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Genomics
 
 

• Manuel Ares, Jr., (MCD) Intron Removal, Alternative Splicing, and Genomics
• Angela Brooks (BME) Transcriptome Analysis of RNA Splicing and Cancer
• Ed Green, (BME) Genome Sequence Assembly and Comparative Genome Analysis
• David Haussler (BME) Bioinformatics, Computational Genomic Data Analysis, Molecular Evolution and Comparative Genomics
• Rohinton Kamakaka (MCD) Chromosome Structure and Gene Regulation
• Todd Lowe (BME) Large Scale Approaches to Study Whole-Genome Biology
• Nader Pourmand (BME) Single Cell Analysis and Manipulation, Biosensor, Nanotechnology, DNA Sequencing
• Jevgenij Raskatov (Chem) Disease-Oriented Chemical Biology
• Jeremy Sanford (MCD) Post Transcriptional Control of Gene Expression
• Holger Schmidt (EE) Integrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip
• Beth Shapiro (EEB) Inferring the Evolutionary Dynamics of Species and Populations Using Genome-scale Data Sampled Over Time
• John Tamkun (MCD) Regulation of Chromatin Structure and Gene Expression
• Alan Zahler (MCD) Regulation of Pre-mRNA Splicing and Post-Transcriptional Regulation by Micro RNAs
• Fitnat Yildiz (METX) Ex-vivo Survival Mechanisms of Vibrio choleraes

Manny AresIntron Removal, Alternative Splicing, and Genomics

Manuel Ares, Jr., MCD Biology

The work of the Ares lab centers on the mechanisms and regulation of splicing. Splicing is required to remove intron sequences from pre-mRNA and create coding sequences for translation. Ares' group tries to understand: (1) the mechanism of action of the core components of the spliceosome, in particular the snRNAs and their rearrangements during assembly of the spliceosome and catalysis of the splicing reactions, (2) the regulation of alternative splicing at a mechanistic level including the coupling of splicing to transcription and RNA decay mechanisms, and (3) the coordinate regulation of splicing events in developing systems. [More]

Ares Publications
Manny Ares' E-Mail

Prof. Angela BrooksTranscriptome Analysis of RNA Splicing and Cancer

Angela Brooks, Dept. of Biomolecular Engineering

The Brooks lab focuses on the study of somatic mutations that cause changes to the transcriptome, particularly through mRNA splicing. We aim to gain a better understanding of how alternative splicing is regulated and the functional consequences of splicing dysregulation through the study of these cancer genome alterations. We are developing computational approaches to analyze genome and transcriptome sequencing data and developing high-throughput experimental approaches to characterize the functional impact of cancer variants. [More]

Brooks' Publications Brooks' E-Mail

Prof Ed GreenGenome Sequence Assembly and Comparative Genome Analysis

Ed Green, Dept. of Biomolecular Engineering

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]

Green's Publications Green's E-Mail

Prof David HausslerBioinformatics, Computational Genomic Data Analysis, Molecular Evolution and Comparative Genomics

David Haussler, Dept. of Biomolecular Engineering

David Haussler’s research lies at the interface of mathematics, computer science, and molecular biology. He develops new statistical and algorithmic methods to explore the molecular function and evolution of the human genome, integrating cross-species comparative and high-throughput genomics data to study gene structure, function, and regulation. [More]

Haussler Publications David Haussler's E-Mail

Prof Roh KamakakaChromosome Structure and Gene Regulation

Rohinton Kamakaka, Dept. of MCD Biology

The primary DNA sequence of an organism determines their unique genetic makeup. DNA in the eukaryotic nucleus associates with several structural and enzymatic proteins to form chromatin. This packaging affects the ability of genes to be transcribed into RNA and only a subset of genes undergo active transcription in any given cell at any particular time. Specific gene transcription is achieved by enhancer bound transcription factors that recruit specific chromatin remodeling and modifying enzymes to form open euchromatin. Conversely, silencer bound factors recruit distinct enzyme machineries and repressor proteins to modify chromatin resulting in the formation of condensed heterochromatin that silences genes ... [More]

Kamakaka's Publications Roh Kamakaka's Email

Prof Todd LoweLarge Scale Approaches to Study Whole-Genome Biology

Todd Lowe, Dept. of Biomolecular Engineering

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]

Lowe Publications Todd Lowe's Email

Prof Nader PourmandSingle Cell Analysis and Manipulation, Biosensor, Nanotechnology, DNA Sequencing

