Lab Alumni

Postdocs

2012 to 2017     Karen Hayden-Miga, effective 9/1/17, Assistant Research Scientist, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA

2011 to 2014     Maximilian Haeussler, European Molecular Biology Organization (EMBO) Fellow, currently Assistant Research Scientist- Browser, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA

2011 to 2014     Adam Ewing, currently research fellow, the Mater Medical Research Institute and honorary fellow, the University of Queensland

2009 to 2014     Frank Jacobs, Assistant Professor, Faculty of Science, University of Amsterdam, The Netherlands

2011 to 2013     Glenn Hickey, currently Research Consultant, Arenaria Inc., Canada

2010 to 2013     Daniel Zerbino, currently Team leader, Genome Analysis, EMBL-EBI, Cambridge, UK

2010 to 2011     Charlie Vaske, currently Research Associate, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA and Chief Scientific Officer, Nantomics (formerly Five3 Genomics), Santa Cruz, CA

2007 to 2012     Benedict Paten, currently Assistant Professor, University of California, Santa Cruz, CA

2006 to 2011     Jing Zhu, currently Assistant Research Scientist-Cancer Genomics, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA

2006 to 2010     Jason Underwood, currently Principal Scientist, Pacific Biosciences, Menlo Park, CA

2007 to 2009     Jian Ma, currently Associate Professor, Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA

2006 to 2009     Ting Wang, Helen Hay Whitney Fellow, currently Associate Professor, Genetics and Computer Science and Engineering, School of Medicine, Washington University, St. Louis, MO

2006 to 2007     Mario Stanke, currently Professor, Bioinformatics, The Institute for Mathematics and Computer Science, University of Greifswald, Greifswald, Germany

2005 to 2008     Andrew Kern, currently Associate Professor, Department of Genetics, Rutgers University, New Brunswick, NJ

2005 to 2006     Chen-Hsiang Yeang, currently Associate Research Fellow, the Institute of Statistical Science, Academia Sinica, Taipei, Taiwan

2004 to 2007     Jakob Skou Pedersen, currently Professor, Bioinformatics, Department of Molecular Medicine, University of Aarhus, Denmark

2003 to 2007     Gill Bejerano, currently Associate Professor of Developmental Biology, Associate Professor of Computer Science, Associate Professor of Pediatrics (Medical Genetics), Stanford University, Palo Alto, CA

2003 to 2005     Katherine Pollard,(Co-supervised by Todd Lowe),  currently Lead Scientist and Senior Investigator, Gladstone Institute, Professor, Division of Biostatistics, University of California, San Francisco School of Medicine, CA

2003 to 2004     Brian Lucena, currently Assistant Professor, Mathematics, American University, Cairo

2002 to 2004     Terry Furey, currently Assistant Professor, Genetics, University of North Carolina

2002 to 2003     Mathieu Blanchette, currently Assistant Professor, Computer Science, McGill University, Montreal, Canada

2000 to 2001     Rune Lyngsoe, currently Research Developer, Undisclosed Company, Oxford, UK, Oxford University, UK

1998 to 1999     Bill Noble, currently Professor, Computer Sciences and Engineering, University of Washington, Seattle, WA

1998                Tommi Jaakkola, currently Professor, Electrical Engineering & Computer Science, MIT

1996 to 1998    Betty Lazareva, currently an Independent Biotechnology Professional

1992                Anders Krogh, Postdoctoral Scholar, currently Professor, Computational and RNA Biology, University of Copenhagen, Denmark

Ph.D. Recipients

2013 to 2017     Adam Novak, “Comparing methods for aligning multiple genomes and developing computer algorithms to map changes in ambiguous areas of the genome,” currently Senior Software Engineer, Computational Genomics, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA

2009 to 2015     Amie Radenbaugh, “Identification of DNA and RNA mutations in cancer using High-Throughput Sequencing Data,” currently on Bioinformatics Scientist, NantOmics, Santa Cruz, CA

2008 to 2015     Tracy Ballinger, “Characterizing insertions in cancer genomes to look for evidence of retrotransposition in tumors,” currently Bioinformatician Research Fellow, Colin Semple’s lab, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland

