Alumni of UCSC's Bioinformatics Graduate Program
| Name | Year | Degree | Thesis title | Adviser | Placement |
|---|---|---|---|---|---|
| Bellows, Miriam | 2009 | M.S. | Analysis of Additional Cystenines in HIV-1 Subtype E Envelope Glycoprotein gp 120 V4 Domain | Berman | |
| Kanabar, Pinal | 2009 | M.S. | Joint Intervention Networks: Multi-Perturbation Probabilistic Epstasis Analysis for Predicting Pathways | Stuart | continuing Ph.D student |
| Vaske, Charles | 2009 | Ph.D | Prediction and Expansion of Biological Pathways From Perturbation Effects | Stuart | Post Doc, Princeton |
| Samayoa, Josue | 2009 | Ph.D | A Bioinformatic Analysis of Simple Repeats and Small Proteins in Prokaryotic Genome | Karplus | Post Doc, Johns Hopkins |
| Weirauch, Matthew | 2009 | Ph.D | Data Integration Methods for Systems-Level Investigation of Gene Functional Association Networks | Stuart | Post Doc, U Toronto |
| Khatib, Firas | 2008 | Ph.D | Topological Filters for Use with Protein Structure Prediction | Karplus | Post Doc, U Washington |
| Dreszer, Timothy | 2006 | M.S. | Biased Clustered Substitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution | Haussler | Software Developer, CBSE |
| Pohl, Andrew | 2006 | M.S. | Three Topics in Bioinfomatics | Lowe | Software Developer, CBSE |
| Thomas, Daryl | 2006 | Ph.D | Using Variation and Constraint to Understand Functional Elements in the Human Genome | Haussler | Scientist, Navigenics |
| Wu, Chiung-Yuan | 2004 | M.S. | Establishing Computational Approaches in Genome-Wide Partnership Predictions of Synaptic PDZ Proteins and Their Targets | Rohl | Medical College of Georgia |
Before we had a graduate program in bioinformatics, we had several grad students in bioinformatics graduating with other degrees. This is a partial list, reconstructed from faulty memories.
| Name | Year | Degree | Dept | Thesis title | Adviser | Placement |
|---|---|---|---|---|---|---|
| Yontao Lu | 2007 | Ph.D. | CMPS | Identification and analysis of pseudogenes in the human and mouse genomes | Haussler | |
| Daryl Thomas |
2006 (M.S. 2003) |
Ph.D. | CMPS | Using variation and constraint to understand functional elements in the human genome | Haussler | Research Scientist, Navigenics, Inc., Redwood Shores, CA |
| Adam Siepel | 2005 | Ph.D. | CMPS | Comparative mammalian genomics : models of evolution and detection of functional elements | Haussler | Assistant Professor, Biological Statistics & Computational Biology, Cornell University, Ithaca, NY |
| Chuck Sugnet | 2005 | Ph.D. | CMPS | Discovery and detection of alternative splicing | Haussler | Research Scientist, Affymetrix, Inc. |
| Rachel Karchin |
2003 (MS 2000, Haussler) |
Ph.D. | CMPE | Evaluating local structure alphabets for protein structure predicition | Karplus | Assistant Professor, Biomedical Engineering, Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD |
| Hui Wang | 2003 | Ph.D. | CMPS | Splice variant chip design and variant-based expression analysis | Haussler | Research Scientist, Affymetrix, Inc. |
| David Kulp | 2003 | Ph.D. | CMPE | Protein-coding gene structure prediction using generalized hidden Markov models | Haussler | Assistant Professor, Computer Science, University of Massachusetts, Amherst |
| Stephen Winters-Hilt | 2003 | Ph.D. | CMPS | Machine learning methods for channel current cheminformatics, biophysical analysis, and bioinformatics | Haussler | Associate Professor, Computer Science, University of New Orleans, LA |
| Terry Furey | 2002 | Ph.D. | CMPS | Analysis and annotation of the draft human genome sequence | Haussler | Assistant Research Professor, Biostatistics & Bioinformatics, Duke University, Durham, NC |
| Christian Barrett | 2001 | Ph.D. | CMPS | Investigation of Non-pairwise Protein Structure Score Functions Using Sets of Decoy Structures | Karplus | Bioinformatics Research Scientist, UC San Diego |
| Matt Xia | 2002 | M.S. | CMPS? | Haussler | ||
| Wei Wu | 2002 | M.S. | CMPS? | Haussler | ||
| Rachel Bevan | 2002 | M.S. | CMPS? | Haussler | ||
| Trevor Bruen | 2002 | M.S. | CMPS? | Haussler | ||
| Fan Shen | 2001 | M.S. | CMPS? | Haussler | ||
| Sugato Basu | 2000 | M.S. | CMPE | Data Structures for a Mini-Threading Algorithm for Protein Structure Prediction |
Karplus | senior research scientist, Google |
| Birong Hu | 2000 | M.S. | CMPS? | Evaluation of SAM-T99 as a Multiple Sequence Alignment Program |
Karplus | |
| Melissa Cline | 2000 | Ph.D. | CMPS | Protein Sequence Alignment Reliability: Prediction and Measurement | Haussler+Karplus | Project Scientist, Molecular, Cell, & Developmental Biology, UC Santa Cruz, CA |
| Albion Baucom | 2000 | M.S. | CMPS? | Haussler | ||
| Michael Brown | 1999 | Ph.D. | CMPS | RNA Modeling Using Stochastic Context-Free Grammars | Haussler | Research Scientist, HNC Software LLC, San Diego, CA |
| Leslie Grate | 1999 | Ph.D. | CMPE | Computer Analysis of RNA | Haussler | |
| David Lin | 1999 | M.S. | CMPS? | Deriving Reliable Intron and Splice Site Evidence From ESTs to Improve Gene-finding |
Haussler | Senior Director, Informatics and Automation at Complete Genomics |
| Kimmen Sjölander | 1997 | Ph.D. | CMPS |
A Bayesian-information theoretic method for evolutionary inference in proteins |
Haussler+Karplus | Associate Professor, Bioengineering, UC Berkeley, Berkeley CA |
| Brad Gulko | 1995 | M.S. | CMPS? | Haussler | ||
| R. Underwood | 1994 | M.S. | CMPS? | Haussler | ||
| Yoav Freund | 1993 | Ph.D. | CMPS | Data filtering and distribution modeling algorithms for machine learning | Haussler | Professor, Computer Science and Engineering, UC San Diego |
| Aleksandar Milosavljević | 1990 | Ph.D. | CMPS | Categorization of macromolecular sequences by minimal length encoding | Haussler | Associate Professor, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX |
| Jeanne Rich | 1989 | M.S. | CMPS? | Haussler | ||
| Jean Cailton | 1988 | M.S. | CMPS? | Haussler |