(Last Update: 2021 October 7 15:41 PDT )
WARNING: this web page has not been maintained since about 2013. It is badly in need of updating.| Name | MS year | PhD Year | Thesis title | Adviser | Placement |
|---|---|---|---|---|---|
| Kim, Hyunsung John | 2011 | 2014 | Applications of High-Throughput Sequencing for Immunology and Clinical Diagnostics | Pourmand | Illumina |
| Timothy Sterne-Weiler | 2011 | 2013 | Integrated Analysis of cis-acting RNA Elements in Posttranscriptional Gene Regulation and Human Inhereited Disease | Sanford | postdoc, Blencowe lab, Univ. of Toronto |
| Goldstein, Theodore | 2011 | 2013 | Tools for Extracting Actionable Medical Knowledge from Genomic Big Data | Haussler | creating startup: MedBook Foundation |
| Uzilov, Andrew | 2010 | 2013 | Novel Applications of High-throughput RNA Sequencing: mapping RNA Structure and Discovering Circular RNAs | Lowe | Mt. Sinai Medical Center |
| Konneker, Thomas | 2013 | project | |||
| Sanborn, John "Zack" | 2010 | 2012 | Tumor vs. Matched-normal Sequencing: Analysis and Data Integration | Haussler | Five-Three Genomics |
| Benz, Stephen | 2010 | 2012 | Sample-specific Cancer Pathway Analysis Using PARADIGM | Haussler | CEO, Five3 Genomics |
| Castro, Paula | 2012 | project | Engineer, Survey Monkey | ||
| Heller, Phil | 2012 | project | Zehr | continuing Ph.D. | |
| Paull, Evan | 2012 | project | Stuart | continuing Ph.D. | |
| Sam, Daniel | 2012 | project | Stuart | ||
| Magasin, Jonathan | 2012 | project | Gerloff | continuing Ph.D. | |
| Botvinnik, Olga | 2012 | project | Pourmand | UCSD doctoral program | |
| Fyfe, Alastair | 2012 | Hydration of r(UGGGGU) Quadriplexes | Scott | UCSC postdoc | |
| Hahner, Nicholas | 2012 | project | |||
| Liaw, Edward | 2012 | project | Analyst, UC Riverside | ||
| Khwaja, Kaleem | 2011 | project | Lowe | Researcher, Children's Hospital, Oakland | |
| Lui, Lauren | 2011 | project | Lowe | continuing Ph.D. | |
| Ng, Samuel | 2011 | project | Stuart | continuing Ph.D. | |
| Onodera, Courtney | 2010 | 2011 | Characterization of Transcriptional Enhancers in the Human and Mouse Genome | Haussler | postdoc, Institute for Human Genetics, UCSF |
| Radenbaugh, Amie | 2011 | project | Haussler | continuing Ph.D. | |
| St. John, John | 2011 | project | Green | VP and Director of Bioinformatics at Cancer Therapeutics Innovation Group | |
| Gifford, Mia | 2011 | project | Haussler | Continuing Ph.D. | |
| Lee, Mei-Chong Wendy | 2011 | project | Pourmand |
Continuing Ph.D. |
|
| Long, Jeffrey | 2011 | project | Haussler | ||
| Ballinger, Tracy | 2011 | project | Haussler | continuing Ph.D | |
| Brumbaugh, Chris | 2011 | project |
MS Pourmand, Phd Karplus |
continuing Ph.D | |
| Carlin, Dan | 2010 | project | continuing Ph.D | ||
| Nguyen, Ngan | 2010 | project | Haussler | continuing Ph.D | |
| Earl, Dent | 2010 | project | Haussler | continuing Ph.D | |
| Velasquez, Elinor | 2010 | project | continuing Ph.D | ||
| Suh, Bernard | 2010 | project | Haussler | ||
| Raney, Brian | 2010 | Haussler | Bioinformatics Engineer, UCSC | ||
| Boyarsky, Sam | 2010 | project | Naturalist, Exploring New Horizons | ||
| Meyer, Lawrence | 2010 | project | |||
| Wong, Christopher | 2010 | project | |||
| Chan, Patricia | 2010 | Characterization of Archaeal Species through RNAse P and Transfer RNAs | Lowe | Chief Technology Officer, Maverix Biomics | |
| Atkins, Alex | 2010 | project | Hughey | Bioinformatics Engineer, Novartis | |
| Shackelford, George | 2010 | Residue-residue Contact Predictions Using Neural Networks and Selected Statistics | Karplus | ||
| Williams, Alex | 2010 | project | Stuart | Biostatistician The Gladstone Institutes (UCSF) |
|
| Thiltgen, Grant | 2010 | 2010 | Creating New Local Structure Alphabets for Protein Structure Prediction | Karplus | Post Doc, National Institute for Medical Research, London |
| Baertsch, Robert | 2010 | Improving Gene Annotation and Understanding of Mammalian Evolution by Identifying Retrocopies of mRNA Transcripts | Haussler | VP of Engineering, SkyTran | |
| Draper, Jenny | 2010 | 2010 | Discovery of CZB, a Novel Zinc-binding Domain in Bacterial Chemoreceptors, and the Genome Sequence of Helicobacter pylori strain SS1 | Ottemann | postdoc, Massey University, Palmerston North, New Zealand |
| Dougherty, Greg | 2010 | project | Stuart | Bioinformatics Programmer, Mayo Clinic, Minnesota | |
| Vasili, Shyamini | 2010 | project: Analysis of Alternative Splicing Events Across Human and Mouse |
Stuart | bioinformatics programmer, Zymo Research | |
| Lui, Lauren | 2010 | project | Lowe | continuing Ph.D | |
| Bernick, David | 2010 | Sequential Discovery—from Small RNA to Genomes, an Investigation of the Hyperthermophilic Genus Pyrobaculum | Lowe | Project scientist, UCSC | |
