Computational Biology

Faculty working in computational biology:


Paul Adams
Adjunct Professor, Department of Bioengineering; Senior Scientist, Lawrence Berkeley Laboratory; Head, Berkeley Center for Structural Biology

Room 248, Building 64, Lawrence Berkeley Laboratory, 510-486-4225, vog.lblnull@smadADP

Research Interests: Development of new algorithms and methods for structural biology.  Structural studies of large macromolecular machines. Development of  cellulosic biofuels

Adam Arkin
Dean A. Richard Newton Memorial Professor, Bioengineering; Director, Physical Biosciences Division, Lawrence Berkeley National Lab; PI and Co-Director, Virtual Institute of Microbial Stress and Survival; Co-Director, BIOFAB: International Open Facility Advancing Biotechnology

512C Energy Biosciences Building, (510) 643-5678, vog.lblnull@nikrapa

Research Interests: My laboratory works on systems biology, cellular biophysics, comparative functional genomics, and synthetic biology. We aim to elucidate the evolutionary design principles of cellular networks and exploit these for design new function and behaviors in cells using a combination of experiment, theory and computation. Projects range from understanding the role of stochastic gene expression and memory in the stress response of Bacillus subtilis, to studies on the evolution of signal transduction pathways in bacteria, to detailed experiments and modeling of the stochastic control of HIV-1 gene expression and its role in latency, to the design and implementation of a tumor killing bacteria. In support of these projects we also develop technology for the statistical analysis of biological data, comparative functional genomics and model-based design of experiments as well as physical theory of cellular processes.

Steven E. Brenner
Affiliated Faculty, Bioengineering and MCB; Professor, Plant & Microbial Biology; Adjunct Professor, Bioengineering & Therapeutic Sciences (UCSF)

461A Koshland Hall, (510) 643-9131, ude.yelekreb.oibpmocnull@rennerb

Research Interests: The Brenner research lab has four key research interests involving computational and experimental genomics.

Gene regulation by alternative splicing and nonsense-mediated mRNA decay
Nonsense-mediated mRNA decay (NMD) is a cellular RNA surveillance system that recognizes transcripts with premature termination codons and degrades them.  Several years ago, we discovered large numbers of natural alternative splice forms that appear to be targets for NMD, and we speculated that this might be a mode of gene regulation which we termed RUST (regulated unproductive splicing and translation).  As part of a modENCODE consortium, we plan to discover the repertoire of cis-regulatory sites for alternative splicing in insects

Prediction of protein function using Bayesian phylogenomics
In collaboration with Michael Jordan’s group, we have developed a statistical approach to predicting protein function that uses a protein family’s phylogenetic tree, as the natural structure for representing protein relationships.

Medical and environmental metagenomics; personal genomics
Our metagenomics studies have included date from the Sorcerer II global ocean sampling project, acid mine drainage, and the role of gut microbiota in Crohn’s disease.  We also have a longstanding interest in personal genome interpretation and developing a genome commons. 

Structural genomics and proteins complexes
We are involved in maintaining the SCOP: Structural Classification of Proteins and ASTRAL databases which are key resources for accessing and understanding protein structure data.  We therefore analyze structural genomics efforts and guide their future directons.

Teresa Head-Gordon
Chancellor's Professor, Department of Chemistry; Professor, Department of Bioengineering and Department of Chemical and Biomolecular Engineering; Faculty Staff Scientist, Lawrence Berkeley National Laboratory

274C Stanley Hall, (510) 666-2744, ude.yelekrebnull@ght

Research Interests: The simultaneous revolutions in molecular biology, scientific computing, and nanotechnology is giving rise to new interdisciplinary research opportunities in bioengineering. My own research program lies at the interfaces of engineering, chemistry, biology, physics, mathematics and computational science, with topics ranging from protein aggregation diseases, muliprotein complex folding and function, protein fold and structure prediction, hydration forces and dynamics, through to glassy dynamics of nanomaterials.