Nader Pourmand, Dept. of Biomolucular Engineering

The Pourmand lab develops new tools and technologies that integrate biology, electronics, and nanofabrication for the detection and study of genes and proteins. These tools are specifically designed to increase the speed and lower the cost of sample analysis. The lab directs particular attention to the development of medically relevant technology, such as instruments for single cell analysis. Pourmand is also Director of Genome Technology Center. [More]

Pourmand Publications Pourmand's Email

Prof. Jevgenij A. RaskatovDisease-Oriented Chemical Biology

Jevgenij A. Raskatov, Dept. of Chemistry and Biochemistry

Raskatov draws inspiration from aging-related medicinally challenging questions, which are becoming increasingly pressing as life expectancy continues to rise (the cancer/inflammation interface is of specific interest). Raskatov's lab identifies biomolecular signaling nodes that are sufficiently well-understood at the molecular level, so that a biology problem can be translated into a chemistry problem. As chemists, their goal is to synthesize molecules and study their properties by means of NMR spectroscopy (1), crystallography (2) and DFT computation (3). Molecular scaffolds that show initial promise are tested in relevant biological systems both in cell culture (4) and in vivo (5). [More]

Jevgenij Raskatov's Publications Jevgenij Raskatov's Email

Prof. Jeremy SanfordPost Transcriptional Control of Gene Expression

Jeremy Sanford , Dept. of MCD Biology

Our work attempts to dissect the myriad roles of RNA binding proteins in mammalian gene expression. RNA processing reactions such as pre-mRNA splicing, mRNA export, translation and mRNA decay are influenced by the interplay of trans-acting proteins with their cognate cis-acting RNA elements. We think that by elucidating the cis-acting RNA elements recognized by specific RNA binding proteins it will be possible to gain a better understanding of both the physiological relevance and mechanisms of action for these critical regulators of gene expression. [More]

Jeremy Sanford's Publications Jeremy Sanford's Email

Prof Holger SchmidtIntegrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip

Holger Schmidt, Dept. of Electrical Engineering

Optofluidics describes the combination of optics and microfluidics and holds great promise for novel devices for biomedical instrumentation, analytical chemistry and other fields that deal with liquid analytes. A highly desirable extension of optofluidics is to use integrated optics to replace the bulky microscopy analysis that is still commonly in use. This would allow development of a fully planar, fully integrated lab on a chip. We are using optofluidic approaches for early infectious disease and cancer detection and genome analysis. [More]

Schmidt Publications Holger Schmidt's Email

Prof Beth ShapiroInferring the Evolutionary Dynamics of Species and Populations Using Genome-scale Data Sampled Over Time

Beth Shapiro, Dept. of Ecology and Evolutionary Biology

The Shaprio lab combines temporal and genetic data to identify periods of growth, decline, dispersal, and replacement in populations. Recent statistical innovations have made it possible to co-estimate molecular rates, demographic histories and phylogenetic relationships in populations that can be sampled through time. While large mammals fall into this category (when ancient samples are available) by far the richest source of these data are RNA viruses, whose fast rate of mutation makes it easy to see evolution happening over only a few years. [More]

Shapiro Publications Beth Shapiro's Email

Prof John TamkunRegulation of Chromatin Structure and Gene Expression

John Tamkun, Dept. of MCD Biology

The Tamkun lab investigates regulation of chromatin's high order structure and its role in gene expression. Composed of DNA and proteins, chromatin's ability to fold enables the eukaryotic genome to be packaged into an extremely small space inside the nucleus of the cell. Proper transcription and replication of the genome also depend upon precise regulation of these dynamic structures, with defects in these processes believed to underly many human diseases. [More]

Tamkun Publications John Tamkun's E-Mail

Prof Al ZahlerRegulation of Pre-mRNA Splicing and Post-Transcriptional Regulation by Micro RNAs

Alan Zahler, MCD Biology

The human genome carries the blueprint for the creation of proteins, the molecular machines that carry out most of the work in the body. However, the diversity of the pool of available proteins is greatly enhanced by alterative splicing of our genes. The Zahler laboratory examines the nematode Caenorhabditis elegans in order to understand the regulatory mechanisms of this alternative splicing. Small RNAs such as miRNAs, piRNAs, and siRNAs play important roles in gene regulation at many different levels. Zahler's group is studying small RNA biogenesis and the role of small RNAs in the regulation of genomic rearrangements in ciliated protozoans. [More]

Zahler Publications Alan Zahler's E-Mail

Prof Fitnat YildizEx-vivo Survival Mechanisms Used by Vibrio cholerae between Epidemics

Fitnat Yildiz, Dept. of Microbiology and Environmental Toxicology

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]

Yildiz Publications Fitnat Yildiz's E-Mail
 

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