| Lowe, Craig | 2010 | The Contribution of Mobile Elements to Gene Regulatory Innovations on the Human Lineage | Haussler | Post Doc, Stanford Medical School | |
| Katzman, Sol | 2010 | Evolutionary Forces at Work in the Human Genome | Haussler | CBSE | |
| Koeva, Martina | 2009 | Stemness Revisited: a Meta Analysis of Stem Cell Signatures Using High-throughput Data Integration |
Stuart | Post Doc, Whitehead Institute | |
| Bellows, Miriam | 2009 | Analysis of Additional Cysteines in HIV-1 Subtype E Envelope Glycoprotein gp 120 V4 Domain | Berman | ||
| Kanabar, Pinal | 2009 | Joint Intervention Networks: Multi-Perturbation Probabilistic Epstasis Analysis for Predicting Pathways | Stuart | Waksman Genomics Core Facility, Rutgers | |
| Vaske, Charles | 2009 | Prediction and Expansion of Biological Pathways From Perturbation Effects | Stuart | Five-Three Genomics | |
| Samayoa, Josue | 2009 | A Bioinformatic Analysis of Simple Repeats and Small Proteins in Prokaryotic Genome | Karplus | Post Doc, Johns Hopkins | |
| Weirauch, Matthew | 2009 | Data Integration Methods for Systems-Level Investigation of Gene Functional Association Networks | Stuart | Assistant Professor, Department of Pediatrics,Univ. Cincinnati |
|
| Khatib, Firas | 2008 | Topological Filters for Use with Protein Structure Prediction | Karplus |
Assistant Professor,
Department of Computer and Information Science,
University of Massachusetts Dartmouth
|
|
| Dreszer, Timothy | 2006 | Biased Clustered Substitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution | Haussler | Software Developer, CBSE | |
| Powell, Corey | 2006 | Bioinformatics Scientist,Buck Institute for Age Research |
|||
| Pohl, Andrew | 2006 | Three Topics in Bioinfomatics | Lowe | Software Developer, CBSE | |
| Thomas, Daryl | 2006 | Using Variation and Constraint to Understand Functional Elements in the Human Genome | Haussler | Associate Director, Life Technologies | |
| Wu, Chiung-Yuan | 2004 | 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. Some students in other programs still do bioinformatics theses. This is a partial list, reconstructed from faulty memories.
| Name | Year | Degree | Dept | Thesis title | Adviser | Placement |
|---|---|---|---|---|---|---|
| Krishna Roskin | 2011 | Ph. D. | CMPS | Past, Present, and Future of Sequence Alignment | Haussler | Postdoc, Scott Boyd, Stanford |
| Yontao Lu | 2007 | Ph.D. | CMPS | Identification and analysis of pseudogenes in the human and mouse genomes | Haussler | Bioinformatics Scientist, Affymetrix |
| Daryl Thomas |
2003 |
M.S. | CMPS | Sequence variation in the UCSC genome browser |
Haussler | Associate Director, Life Technologies |
| Adam Siepel | 2005 | Ph.D. | CMPS | Comparative mammalian genomics : models of evolution and detection of functional elements | Haussler | Associate Professor, Biological Statistics & Computational Biology, Cornell University, Ithaca, NY |
| Chuck Sugnet | 2005 | Ph.D. | CMPS | Discovery and detection of alternative splicing | Haussler | Ion Torrent |
| Rachel Karchin |
2003 (MS 2000, Haussler) |
Ph.D. | CMPE | Evaluating local structure alphabets for protein structure predicition | Karplus | Associate Professor, Biomedical Engineering, Institute of Computational Medicine, Johns Hopkins University, Baltimore, MD |
| Eva Hui Wang | 2003 | Ph.D. | CMPS | Splice variant chip design and variant-based expression analysis | Haussler | Senior Director, Information Sciences and Biostatistics, XDx (previously at Affymetrix) |
| 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 |
| Matt Xia | 2002 | M.S. | CMPS | Haussler | Software Engineer, Life Technologies | |
| Wei Wu | 2002 | M.S. | CMPS | Haussler |
Associate Research Professor,Lane Center for Computational Biology, Carnegie-Mellon |
|
| Rachel Bevan | 2002 | M.S. | CMPS | Haussler | ? | |
| Trevor Bruen | 2002 | M.S. | CMPS | Haussler | Assistant Professor, St. Francis Xavier College, Canada | |
| 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 |
| Fan Shen | 2001 | M.S. | CMPE | Haussler | Bioinformatics scientist, Affymetrix | |
| 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, MCD Biology, UC Santa Cruz, CA |
| Albion Baucom | 2000 | M.S. | CMPS | Protein structure and function prediction: tools and techniques | Haussler | Systems Architect, Genentech |
| 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 | Software Engineer, Qualitau |
| 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 | Using phylogenetic Markov trees to detect conserved structure in RNA multiple alignments | Haussler | Ph.D. sudent, Cornell |
| Rebecca Underwood | 1994 | M.S. | CMPS | Stochastic context-free grammars for modeling three spliceosomal small nuclear ribonucleic acids | 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 |
If anyone has information to update the placement information for either alumni table, please send it to Kevin Karplus karplus@soe.ucsc.edu