Ian Holmes
Associate Professor, Bioengineering

374C Stanley Hall, (510) 666 - 2790, ude.yelekrebnull@hhi

Research Interests: We have several areas of interest around the general theme of using bioinformatics in the investigation of genomes, their evolution and ecology.These include(1) Developing new software for genomics (from Web 2.0/AJAX genome browsers to phylogeny and molecular evolution, ');(2) Developing, analyzing and applying probabilistic models for sequence analysis (example methods include stochastic grammars or finite-state machines; example biological applications include multiple genome alignment, ncRNA gene evolution and transposon analysis, ');and (3) Developing computational methods for synthetic biology, such as ribocircuit design or metagenomics.

Richard Karp
University Professor, Bioengineering and Electrical Engineering & Computer Science and Industrial Engineering & Operations Research and Mathematics

621 Soda, (510) 642-5799, ude.yelekreb.scnull@prak

Research Interests:

I have worked on a variety of problems in computational molecular biology, including physical mapping, sequence assembly, sequence comparison, finding hidden structure in gene expression data, design of DNA probes, analysis of transcriptional regulation, discovery of regulatory structure from protein-protein interaction data, haplotype inference and estimation of haplotype frequencies from pooled genotype data.

Jitendra Malik
Professor, Bioengineering; Arthur J. Chick Professor, Computer Science

, (510) 642-7597, ude.yelekreb.scnull@kilam

Research Interests:

Mohammad Mofrad
Professor, Bioengineering and Mechanical Engineering; Faculty Engineer, Physical Biosciences Division, Lawrence Berkeley National Lab

208A Stanley Hall, (510) 643-8165, ude.yelekrebnull@darfom

Research Interests:

Mechanical phenomena affect nearly every aspect of cellular biology and function, yet the underlying mechanisms of how mechanical forces and biochemical signals interact is not clearly understood. We are interested in understanding the molecular basis of cell mechanics and mechanotransduction and shedding light on the role of these processes in human disease. Our specific attention is on the role of two macromolecular systems in cellular function, namely the integrin-mediated focal adhesions at the interface between the cell and extracellular matrix (ECM) and the nuclear pore complex (NPC). Focal adhesions are the immediate sites of cell interaction with the extracellular matrix, and as such they play a key role in mechanosensing and mechanotransduction at the the edge of the cell. Nuclear pores could also play a role in the overall process of cellular mechanotransduction by exquisitely controlling the material transport in and out of the nucleus, thereby regulating the gene expression and protein synthesis. Our current projects are as follows: 
 1. Molecular Mechanics of Integrin-Mediated Focal Adhesions 2. Mechanics of the Nuclear Pore and Nucleocytoplasmic Transport 3. Mechanics and Mechanotransduction in Cardiovascular Disease

Boris Rubinsky
Professor Emeritus, Bioengineering; Professor of the Graduate School, Mechanical Engineering

6105B Etcheverry Hall, (510) 642-8220, ude.yelekreb.emnull@yksnibuR

Research Interests: Research in several different areas. Heat and mass transfer in bioengineering with particular emphasis on low temperature biology and cryosurgery. Tissue engineering with emphasis on production of artificial tissue through freezing and preservation of engineered tissue. Bioengineering devices with emphasis on devices that interface between biological systems and inanimate electronics; such as the bionic micro technology. Imaging with emphasis on introducing imaging systems (suchas MRI and Electrical Impedance Tomography) in the control loop of minimally invasive surgical procedures. Genomic computation witrh emphasis on genetic algorithm simulation of gene behavior and properties.

David Schaffer
Professor, Bioengineering and Chemical Engineering and Helen Wills Neuroscience Institute; Chemist Faculty, Lawrence Berkeley National Lab

274 Stanley Hall, (510) 643-5963, ude.yelekrebnull@reffahcs

Research Interests:

Our research program employs molecular and cellular engineering approaches to investigate biomedical problems. Our laboratory is a part of the Department of Chemical Engineering, the Helen Wills Neuroscience Institute, and the Bioengineering Graduate Group at Berkeley. We are interested in the related areas stem cell bioengineering, gene delivery systems, and molecular virology, with applications in regenerative medicine and tissue engineering.

We will develop a research program that employs molecular and cellular engineering approaches to attempt to investigate biomedical problems. In particular, our lab is interested in the related areas of stem cell bioengineering and gene delivery, with applications in regenerative medicine and tissue engineering.

