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• Mannuel Ares (MCD) Intron Removal, Alternative Splicing, and Genomics
• Phil Berman (BME) Biotechnology and Infectious Diseases
• Angela Brooks (BME) Transcriptome Analysis of RNA Splicing and Cancer
• Manel Camps (METX) Use of Random Mutagenesis for Studies of Evolution and for Therapy
• Phil Crews (Chem) Marine Natural Products as Anti-Cancer Compounds
• Dave Draper (AMS) Bayesian Statistics, Hierarchical Modeling, and Bayesian Non-parametric Methods
• Camilla Forsberg (BME) How Is Stem Cell Fate Decided?
• Ed Green (BME) Genome Sequence Assembly and Comparative Genome Analysis
• David Haussler (BME) Bioinformatics, Computational Genomic Data Analysis, Molecular Evolution and Comparative Genomics
• Richard Hughey (CE) Bioinformatic Tools for Sequence Analysis and Prediction
• Kevin Karplus (BME) Long-read DNA Sequencing
• Juhee Lee (AMS) Applications of Bayesian Models to Bioinformatics Data
• Todd Lowe (BME) Large Scale Approaches to Study Whole-Genome Biology
• Harry Noller (MCD) Structure and Function of the Ribosome
• Karen Ottemann (METX) Bacterial Pathogens Sense and Respond to Host Environments
• Raquel Prado (AMS) Application of Bayesian Analysis to Biomedical Questions
• Jeremy Sanford (MCD) Post Transcriptional Control of Gene Expression
• Nik Sgourakis (Chem) Modelling the Structures of Protein Complexes from Sparse Experimental Data
• Susan Strome (MCD) Regulation of Germ Cell Development in C. elegans
• Josh Stuart (BME) Computational Functional Genomics, with Application to Integrative Analysis of Cancer
• Fitnat Yildiz (METX) Ex-vivo Survival Mechanisms Used by Vibrio cholerae between Epidemics

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 Phil BermanBiotechnology and Infectious Diseases

Phil Berman, Dept. of Biomolecular Engineering

Professor Berman is a pioneer in the development of recombinant vaccines for AIDS and other infectious diseases. His research interests include the development of vaccines, therapeutics, and diagnostics for the prevention and treatment of infectious diseases, as well as the development of new technology for commercial production of complex recombinent glycoproteins. [More]

Berman Publications Phil Berman's Email

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 Manel CampsUse of Random Mutagenesis for Studies of Evolution and for Therapy

Manel Camps, Microbiology and Environmental Toxicology

The Camps laboratory studies how random changes in genetic information (mutations) facilitate the acquisition of new biochemical activities. They couple the generation of random mutant libraries with specific selections or screens to study the functional impact of individual point mutations and to establish how genes evolve in response to selective pressure. As model systems they use extended-spectrum beta-lactamase resistance and the evolution of alterations in the substrate specificity of the demethylase ALKBH2. This work is combined (in a collaboration) with high-end computational approaches aimed at anticipating the effect of individual mutations, alone, or in combination. A separate application of random mutant library generation in vivo is the use of mutation footprints to dissect the role of individual players involved in DNA replication. Finally, the Camps laboratory is applying concepts of directed evolution to whole genomics analysis, with an emphasis on cancer. The goal of these studies is to help understand the contribution of DNA repair genes to resistance to chemotherapy and to oncogenesis. [More]

Camps' Publications Manel Camps' Email

Prof Phil CrewsMarine Natural Products as Anti-Cancer Compounds

Phil Crews, Dept. of Chemistry and Biochemistry

The Crews laboratory investigates the chemical structure and biological activity of chemical compounds that are derived from marine organisms. Among its many research projects, the laboratory collaborates with scientists at other research institutions and pharmaceutical industries to explore the identification and development of naturally occuring compunds in the fight against cancer. [More]

Crews' Publications Phil Crews' E-Mail

Bayesian Statistics, Hierarchical Modeling, and Bayesian Nonparametric Methods

David Draper, Dept. of Applied Math & Statistics

David Draper's bio-medical research focuses on methodological developments in Bayesian statistics, with particular emphasis on hierarchical modeling, Bayesian non-parametric methods, and Bayesian model specification and model uncertainty. His applied work has been concentrated on quality-of-care assessment in health policy, controlled experiments and observational studies in medicine, and environmental risk assessment. Previous projects have included the use of real-time electronic medical records to measure processes and outcomes of health care, hierarchical methods for the evaluation of quality of medical care in hospitals, and the assessment of risks arising from nuclear waste disposal. [More]

Draper's Publications Dave Draper's E-Mail

Prof Camilla ForsgergHow Stem Cell Fate Is Decided

Camilla Forsberg, Dept. of Biomolecular Engineering

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]

Forsberg Publications Camilla Forsberg's Email

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 Richard HugheyBioinformatic Tools for Sequence Analysis and Prediction

Richard Hughey, Dept of Biomolecular Engineering and Dept. of Computer Engineering

