Phil Berman's lab develops products and methods useful for the diagnosis, prevention, and treatment of infectious diseases, particularly HIV-1. This work involves molecular epidemiology to characterize viruses responsible for new infections and to understand the evolution of the virus within individuals. They also analyze the immune response to HIV-1 and the identification of epitopes recognized by broadly neutralizing antibodies. Based on results from these studies, new antigens are selected, mutagenized, expressed in mammalian cells, purified, and evaluated as candidate HIV-1 vaccine antigens. Because the HIV-1 envelope glycoprotein, gp120, is highly glycosylated and difficult to express, Berman's lab has developed special expertise in commercially useful methods to improve the yield and quality of complex recombinant  glycoproteins in mammalian cells. In collaborative studies, they also analyze host factors that affect susceptibility and resistance to HIV-1 infection. [More]

Camila Forsberg's research group focuses on stem cell fate decisions that give rise to variant blood cell types. Are such decisions made by the stem cell itself, by its descendant multipotent progenitors, or both? To answer such questions, Forsberg's group conducts molecular lineage tracing of HSC differentiation in vivo. In order to elucidate the mechanisms of fate decisions, they employ global analyses, such as genome-wide gene expression analysis and chromatin remodeling assays. The ultimate goal of this research is to facilitate our ability to direct specific fates and improve clinical applications of hematopoietic and non-hematopoietic stem cell therapy. [More]

Dietlind Gerloff leads a bioinformatics research group that examines the structural/evolutionary principles of interactions between proteins. Her research team combines such principles with computer science to make sense of the recent, vast accumulation of functional genomics data. The group has produced several protein structure models for biomedically important target proteins, including the malaria transmission-blocking vaccine candidate, Pfs230. They have also developed visualization tools for yeast and malaria functional genomic data. [More]

The Green lab is interested in understanding molecular and evolutionary biology through comparative genomics. They are particularly focused on the many applications of high-throughput sequencing including genome assembly, gene expression analysis, and population genetics. Green maintains a wide range of collaborative projects that currently include: investigating sex-specific gene expression and splicing, denovo assembly of bacterial genomes that produce potentially useful natural products, and application of Neandertal and other ancient hominin genomes to detect and interpret positive selection in humans. [More]

Dr. Haussler's research lies at the interface of mathematics, computer science, and molecular biology. He has focused on computational analysis and classification of DNA, RNA, and protein sequences. As a collaborator on the public Human Genome Project, his team posted the first publicly available computational assembly of the human genome sequence on the Internet, and it now maintains UCSC's Genome Browser, which is used extensively in biomedical research. [More]

Richard Hughey's research group focuses on two areas: the Kestrel programmable sequence analysis accelerator and the SAM Hidden Markov Modeling system. Kestrel is a single-board parallel processor designed to speed biological sequence analysis. The Kestrel research group, which includes Professor Kevin Karplus, designed and built the system, and has applied the machine to Smith & Waterman searching, SAM HMMs, conformational chemistry, graph coloring, and other areas. Hughey and Dr. Anders Krogh originally developed SAM -- a collection of algorithms and software used to create statistical models of RNA, DNA, and protein families with profile hidden Markov models. Since then, the Hughey and Karplus groups have collaborated to extend and improve SAM. [More]

Kevin Karplus' research group develops tools and techniques for protein structure prediction and protein design. He collaborates with Richard Hughey's group on the development of the SAM tool suite for profile hidden Markov models, particularly on developing protocols for using the tools for high-accuracy detection of remote relationships between proteins. Karplus' group has used these tools themselves to earn an international reputation for accurate prediction of protein structure: secondary structure, tertiary structure, and contact prediction. In the biannual Critical Assessment of Structure Prediction "contests", his group has presented papers (the "prize" for the contest) in CASP2 through CASP7. The group also collaborates extensively with UCSC wet-lab biologists in predicting structure and function for proteins of interest to them, and is starting work on designing novel proteins. [More]

Todd Lowe's research group uses a mixture of computational and experimental genomics to identify and characterize non-coding RNA (ncRNA) genes and to study the unique biology of Archaeal “extremophiles” – microbes that live at the edge of the limits of life.  His team has created several classes of non-coding RNAs gene-finders, and has created full-genome DNA microarrays for two different hyperthermophile species to study ancient forms of respiration and strategies for thermo-tolerance.  The group has also created a genome browser and functional genomics resource for all archaeal and extremophile species (archaea.ucsc.edu), now funded by the NSF. [More]

Professor Karen Ottemann's laboratory investigates how bacteria translate chemical and physical cues in their host environment into adaptive responses. Mistakes in sensation and subsequent gene expression by bacteria may result in their elimination by the host immune response or peristaltic flow. Elucidation of such processes will hopefully lead to identification of anti-bacterial drug targets. Ottemann is particularly interested in the role of chemoreceptors and chemotaxis associated with the bacterium Helicobacter pylori. This pathogen infects some 3 billion humans and can lead to serious disease, including ulcers and cancer. Ottemann and her colleagues have discovered two of the first chemoreceptors known to aid in the process of bacterial colonization. [More]

Dr. Prado is a statistician whose research deals with developing sophisticated Bayesian models and methodology to analyze data that arise in various biomedical applications. She is currently working on statistical genetics and non-stationary time series modeling. Her areas of application include studying the effect of natural selection in DNA sequences from malaria antigens that are candidates for vaccine development, and modeling biomedical signals such as electroencephalograms. [More]

Germ cells (the cells that give rise to eggs and sperm) have special properties.  Their immortality allows them to be perpetuated from generation to generation, and their totipotency allows them to generate all of the diverse cell types of the body in each generation.  The Strome lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency.  They study germ cells in the model organism C. elegans using a wide variety of approaches, including forward genetics, RNAi, imaging, molecular biology, biochemistry, and whole genome microarray-based technologies.  Their current focus areas are control of gene expression in germ cells by regulation of chromatin, and control of RNA metabolism by germline-specific cytoplasmic "P granules". [More]

Josh Stuart's research group develops computational approaches for predicting gene function and discovering how gene activity is regulated and modulated in response to cellular events and processes. Their methods combine genome-wide functional data across multiple organisms to identify conserved genetic mechanisms. The group has three broad aims: 1) to develop computational models to predict gene function, 2) to integrate datasets across multiple organisms to identify core molecular pathways, and 3) to develop algorithms and resources for biological discovery. Stuart also collaborates with numerous colleagues at UCSC and elsewhere to predict molecular targets of drugs, causal networks in disease, and pathways involved in stem cell differentiation. [More]

Ex-vivo Survival Mechanisms used by Vibrio cholerae between Epidemics: Fitnat Yildiz's laboratory investigates signaling and regulatory networks of Vibrio cholerae, the causative agent of the Asiatic cholera. She and her colleagues are particularly interested in those mechanisms that allow the pathogen to adapt to changes in its habitat. The bacteria's ability to survive in different growth modes in aquatic environments is closely linked to seasonal epidemics of cholera. Yildiz's laboratory is attempting to identify and characterize genes and processes associated with phase variations of the pathogen. Their results will be useful for prediction and control of epidemics of this devastating disease. [More]