Biomolecular Engineering

2015-16 General Catalog

Baskin School of Engineering
335 Baskin Engineering Building
(831) 459-2158
http://www.soe.ucsc.edu

Program Statement | Course Descriptions


Faculty and Professional Interests

Professor

Mark Akeson
Development of nanopore sensors for single molecule identification, epigenetics, bioethics

Phillip Berman
Baskin Distinguished Professor
Drug development, vaccines, AIDS, monoclonal antibody therapeutics, immunology, molecular cell/biology, recombinant protein production (commercial scale)

Camilla Forsberg
Hematopoietic stem cells. transcriptional regulation, chromatin, blood cell development, cell surface receptors, genomics

David Haussler
Bioinformatics, genomics, computational genomic data analysis, molecular evolution and comparative genomics, genomic and clinical data sharing and standards, cancer genomics, neurodevelopment, stem cell research, immunogenomics, information theory, pattern recognition, machine learning, artificial intelligence, information theory, theoretical computer science

Richard Hughey (joint with Computer Engineering)
Bioinformatics, hidden Markov models, computer architecture, parallel computation

Kevin Karplus
Genome assembly from next-generation sequence data (Formerly protein structure prediction), signal processing and statistics for nanopore signals

Todd Lowe
Experimental and computational genomics, non-coding RNA gene finders, and high-throughput small RNA sequencing small RNA roles in cancer, evolution of RNA-based gene regulation

Nader Pourmand
Bioelectronics, biosensors, chemosensors, nanotechnology, single-cell characterization, sequencing, genotyping, pathogen detection, DNA fingerprinting

Joshua Stuart
Jack Baskin Endowed Chair of Biomolecular Engineering

Computational functional genomics, comparative analysis of gene regulation, cross-species inference of gene networks, probabilistic graphical models

Assistant Professor

Angela Brooks
Genomics, functional genomics, cancer genomics, RNA processing, gene regulation, gene variant function

Rebecca M. Dubois
Protein engineering; structural virology and biomedical applications

Richard “Ed” Green
Genomics, computational molecular biology, genome assembly, human evolutionary genetics, ancient DNA, high-throughput sequencing, mRNA-processing and alternative splicing

Christopher Vollmers
Developing DNA sequencing tools to analyze B cells on a population and single cell level

Research Professor

David W. Deamer (UC Davis Emeritus)
Membrane biophysics, nanopore analysis, DNA sequencing, biomolecular self-assembly

Adjunct Professor

Robert Coffman
Regulation of innate and adaptive immunity, systems biology of human immune responses, development of novel vaccines and oligonucleotide-based drugs

Jonathan Trent
Organic aggregates, marine snow, microbial physiology, microenvironments, robust proteins, genetic engineering for nanotechnology

Zemin Zhang
Cancer genomics, bioinformatics, anti-cancer target and biomarker discovery, tumor immunology, drug-genome interaction

Assistant Adjunct Professor and Lecturer

David Bernick
Biofuel production using reengineered extremophiles, especially halophiles; next-generation sequencing applications including genome assembly, metagenome assembly and RNA transcriptomics; extremozymes - viral/microbial gene discovery - RNA/RNA packing motors and porins; single-molecule sequencing of highly structured/modified tRNA; novel halo virus discovery

Lecturer

Wendy Rothwell
Biotechnology, molecular genetics

♦ ♦ ♦

Manuel Ares, Jr. (Molecular, Cell, and Developmental Biology)
RNA processing, structure and function of RNA

Hinrich Boeger (Molecular, Cell, and Developmental Biology)
Chromatin structure and gene regulation

Manel Camps (Microbiology and Environmental Toxicology)
Molecular mechanisms of reactive DNA methylation toxicity

William Dunbar (Computer Engineering)
Theory and application of feedback control, single-molecule biophysics, nanopore sensors, dynamics and control of biomolecules

Lars Fehren-Schmitz (Anthropology)
Palaeogenetics/anthropological genetics, human evolutionary ecology, evolutionary demography, gene-culture coevolution, migration theories, population history of the Americas, archaeology of South America

A. Russell Flegal (Microbiology and Environmental Toxicology)
Anthropogenic perturbations of biogeochemical cycles, applications of isotopic tracers in anthropology and archaeology

Robert S. Lokey (Chemistry and Biochemistry)
Organic chemistry, combinatorial synthesis, biotechnology, molecular cell biology

Glenn L. Millhauser (Chemistry and Biochemistry)
Electron spin resonance; nuclear magnetic resonance, melanocortin receptor signaling, agouti proteins, prions, peptide synthesis

Karen Ottemann (Microbiology and Environmental Toxicology)
How bacterial pathogens are able to chronically colonize mammalian hosts and cause disease outcomes such as inflammation and cancer

Beth Shapiro (Ecology and Evolutionary Biology)
Evolutionary and molecular ecology, ancient DNA, genomics, pathogen evolution

John W. Tamkun (Molecular, Cell, and Developmental Biology)
Transcriptional regulation, molecular genetics of Drosophila development, regulation of gene expression

Hongyun Wang (Applied Mathematics and Statistics)
Single molecule studies and biophysics, statistical physics, stochastic processes and stochastic differential equations, classical analysis, numerical analysis

Manfred K. Warmuth (Computer Science)
Online learning, machine learning, statistical decision theory, game theory, analysis of algorithms

W. Todd Wipke, Emeritus (Chemistry and Biochemistry)

Fitnat H. Yildiz (Microbiology and Environmental Toxicology)
Understanding processes controlling transmission of bacterial pathogens

Alan M. Zahler (Molecular, Cell, and Developmental Biology)
Alternative pre-mRNA splicing and small RNA function

Revised: 09/01/15