Graduates from Bioinformatics Grad program
Name MS year PhD
Thesis title Adviser Placement
Lui, Lauren  2010 2015 Evolution of Structure and Function of Kink-turn-containing RNAs in the Domain Archaea Lowe  Postdoc, Arkin Lab, LANL
Ballinger, Tracy  2011 2015 Analysis of Genomic Rearrangements in Cancer from High-throughput Sequencing Data Haussler  Edinburgh
Woehrmann, Marcos   2015 Predicting the Mode of Action of Bioactive Compounds via High Throughput Screening and Computational Algorithms Stuart  
Heller, Philip 2012 2014 Bioinformatic Investigations in Marine Microbial Ecology Zehr Asst. Professor, CS, San Jose State Univ.
Lee, Mei-Chong Wendy 2011 2014 Single-cell Analyses of Transcriptional Heterogeneity
during Drug ToleranceTransition in Cancer Cells by
RNA Sequencing
Pourmand Maverix Biomics
Shelansky, Robert 2014        
Bivol, Adrian 2014     Stuart continuing to PhD
Oliver, Dorothy 2013    Evaluating Error Frequencies from Sequencing Short Tandem Repeats Akeson Affymetrix
Grifford, Mia  2011 2014 Using High-throughput Sequencing to Study the Progression of Cancer Haussler  
Earl, Dent  2010 2014 Evaluation and Application of the Three A's of Genomics: Assembly, Alignment, Annotation Haussler  Google
Nguyen, Ngan 2010 2014 Addressing the Omics Data Explosion: a Comprehensive Reference Genome Representation and the Democratization of Comparative Genomics and Immunogenomics Haussler  
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
Nguyen, Andrew   2013 Molecular Mechanisms of Hematopoietic Stem Cell Migration and Engraftment  Forsberg  
Uzilov, Andrew 2010 2013 Novel Applications of High-throughput RNA Sequencing: mapping RNA Structure and Discovering Circular RNAs Lowe Mt. Sinai Medical Center
Newton, Yulia 2013   project Stuart continuing PhD
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
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   Driver Group, LLC
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
Wilks, Chris



  Exploiting MAINE/FAIRE Experimental Data for Gene-Finding in
Plasmodium falciparum Using Random Forests
Gerloff Cancer Genomics Hub
Radenbaugh, Amie 2011    project Haussler continuing Ph.D.
St. John, John 2011    project Green VP and Director of Bioinformatics at Cancer Therapeutics Innovation Group
Long, Jeffrey 2011    project Haussler  
Brumbaugh, Chris 2011   project

 MS Pourmand,

Phd Karplus

continuing Ph.D
Carlin, Dan 2010   project   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   The Iron Yard
Durham, NC
Meyer, Lawrence 2010   project   Google
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 ThermoFisher Scientific
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
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.

Bioinformatics Graduates from other programs
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


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