2010 to 2014     Mia Gifford, “Emergence of drug resistance in cancer” currently on sabbatical

2008 to 2014     Dent Earl, “Evaluations and Application of the three A’s of Genomics: Assembly, Alignment, Annotation,” currently Software Engineer, Google, Mountain View, CA

2008 to 2014     Ngan Nguyen, “Immunogenomics, Database of the Genome 10K Project,” currently Bioinformatics Scientist, Atreca, San Carlos, CA

2006 to 2014     David Greenberg, “An evolutionary arms race between zinc finger proteins and retrotransposons in ape genomes,” currently Scientist and Process Manager, TwoPore Guys, Santa Cruz, CA

2008 to 2013     Ted Goldstein, “Tools for Extracting Actionable Medical Knowledge from Genomic Big Data,” currently Scientific Program Director, Institute of Computational Health Sciences, University of California, San Francisco; Adjunct affiliation, University of California, Santa Cruz, CA

2006 to 2013     Chris Szeto, “Discovery of clinically relevant molecular signatures in cancer,” currently Bioinformatics Scientist, NantOmics, Santa Cruz, CA (formally Five3 Genomics)

2007 to 2012     Stephen Benz, “Sample-specific cancer pathway analysis using PARADIGM,” currently Chief Executive Officer, NantOmics, Santa Cruz, CA (formally Five3 Genomics)

2005 to 2012     Zack Sanborn “Tumor vs. Matched-Normal Sequencing Analysis and Data Integration,” currently Chief Technology Officer, NantOmics, Santa Cruz, CA (formally Five3 Genomics)

2004 to 2011     Courtney Onodera, UCSC Predoctoral CIRM Scholar, “Characterization of Transcriptional Enhancers in the Human and Mouse Genomes,” currently Scientific Programmer Analyst, Pathology UCSF School of Medicine, University of California, San Francisco, CA

2004 to 2010     Craig Lowe, “The contribution of mobile elements to regulatory innovations on the human lineage,” currently Postdoctoral Scholar, David Kingsley lab, Howard Hughes Medical Institute, Stanford University, Palo Alto, CA. Effective 2018: Assistant Professor, Department of Molecular Genetics and Microbiology, Duke University Medical Center

2004 to 2010     Solomon Katzman, “Evolutionary Forces at Work in the Human Genome,” currently High-Throughput Sequencing Analyst, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA

2003 to 2009     Brian Raney, “Reconstructing Ancestral Genomes: A case study of small inversions on the human lineage since the eutherian explosion,” currently Software Developer, Genome Browser Project, UC Santa Cruz Genomics Institute, University of California, Santa Cruz

2002 to 2010     Krishna Roskin, “Past, present, and future of sequence alignment,” currently Associate Professor, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center

2002 to 2010     Robert Baertsch, “Burst of exapted human retrogenes not found in mouse and improved methods for identifying retrocopies,” currently VP, Engineering, SkyTran, NASA Ames, Moffett Field, CA

2002 to 2005     Adam Siepel, “Comparative mammalian genomics : models of evolution and detection of functional elements,” Professor and Director of the $50M Simons Center, Cold Spring Harbor Laboratory

2001 to 2007     Yontao Lu, “Identification and analysis of psuedogenes in the human and mouse genomes”, Director of Bioinformatics, Accuragen, Fremont, CA

2001 to 2006     Daryl Thomas, “Using variation and constraint to understand functional elements in the human genome,” currently Associate Director, Life Technologies, Carlsbad, CA

1999 to 2005     Charles Sugnet, “Discovery and detection of alternative splicing,” currently Sr Bioinformatics Engineer, Ion Torrent, South San Francisco, CA

1999 to 2003     Hui Wang, “Splice variant chip design and variant-based expression analysis,” currently Bioinformatics/Biostatistics Head, HTG Molecular Diagnostics, Tucson, AZ

1998 to 2002     Terry Furey, ARCS Scholar, “Analysis and annotation of the draft human genome sequence,” currently Assistant Professor, Genetics, University of North Carolina, Chapel Hill, NC

