Lab Alumni
Postdocs
| 2016 to 2019 | Jason Fernandes | Biomedical Scientist at Scribe Therapeutics, Alameda, CA |
| 2013 to 2017 | Olena Morozova-Vaske | Assistant Professor of MCD Biology, University of California, Santa Cruz, CA |
| 2012 to 2017 | Karen Hayden-Miga | Assistant Research Scientist, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA |
| 2011 to 2014 | Maximilian Haeussler | Assistant Research Scientist-Browser, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA |
| 2011 to 2014 | Adam Ewing | Research fellow, the Mater Medical Research Institute and honorary fellow, the University of Queensland |
| 2009 to 2014 | Frank Jacobs | Associate Professor, Faculty of Science, University of Amsterdam, The Netherlands |
| 2011 to 2013 | Glenn Hickey | Research Consultant, Arenaria Inc., Canada |
| 2010 to 2013 | Daniel Zerbino | Head of Data Science, Mosaic, England, UK |
| 2010 to 2011 | Charlie Vaske | Vice President of Bioinformatics, Clear Labs, San Carlos, CA |
| 2007 to 2012 | Benedict Paten | Associate Professor, University of California, Santa Cruz, CA |
| 2006 to 2011 | Jing Zhu | Assistant Research Scientist-Cancer Genomics, UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA |
| 2006 to 2010 | Jason Underwood | Principal Scientist, Pacific Biosciences, Menlo Park, CA |
| 2007 to 2009 | Jian Ma | Ray and Stephanie Lane Professor of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA |
| 2006 to 2009 | Ting Wang | Inaugural Sanford C. and Karen Loewentheil Distinguished Professor of Medicine, School of Medicine, Washington University, St. Louis, MO |
| 2006 to 2007 | Mario Stanke | Professor, Bioinformatics, The Institute for Mathematics and Computer Science, University of Greifswald, Greifswald, Germany |
| 2005 to 2008 | Andrew Kern | Associate Professor, Evolutionary Genomics, University of Oregon |
| 2005 to 2006 | Chen-Hsiang Yeang | Associate Research Fellow, the Institute of Statistical Science, Academia Sinica, Taipei, Taiwan |
| 2004 to 2007 | Jakob Skou Pedersen | Professor, Bioinformatics, Department of Molecular Medicine, University of Aarhus, Denmark |
| 2003 to 2007 | Gill Bejerano | Chief Scientist, SAIVA, Inc., Los Altos, CA and 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 | Director, Gladstone Institute of Data Science and Biotechnology, Gladstone Institute, Professor, Division of Biostatistics, University of California, San Francisco School of Medicine, CA |
| 2003 to 2004 | Brian Lucena | Assistant Professor, Mathematics, American University, Cairo |
| 2002 to 2004 | Terry Furey | Professor, Genetics, University of North Carolina |
| 2002 to 2003 | Mathieu Blanchette | Director, School of Computer Science, McGill University, Montreal, Canada |
| 2000 to 2001 | Rune Lyngsoe | Principal Analyst, Oodle Car Finance, Oxford, UK |
| 1998 to 1999 | Bill Noble | Professor, Computer Sciences and Engineering, University of Washington, Seattle, WA |
| 1998 | Tommi Jaakkola | Professor, Electrical Engineering & Computer Science, Massachusetts Institute of Technology |
| 1996 to 1998 | Betty Lazareva | Senior Principal Bioinformatics Scientist, Santa Clara, CA |
| 1992 | Anders Krogh | Professor, Computational and RNA Biology, University of Copenhagen, Denmark |
Ph.D. Recipients
| 2017 to 2020 | Lauren Sanders | “Multi-omic analyses and organoid models for identification of therapeutic vulnerabilities and developmental origins in childhood cancer,” currently Staff Scientist at Blue Marble Space Institute of Science, NASA GeneLab |
| 2016 to 2019 | Jacob Pfeil | “Novel Gene Expression Analyses to Accelerate Precision Pediatric Oncology Research,” currently Senior Scientist II: Computational Biology, AbbVie, San Francisco, CA |
