Lab Alumni


2016 to 2019     Jason Fernandes Effective July 2019, Assistant Project Scientist, UC Santa Cruz Haussler-Salama Lab, University of California, Santa Cruz, CA
2013 to 2017     Olena Morozova Assistant Professor of MCD Biology, University of California, Santa Cruz, CA and Colligan Presidential Chair in Pediatric Genomics
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 Assistant Research Scientist-Genome 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 
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 VP Bioinformatics, Claret Bioscience, 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 Inaugural Sanford and Karen Loewentheil Distinguished Professor of Medicine, 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 Associate Professor, University of Oregon
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 Professor at UCSF and the Director of the Gladstone Institute of Data Science and Biotechnology
2003 to 2004     Brian Lucena Currently Assistant Professor, Mathematics, American University, Cairo and Consulting Data Scientist, Agentero and Principal, Lucena Consulting
2002 to 2004     Terry Furey Currently Assistant Professor, Genetics, University of North Carolina
2002 to 2003     Mathieu Blanchette Associate 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 Sr. Bioinformatics Scientist, Bina Technologies, Part of Roche Sequencing Solutions, Redwood City, CA
1992                    Anders Krogh Currently Professor, Computational and RNA Biology, University of Copenhagen, Denmark


Ph.D. Recipients

2015 to 2019      John Vivian Bioinformatics Scientist, Atreca Inc., Redwood City, CA
2012 to 2019      Joel Armstrong Software Engineer, Google, Sunnyvale, CA
2014 to 2018     Arjun Rao Research Specialist, Postdoc with Max Krummel in UCSF
2014 to 2017     Ian Fiddes Comparative Annotation Toolkit (CAT) – simultaneous annotation of related genomes, currently Senior Manager of Content and Curation, Inscripta Inc., Pleasanton, CA
2010 to 2017     Andrew Field Postdoctoral fellow, Karen Adelman’s Lab, Harvard Medical School, California Institute for Regenerative Medicine (CIRM) Fellow, Regulation of cortical neuron development from embryonic stem cells, focusing on the role ncRNAs play in this process
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 Associate Director, Bioinformatics, Atreca, San Carlos, CA
2006 to 2014     David Greenberg “An evolutionary arms race between zinc finger proteins and retrotransposons in ape genomes,” Inside Sales and Technical Support Specialist, Diagenode, San Francisco Bay Area, CA
2008 to 2013     Ted Goldstein “Tools for Extracting Actionable Medical Knowledge from Genomic Big Data,” currently Chief Artificial Intelligence Officer, Anthem Inc., San Francisco Bay Area, CA
2006 to 2013     Chris Szeto “Discovery of clinically relevant molecular signatures in cancer,” currently Director of Machine Learning, ImmunityBio, Culver City, CA
2007 to 2012     Stephen Benz “Sample-specific cancer pathway analysis using PARADIGM,” currently President, ImmunityBio, Culver City, CA
2005 to 2012     Zack Sanborn “Tumor vs. Matched-Normal Sequencing Analysis and Data Integration,” currently Chief Technology Officer, NantOmics, Santa Cruz, CA (formerly 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,” Director of Product Management, Personalis, Menlo Park, CA
1999 to 2005     Charles Sugnet “Discovery and detection of alternative splicing,” currently Staff Software Engineer, Google, Mountain View, CA
1999 to 2003     Eva Wang “Splice variant chip design and variant-based expression analysis,” currently Director, Bioinformatics, Gladstone Institutes, San Francisco, CA and Startup Advisor, PreCyte Inc, Sentrix, NTLP
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 Sole Proprietor, Meta Logos Systems
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,” Research Associate, Steve McCaroll’s Lab Neurobiology Lab, Department of Genetics, Harvard Medical School 
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 Self-employed Computational Biologist and Genomics Scientist, Amsterdam, Netherlands
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 Director, Program in Quantitative & Computational Biosciences (QCB), Baylor College of Medicine, and Co-Director, Computational and Integrative Biomedical Research Center (CIBR), Baylor College of Medicine, and Member, Dan L Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, Texas, United States
1989                      Nick Littlestone “Mistake bounds and logarithmic linear-threshold learning algorithms,” currently Computer Programmer,, Berkeley, CA
1985                      Janet Blumer “Algorithms for the directed acyclic word graph and related structures”