1997 to 2003      Stephen Winters-Hilt, “Machine learning methods for channel current cheminformatics, biophysical analysis, and bioinformatics,” currently Visiting Associate Professor, Computer Science and Biology, Connecticut College

1995 to 2000      Melissa Cline, “Protein sequence alignment reliability: prediction and measurement,” currently Project Scientist, Molecular, Cell, & Developmental Biology, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA

1994 to 2003      David Kulp, “Protein-coding gene structure prediction using generalized hidden Markov models,” co-founder of Neomorphic, which was acquired by Affymetrix; currently Assistant Professor, Computer Science, University of Massachusetts, Amherst

1999                 Michael Brown, “RNA modeling using stochastic context-free grammars,” currently a research scientist in the biotech industry

1997                 Kimmen Sjölander, “A Bayesian-information theoretic method for evolutionary inference in proteins,” currently Associate Professor, Bioengineering, University of California, Berkeley, Berkeley, CA. Won a U.S. Presidential Early Career Award in Science and Engineering

1993                 Yoav Freund, “Data filtering and distribution modeling algorithms for machine learning,” currently Professor, Computer Science &Engineering, University of California, San Diego, La Jolla, CA, won Gödel Prize for 2003

1992                 Phil Long, “Towards a more comprehensive theory of learning in computers,” currently Research Scientist, Google, Mountain View, CA

1990                 Giulia Pagallo, “Adaptive decision tree algorithms for learning from examples,” currently Software Manager, Apple Computer, Cupertino, CA

1990                 Alexander Milosavljevic, “Categorization of macromolecular sequences by minimal length encoding,” currently Associate Professor, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX

1989                 Nick Littlestone, “Mistake bounds and logarithmic linear-threshold learning algorithms,” currently Computer Programmer, Patternlanguage.com, Berkeley, CA

1985                 Janet Blumer, “Algorithms for the directed acyclic word graph and related structures”

M.S. Recipients

2012              Jeffrey Long

2011              Chris Wilks, “Exploiting MAINE/FAIRE Experimental Data for Gene-Finding in Plasmodium falciparum Using Random Forests,” currently PhD student, Johns Hopkins University: Home, Baltimore, Maryland

2006              Timothy Dreszer, “Biased Clustered Substitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution”

2002              Matt Xia, “Study of molecular evolution by comparison of vertebrate genomes,” currently Software Engineer, Life Technologies

2002              Wei Wu (project option), currently Associate Research Professor, Lane Center for Computational Biology, Carnegie-Mellon

2002              Rachel Bevan (project option)

2002              Trevor Bruen (project option), currently Assistant Professor, St. Francis Xavier College, Canada

2001              Fan Shen (project option), currently Bioinformatics Scientist, Affymetrix, Santa Clara, CA

2000              Albion Baucom, “Protein structure and function prediction: tools and techniques,” currently Systems Architect, Genentech, San Francisco, CA

2000              Rachel Karchin, “Classifying G-protein coupled receptors with support vector machines,” Associate Professor, Department of Biomedical Engineering, John Hopkins University, Baltimore, MD

1999              David Lin, “Deriving reliable intron and splice site evidence from ESTs to improve gene finding,” currently Senior Director, Informatics and Automation, Complete Genomics, Mountain View, CA

1995              Brad Gulko, “Using phylogenetic Markov trees to detect conserved structure in RNA multiple alignments,” currently Doctoral Student, Computer Science Department, Cornell University, Ithaca, NY

1994              Rebecca Underwood, “Stochastic context-free grammars for modeling three spliceosomal small nuclear ribonucleic acids”

1994              Anne Urban, “Hidden Markov models in characterization, discrimination and alignment of the Helicase family of proteins”

1989              Jeanne Rich, “Training an animated arm to reach for objects in space using a neural network”

1988              Jean Cailton, “Constrained backpropogation: an algorithm for learning in artificial neural networks”

Senior Thesis & Undergraduate Awards

2002              Krishna Roskin, Huffman Prize, currently Post-Doctoral Fellow, Scott Boyd lab, Pathology, Stanford University, Palo Alto, CA

1995              David Konerding, currently Director of Genomics, Google, Mountain View, CA

1995              Jesse Reklaw (received the Chancellor’s award for undergraduate research)