| 2015 to 2019 | John Vivian | “Tools for large-scale genomic analysis and gene expression outlier modeling for precision therapeutics,” currently Bioinformatics Scientist II, Atreca, Inc. Redwood City, CA |
| 2012 to 2019 |
Joel Armstrong |
“Enabling comparative genomics at the scale of hundreds of species,” currently Software Engineer, Google, Mountain View, CA |
| 2014 to 2018 |
Arjun Rao |
“Precision Immunotherapy for Cancer treatment,” currently Research Specialist, Krummel Lab, Department of Pathology, University of California San Francisco, CA |
| 2014 to 2017 | Ian Fiddes | “Comparative Annotation Toolkit (CAT) – simultaneous annotation of related genomes,” currently Director of Genomics and Biosecurity, 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, ImmunityBio, Santa Cruz, CA (formerly Five3 Genomics & NantOmics) |
| 2008 to 2015 |
Tracy Ballinger |
“Characterizing insertions in cancer genomes to look for evidence of retrotransposition in tumors,” currently Scientist, Rancho BioSciences, San Diego, CA |
| 2010 to 2014 | Mia Bosinger | “Emergence of drug resistance in cancer” currently Bioinformatics Consultant, Diamond Age Data Science and Adjunct Teaching Professor at Worcester Polytechnic Institute |
| 2008 to 2014 | Dent Earl | “Evaluations and Application of the three A’s of Genomics: Assembly, Alignment, Annotation,” currently L7 Software Engineer Manager, Google, Mountain View, CA |
| 2008 to 2014 | Ngan Nguyen | “Immunogenomics, Database of the Genome 10K Project,” currently Associate Director, Atreca, San Carlos, CA |
| 2006 to 2014 | David Greenberg | “An evolutionary arms race between zinc finger proteins and retrotransposons in ape genomes,” currently Account Manager, Axion BioSystems, San Francisco, CA |
| 2008 to 2013 | Ted Goldstein | “Tools for Extracting Actionable Medical Knowledge from Genomic Big Data,” currently Member of the Accessibility and Affordability Working Group, CIRM, CA |
| 2006 to 2013 | Chris Szeto | “Discovery of clinically relevant molecular signatures in cancer,” currently Senior Director, Discovery Bioinformatics, Exelixis, Alameda, CA |
| 2007 to 2012 | Stephen Benz | “Sample-specific cancer pathway analysis using PARADIGM,” currently Chief Technology Officer, Sagittarius Bio, Santa Cruz, CA |
| 2005 to 2012 | Zack Sanborn | “Tumor vs. Matched-Normal Sequencing Analysis and Data Integration,” currently Chief Technology Officer, ImmunityBio, Santa Cruz, CA (formerly Five3 Genomics & NantOmics) |
| 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 Assistant Professor of Molecular Genetics and Microbiology, Assistant Professor of Cell Biology, and Member of the Duke Cancer Institute, Duke University |
| 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”, currently Director of Clinical Informatics & Data Science, Freenome, Sunnyvale, CA |
| 2001 to 2006 | Daryl Thomas | “Using variation and constraint to understand functional elements in the human genome,” currently Director of Product Management, Personalis, Menlo Park, CA |
| 1999 to 2005 | Charles Sugnet | “Discovery and detection of alternative splicing,” currently Staff Software Engineer, Google, 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 Sole Propprietor, Meta Logos Systems, Denver, CO |
| 1995 to 2000 | Melissa Cline | “Protein sequence alignment reliability: prediction and measurement,” currently Program Manager, BRCA Exchange, 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,” currently Vice President Research Informatics, Olema Onocology, Ashfield, MA |
| 1999 | Michael Brown | “RNA modeling using stochastic context-free grammars,” currently Research scientist, undisclosed Biotech company |
