplies.
Tuberculosis Structural Genomics Consortium
The TB Structural Genomics Consortium is a world-wide consortium of scientists developing a foundation for tuberculosis diagnosis and treatment by determining the 3-dimensional structures of proteins from M. tuberculosis.
Virtual Institute of Microbial Stress and Survival
The Virtual Institute of Microbial Stress and Survival (VIMSS), based at Lawrence Berkeley National Laboratory, supports an integrated and multi-institutional program to understand the ability of bacteria and other microorganisms to respond to and survive external stresses. Dr. Adam Arkin co-directs the Institute.