Many of our efforts are dedicated to understanding the biology and exploring the therapeutic potential of stem cells. Stem cells are immature cells that exist in various locations of our bodies. Throughout our lifetimes, these cells divide and develop into the specialized cells that perform the functions necessary for life. Therefore, if we contract a disease that kills those specialized cells, our stem cells are a potential source for replacing lost cells to counteract or even cure the disorder.

There are several challenges that must be overcome in this field. In particular, efforts to engineer tissues rely upon the ability to control stem cells. That is, the signals that control stem cell function and fate must first be discovered, and then integrated into cellular microenvironments to control stem cell expansion and lineage-specific differentiation. We have efforts in novel signal discovery, computational and experimental analysis of the biological networks that cells use to interpret and implement these signals, and on the integration of these signals into synthetic, polymeric microenvironments for optimal stem cell control in collaboration with the group of Prof. Kevin Healy (Bioengineering). This blend of stem cell biology, systems biology analysis, and biomaterials engineering has led to significant advances in the application of stem cells for tissue repair.

Our second major research thrust is dedicated to understanding the biology and exploring the therapeutic potential of gene delivery, which serves as an effective means to control stem cells. Gene therapy can be defined as the introduction of genetic material to the cells of an individual for therapeutic benefit. A variety of approaches are under development to use gene therapy for treating cancer, AIDS, and a number of inherited genetic disorders. For example, gene therapy could be used to replace the genes hemophilia patients are missing, to bolster the immune system to recognize and combat tumors, or to inhibit the replication of HIV virus. However, significant progress must still be made before these developing strategies become therapeutic realities.

One of the most formidable obstacles to gene therapy is how to efficiently deliver genes to a sufficient number of cells to yield a therapeutic effect. A number of gene delivery vehicles, or vectors, are in development, and most exploit or emulate the abilities many viruses have evolved to deliver their genes to cells as part of their life cycles. However, while viruses have developed numerous strategies to deliver genes over millions of years of evolution, the efficiency and safety of vehicles based upon recombinant viruses must still be further improved. We have developed numerous high-throughput directed evolution approaches to engineer the properties of viral vehicles at the molecular level to enhance their abilities to deliver genes. These successful efforts are enhancing the abilities of several vectors to make them more effective at delivering gene “medicines.”

In parallel, we are interested in studying some basic aspects of viral biology. Specifically, viruses have evolved gene circuits that after infecting a cell execute programs to harness cells to reproduce the virus. We apply integrated systems biology approaches, composed of computational and experimental efforts, in collaboration with the group of Prof. Adam Arkin (Bioengineering) to how the structures of these gene circuits have dynamically evolved to optimize the virus’ ability to hijack cells to maximize its ability to reproduce. This fundamental work is leading to new insights on how to combat viral infectious disease.

Furthermore, we plan for these related lines of research to converge in the future. If we can effectively deliver a gene, and we can learn much more about what kinds and levels of genes are needed to control stem cell behavior, we can attempt to apply this information to longer term therapeutic goals. These aims could include using gene delivery to stimulate stem cells to divide more rapidly, to generate specific types of cells such as neurons, or to guide the successful integration of specific cell types into tissue for functional repair. It is our hope that this research will not only enhance our understanding of neuroscience, but also eventually alleviate the devastating effects of numerous diseases.

Kimmen Sjölander
Professor, Bioengineering and Plant and Microbial Biology

308C Stanley Hall, (510) 642-9932, ude.yelekrebnull@nemmik

Research Interests: I am primarily interested in phylogenetic tree reconstruction, remote homolog recognition, protein structure prediction, subfamily classification, prediction of critical positions in molecules, multiple sequence alignment, protein-protein interaction, pathway inference, computational prediction of protein domain structure, and other aspects of protein function and structure. The medical applications of genomics and bioinformatics, for the detection of genes involved in disease, or conferring virulence to microbes, and similar problems, is a particular area of interest. My experience in industry, prior to re-joining academia, made me aware of many of the issues confronting scientists working on target and drug discovery, and I have various research interests in these areas as well.