M.S. Recipients

2012                      Jeffrey Long Currently Senior Data Scientist, Genentech, San Francisco, CA
2011                     Chris Wilks “Exploiting MAINE/FAIRE Experimental Data for Gene-Finding in Plasmodium falciparum Using Random Forests,” currently PhD student,  Johns Hopkins University, Baltimore, Maryland
2006                     Timothy Dreszer “Biased Clustered Substitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution,” currently Bioinformatics Contractor, Stanford University
2002                     Matt Xia “Study of molecular evolution by comparison of vertebrate genomes,” currently Sr. Director of Software Engineering, Cepheid, Sunnyvale, CA
2002                     Wei Wu (project option), currently Associate Research Professor, Lane Center for Computational Biology, Carnegie-Mellon and Co-director, the Computational Genomics Core (CDAR)
2002                     Rachel Bevan (project option)
2002                     Trevor Bruen (project option)
2001                     Fan Shen (project option), currently Senio Manager, Thermo Fisher Scientific, San Francisco, CA
2000                     Albion Baucom “Protein structure and function prediction: tools and techniques,” Team Lead at Invitae, San Francisco, CA
2000                     Rachel Karchin “Classifying G-protein coupled receptors with support vector machines,” 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 Owner, Lepton Incorporated, Sausalito, CA
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,” currently Senior Technical Editor, Altair Grid Technologies
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

2020                    Natalie Filippi Currently Research Associate, Haussler-Salama Lab, University of California Santa Cruz, CA
2019                    Paola Angulo UCSC Dean’s Award, “Understanding the role of ZNF765 and/or L1PA retroelements in defining embryonic stem cell phenotypes,currently Junior Specialist, Haussler-Salama Lab, University of California Santa Cruz, CA
2019                    Mason Hargrave UCSC Dean’s Award for undergraduate research, currently National Science Foundation Graduate Student Fellow, The Rockefeller University, New York, CA
2018                    Josh Gu Steck Award, “KRAB Zinc Finger proteins coordinate across evolutionary time scales to battle retroelements“, PhD candidate at UC Irvine School of Medicine
2018                    Yulia Zybina Research Mentoring Institute (RMI) and Diversity Fellowship, “High throughput assay for copy number detection of NOTCH2NL paralogs,” currently Scientist at Merk, Palo Alto, CA
2016                    Lila Whitehead Currently Research Associate, Fate Therapeutics Inc., San Diego, CA
2016                    Erin La Montagne Cortical organoid development from Sumatran Orangutan induced pluripotent stem cells,” currently Bioengineering PhD Graduate Student,  University of California San Diego, CA and NSF GRFP Fellow
2015                    Andrea Reyes-Ortiz UC LEADS Scholar, PhD candidate in Biomedical Sciences at UC Irvine School of Medicine
2015                    Alex Phillips UCSC Dean’s Award, “Reprogramming Orangutan Fibroblasts to Integration-free induced Pluripotent Stem Cells”, PhD Candidate in Microbiology at University of Illinois Urbana-Champaign
2002                    Krishna Roskin Huffman Prize, currently Post-Doctoral Fellow, Scott Boyd lab, Pathology, Stanford University, Palo Alto, CA
1995                    David Konerding “Prediction of gene-encoding regions in E.Coli DNA using an optimal parse method with multiple types of evidence”, currently Software Engineer, Google, Mountain View, CA
1995                    Jesse Reklaw Chancellor’s award for undergraduate research, currently Web Developer, Watermelon Web Works, Portland, Orgeon