Computational Genomics
PhD GraduatesSarah Aerni
PhD in Biomedical Informatics, June 2012 Single-cell gene expression analysis in C. elegans Current position: Principal Data Scientist at Pivotal George Asimenos PhD in Computer Science, June 2009 Methodoologies for comparative genomics and metagenomics Current position: Director of Strategic Projects at DNAnexus Michael Brudno PhD in Computer Science, June 2005 Algorithms for comparison of DNA sequences Current position: Associate Professor and Canada Research Chair in Computational Biology, University of Toronto Tiffany (TJ) Chen PhD in Biomedical Informatics, June 2012 De novo reconstruction of cell cycle and chemotherapeutic mechanisms in cancer Current position: Director of Informatics at Cytobank Eugene Davidov PhD in Computer Science, June 2009 Algorithms for analysis of multiple biological sequences Current position: Senior Software Engineer at Google Omkar Deshpande PhD in Computer Science, June 2008; co-advisor: Luca Cavalli Sforza A simulations approach to the genetic and cultural prehistory of humans Current position: Founder at The Young Socratics Chuong (Tom) Do PhD in Computer Science, June 2009; primary advisor: Andrew Ng Discriminative structured models for biological sequence analysis Current position: Director of Analytics at Coursera Jason Flannick PhD in Computer Science, June 2008 Algorithms for biological network alignment Current position: Research Associate in Genetics, Massachusetts General Hospital Eugene Fratkin PhD in Computer Science, June 2009 Application of non-parametric algorithms to computational biology Current position: Co-Founder, Senior VP of Engineering at Lifecode Sam Gross PhD in Computer Science, June 2010 Computational recognition of protein-coding genes using multiple genomic alignments Current position: Software Engineer at Google Dorna Kashef-Haghighi PhD in Computer Science, June 2015 Algorithms for decoding cancer genomes Curent position: Postdoctoral Scientist, Dennis Wall laboratory Su-In Lee PhD in Computer Science, June 2009 Member of the Batzoglou lab for 1 year, PhD advisor: Daphne Koller Machine learning approaches to understanding the genetic basis of complex traits Current position: Assistant Prof. of CS, EE, Genome Sciences, University of Washington Irene Liu PhD in Biomedical Informatics, June 2006 Computational identification of eukaryotic regulatory elements and application in Caenorhabditis elegans Current position: Breast Imaging Fellow at Stanford Hospital & Clinics Sofia Kyriazopoulou-Panagiotopoulou PhD in Computer Science, June 2014 An integrative model of chromatin and expression variation across human cell types Current position: Computational Biologist at 10X Genomics Brian Naughton PhD in Biomedical Informatics, June 2006; primary advisor: Doug Brutlag Sequence analysis methods for the detection of promoters and transcription factor binding sites Daniel E. Newburger PhD in Biomedical Informatics, December 2014 Analysis of genomic variants for investigating the genetic etiology of disease Current position: Software Engineer at Google Tony Novak Current position: Implementer of things Dmitri Pushkarev PhD in Physics, expected June 2016; primary advisor: Steven Quake Current position: CEO at ClusterK Jesse M. Rodriguez PhD in Biomedical Informatics, June 2014 Accurate methods for ancestry and relatedness inference Current position: Software Engineer at Google Serge Saxonov PhD in Biomedical Informatics, June 2006; primary advisor: Doug Brutlag Genome-scale analysis of DNA regulatory sequences Current position: CEO and Co-Founder, 10X Genomics Marc Schaub PhD in Computer Science, June 2012 Integrative methods for analysis of genome wide association studies Current position: Senior Software Engineer at Google Marina Sirota PhD in Biomedical Informatics, June 2010; primary advisor: Atul Butte Developing and applying integrative computational methods to study autoimmune disease Current Position: Assistant Professor, Institute for Computational Health Sciences, UCSF Balaji Srinivasan PhD in Electrical Engineering, June 2007 Protein interaction networks: integration, analysis, and alignment Current position: CEO and Cofounder of 21; Board Partner at Andreessen Horowitz Andreas Sundquist PhD in Computer Science, June 2008 Algorithms for next-generation sequencing |
Postdoctoral ScientistsRaheleh Salari
Current position: Senior Bioinformatician at Natera Anshul Kundaje Current position: Assistant Professor of Genetics and Computer Science, Stanford University |
VisitorsRunshen (Ryan) Cai
Associate Professor, Tianjin University of Science and Technology, Tianjin, China Thanh Thi-Nguyen Lecturer in Computational Intelligence and Health Informatics, Deakin University, Victoria, Australia. Phuong Tu-Minh |
Undergraduates and Masters Students
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