Members of the UC Santa Cruz Computational Biology Project

Last updated Oct 24 2001:

David Haussler

Professor David Haussler is involved in gene finding, protein homology, RNA secondary structure and other areas bioinformatics. His broader interests include statistcs, decision theory, neural networks, machine learning, and algorithms.

Richard Hughey

Associate Professor Richard Hughey studies hidden Markov modeling, parallel processing, and architectural support for computational biology.

Kevin Karplus

Associate Professor Kevin Karplus is fascinated with Hidden Markov Models and their applications to computational biology. His current work focuses on predicting the structure of proteins from their sequences, and on detecting remote homologies.

Betty Lazareva

Betty Lazereva is a postdoctoral researcher supported by SmithKline Beecham. She is developing new statistical methods to analyze EST data and to detect SNPs.

Albion Baucom

Albion Baucom is a Masters student working on protein structure prediction using neural networks and visualization of protein sequence alignments. Other interests include visualization of organic and biological molecules for use in the classroom as part of the C4 Project at the local community college Cabrillo.

Melissa Cline

Melissa Cline is a PhD candidate working on alignment quality prediction, estimation, and building a better alignment. In her spare time she can be found climbing the walls and/or drinking dark beer, though not necessarily at the same time.

Mark Diekhans

Mark Diekhans is a PhD student, working on methods for detecting remote protein homologies and on genefinding.

Terrence Furey

Terry Furey is a PhD student working on analysis of microarray gene expression data using support vector machines and other statistical techniques. He is also interested in other aspects of gene regulation such as the analysis of the promoter region.

David Kulp

David is a PhD candidate working on gene identification. He has developed "Genie" (postscript paper) -- a gene-finding system based on a generalized hidden Markov model and a modular collection of sensors. His research interests also include data compression, information theory, and algorithm development.

Marc Hansen

Mark Hansen is a Ph.D. student working with Doanna Weissgerber on the visualization and interactive editing of 2D and 3D protein alignments.

Birong Hu

Birong Hu received her Ph.D. in biology from UCLA and is now an M.S. candiadate in Computer Science, working on hidden Markov model methods for biosequence analysis.

Rachel Karchin

Rachel is a Ph.D. student working on support vector classification of proteins.

Doanna Meads

Doanna is a PhD student who is currently working on ProtAlign with Marc Hansen. This work focuses on the visualization and interactive editing of 2D and 3D protein alignments.

Eric Rice

Eric Rice is a Ph.D. candidate working on the Kestrel project.

Spencer Tu

Spencer Tu is a Ph.D. candidate working on generalized hidden Markov model architectures for protein remote homology and secondary structure prediction.

Stephen Winters-Hilt

Stephen Winters-Hilt is a Ph.D. candidate working on the use of discriminative statistical models for genefinding.

Seth Carbon

Seth Carbon is working on genefinding with Stephen Winters-Hilt.

David Dahle

David Dahle has been a key player in the development of the Kestrel chip.

Brian Martin

Brian Martin is working on genefinding and recognition of splice sites. He developed the EMmix suite of tools.

Christian Barrett

Christian is a PhD candidate whose work focuses on hidden Markov models and their application to remote homology detection and protein structure prediction. His thesis work is attempting to discern regularity in protein structures that can be exploited for a protein conformation score function.

Michael Brown

Michael Brown earned his PhD. in 1999. He is currently working at Hecht-Nilsson. His research involved modeling small subunit rRNA with stochastic context-free grammars. He also worked with SVM's in gene expression analysis.

Leslie Grate

Leslie Grate earned PhD in 1999. His research interests included a comprehensive study of yeast introns, work on potential SECIS elements in HIV1, alignment of large RNA molecules, and development of graphical tools for creating models for HMM and SCFG systems. He is currently a postdoctoral researcher with the Kestrel project.

Bill Grundy

Bill Grundy was a Sloan Postdoctoral Fellow at UCSC in 1998 and 1998. He is now an Assistant Professor in Computer Science at Columbia. He has developped the Meta-MEME and Family Pairwise Search servers.

Tommi Jaakkola

Tommi Jaakkola was a Sloan Postdoctoral Fellow at UCSC in 1997 and 1998. He is now an Assistant Professor in Computer Science at MIT.

Anders Krogh

Anders Krogh spent a year at UCSC as a postdoctoral researcher in 1992 and is now an Associate Professor in the Center for Biological Sequence Analysis at the Technical University of Denmark. He continues to be a close collaborator with the group and an excellent reason to visit Denmark.

David Lin

David Lin earned his M.S. in 1999. He is currently working at Incyte Pharmaceuticals, Inc. He previously worked at the Stanford Genome Center and later for Roche Biosciences. He research included working on EST analysis, gene expression data, and alternative splicing.

I. Saira Mian

Doctor Mian spent several years at UCSC as a postdoctoral researcher. She is now at LBNL, but continues to work with us on HMM modeling of proteins.

Yasubumi Sakakibara

Doctor Sakakibara spent a year at UCSC as a postdoctoral researcher, studying stochastic context-free grammars for RNA modeling.

Aleksandar Milosavljevic

Aleksandar Milosavljevic earned his Ph.D. in 1990 and has since been a principal Scientist at the Linus Pauling Institute and later Director of Bioinformatics at CuraGen.

Kimmen Sjolander

Kimmen Sjolander earned her PhD in 1996. Her work focused on hidden Markov models, Dirichlet mixture priors, inferring and incorporating subfamily relationships into statistical models of proteins, and on remote homolog detection. She is now a senior scientist at Molecular Applications Group.

David Konerding

David Konerding has a BA in Biochemistry from UCSC. He studies computational biology at UCSF. His thesis work covered gene finding using a generalized parsing method: Optimal Parse of DNA

Jesse Reklaw

Jesse got the Chancelor's Undergraduate Research Award for his work on RNA secondary structure, and is now a graduate student at Yale.

Christopher Tarnas

Christopher Tarnas got his B.S. in 1996 and now is a research scientist at Pangea.