Richard Hughey's research has focussed on two areas: high-performance VLSI computer architecture and biological sequence analysis. The Kestrel programmable sequence analysis accelerator was a single-board parallel processor designed to speed biological sequence analysis for Smith & Waterman searchin, HMMs, conformational chemistry, graph coloring, and other areas. Hughey, Dr. Anders Krogh, Professors Haussler and Karplus, and UC Santa Cruz student researchers developed developed the Sequence Analysis and Modeling (SAM) software suite. SAM is a a collection of algorithms and software used to create statistical models of RNA, DNA, and protein families with profile hidden Markov models. Dr. Hughey has been active in program development, including the UC Santa Cruz Bioinformatics and Bioengineering programs. He is presently Vice Provost and Dean of Undergraduate Education at UC Santa Cruz. [More]

Hughey's Publications Richard Hughey's Email

Prof Kevin KarplusLong-read DNA Sequencing

Kevin Karplus, Dept. of Biomolecular Engineering

Kevin Karplus' research group develops tools and techniques for genome assembly from next-generation sequence data, signal processing and machine learning for nanopores. [More]

Karplus Publications Kevin Karplus's E-Mail

Applications of Bayesian Models to Bioinformatics DataProf. Juhee Lee

Juhee Lee, Dept. of Applied Math and Statistics

Juhee Lee's research interests include the development of Bayesian models (parametric and nonparametric) and their application of to bioinformatics data. Her work features allocation models (with applications to tumor heterogeneity), roobust statistical modeling with nonparametric Bayesian methods, and clinical trial design. [More]

Lee's Publications
Juhee Lee's E-mail

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 Harry NOller

Structure and Function of the Ribosome

Harry Noller, MCD Biology

The Noller laboratory studies ribosome structure and function using a wide range of approaches, including X-ray crystallography, chemical probing methods, molecular genetics, comparative sequence analysis, fluorescence resonance energy transfer (FRET), including the use of single-molecule methods. The ultimate goal of these studies is to understand how the ribosome works at the molecular level: what are the moving parts of the machine, and how do they move in three dimensions to enable translation? [More]
Noller Publications Harry Noller's E-Mail

Prof Karen OttemannHow Bacterial Pathogens Sense and Respond to Host Environments

Karen Ottemann, Dept. of Microbiology and Environmental Toxicology

Professor Karen Ottemann's laboratory investigates how bacteria translate chemical and physical cues in their host environment into pathogenic outcomes. 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 outer membrane proteins 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. [More]

Ottemann Publications Karen Ottemann's Email

Prof Raquel PradoApplications of Bayesian Analysis to Biomedical Signal Processing

Raquel Prado, Dept. of Applied Mathematics and Statistics

Dr. Prado is a statistician whose research deals with sophisticated Bayesian time series methods to analyze complex and large-dimensional data that arise in various biomedical applications. She is currently working on developing statistical models and computational tools for the analysis of brain signals that are recorded in clinical and non-clinical neuroscience studies, such as electroencephalograms, fMRI data, and magnetoencephalograms. [More]

Prado Publications Raquel Prado '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 Nik SgourakisModelling the Structures of Protein Complexes from Sparse Experimental Data

Nik Sgourakis, Dept. of Chemistry and Biochemistry

Research in the Sgourakis lab focuses on elucidating the structures of important protein complexes involved in Immune recognition of viruses, bacterial secretion and neurodegeneration. Determining the structural basis of protein-protein interactions and self-assembly will help clarify fundamental biological mechanisms and facilitate the design of novel therapeutics. To achieve this, structure-based modelling at sufficient resolution is required. The Sgourakis lab is developing and implementing new tools based on Nuclear Magnetic Resonance spectroscopy and complementary sources of experimental data alongside advanced computational sampling methods. The integration of a range of experimental and computational approaches enables structural studies of proteins and their complexes at high resolution. [More]
Sgourakis Publications Nik Sgourakis' Email

Prof Susan StromeRegulation of Germ Cell Development in C. elegans

Professor Susan Strome, MCD Biology

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. Our lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency. We study germ cells in the model organism C. elegans using a wide variety of approaches, including genetics, imaging, molecular biology, biochemistry, and whole-genome microarray and sequencing technologies. Our current focus areas are transmission of chromatin states and control of gene expression in germ cells, and regulation of RNA metabolism by germline-specific cytoplasmic "P granules". [More]

Strome Publications Susan Strome's E-Mail

Prof Josh StuartComputational Functional Genomics, with Application to Integrative Analysis of Cancer

Josh Stuart, Dept. of Biomolecular Engineering

Josh Stuart's background is in machine-learning applied to high-throughput datasets and an expertise in developing computational models to integrate multiple sources of molecular biology information. His research focuses on discovering how gene networks program cellular responses and search engines to scan large collections of high-throughput results to predict how genes function. His labrecently developed the PARADIGM pathway-based models to integrate multiple sources of gene activity to predict alterations and clinical outcomes in tumor samples to decipher pathway alterations in many cancer cohorts. Stuart co-leads a Genome Data Analysis Center for the TCGA project, co-chairs the pan-cancer TCGA effort, is a member of the bioinformatics pathway’s group for the International Cancer Genome Consortium, and directs the computational pathway analysis for a Stand Up To Cancer Dream Team to identify therapies for resistant prostate cancer. [More]

Stuart Publications Josh Stuart's Email

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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