| 1997 | Kimmen Sjölander | “A Bayesian-information theoretic method for evolutionary inference in proteins,” currently Genomics Scientist, Educator, and Writer, Self-employed, 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 and Computational Biosciences, 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
| 2023 | Hsiang Yun Lu | |
| 2023 | Wenyu Liang |
“Diploid Assembly of the Human 1Q21.1 Region Using Nanopore Reads”
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| 2022 | Gary Mantalas | “Evolution of Human Brain Development”, Co-Founder and CEO OrganOmics |
| 2012 | Jeffrey Long | Senior Statistical Program Analyst Project LeadSenior, 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: Home, Baltimore, Maryland |
| 2006 |
Timothy Dreszer |
“Biased Clustered Substitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution,” currently Film Maker, Music Producer, Self-employed, Santa Cruz, CA |
| 2002 | Matt Xia | “Study of molecular evolution by comparison of vertebrate genomes,” currently Software Engineer, Life Technologies |
| 2002 |
Wei Wu |
Associate Research Professor, Lane Center for Computational Biology, Carnegie-Mellon |
| 2002 |
Rachel Bevan |
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| 2002 |
Trevor Bruen |
Postgraduate in Family Medicine at the Northern Ontario School of Medicine |
| 2001 |
Fan Shen |
Currently Bioinformatics Scientist, Affymetrix, Santa Clara, CA |
| 2000 | Albion Baucom | “Protein structure and function prediction: tools and techniques,” currently Developer Services Team Lead, Genentech, San Francisco, CA |
| 2000 | Rachel Karchin | “Classifying G-protein coupled receptors with support vector machines,” currently 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 Director, Applied Bioinformatics, 10x Genomics, Pleasanton, CA |
| 1995 | Brad Gulko | “Using phylogenetic Markov trees to detect conserved structure in RNA multiple alignments,” currently Co-Founder, Progenic Genomics, San Francisco, 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, Mountain View, CA |
| 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” |
Undergrads
| 2024 | Jax Maya | |
| 2024 | Claudia Paz Flores | |
| 2023 | Sarah Xia | UCSC Deans Award, “Organoid Culture Modifications to Improve Brain Organoid Fidelity” |
| 2023 | Trevor McGuire | “Developing an Organoid-Based Model of Pediatric High-Grade Gliomas, introduces a specially-constructed DNA plasmid with an inducible Diffuse Intrinsic Pontine Glioma (DIPG) tumor driver expression cassette for Cre-Lox recombination into hESCs and, eventually, organoids.” |
| 2022 | Angelica Montevirgen | UCSF Neurology Department, Junior Specialis under Dr. Ari Green |
| 2019 to 2021 | Jennifer Yang | Library Assistant at National Library of Medicine, Los Angeles, CA |
| 2020 | Natalie Filippi | |
| 2020 | Taylor Real | UCSC Dean’s Award, Optimizing Molecular Inversion Probe Assays to Characterize Human-Specific Neurodevelopmental Genes |
| 2020 | Alex Hoefler | |
| 2019 | Paola Angulo | UCSC Dean’s Award, “Understanding the role of ZNF765 and/or L1PA retroelements in defining embryonic stem cell phenotypes” |
| 2019 | Mason Hargrave |
UCSC Dean’s Award for undergraduate research |
| 2018 | Josh Gu |
Steck Award, “KRAB Zinc Finger proteins coordinate across evolutionary time scales to battle retroelements“, PhD candidate at UC Irvine |
| 2018 | Yulia Zybina | Research Mentoring Institute (RMI) and Diversity Fellowship, “High throughput assay for copy number detection of NOTCH2NL paralogs” |
| 2016 | Lila Whitehead |
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| 2016 | Erin La Montagne |
“Cortical organoid development from Sumatran Orangutan induced pluripotent stem cells” |
| 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 Director of Genomics, Google, Mountain View, CA |
| 1995 | Jesse Reklaw | Chancellor’s award for undergraduate research |