Principal Investigator
Lior Pachter
Lab Manager
Lisa Sledd
Postdocs
Shannon McCurdy
Vasilis Ntranos (joint with David Tse)
Valentine Svensson
Akshay Tambe
Graduate students
Sina Booeshaghi
Jase Gehring
Robert Tunney (joint with Liana Lareau)
Lynn Yi
Graduate rotation students
Eduardo Beltrame
Nadezda Volovich
Research assistants
Makenna Herl
Undergraduates
Lauren Liu
Tina Wang
Visitors
Lenka Matejovicova (spring 2016)
Páll Melsted (Spring 2015)
Julie Mitchell (Spring 2010)
Satyan Devadoss (2009-2010)
Anna Kedzierska (March-August 2010)
Rahul Satija (February-March 2009)
Cole Trapnell (2008-2010)
Graduated students (also in the Mathematics Genealogy Project)
Akshay Tambe, Ph.D. (2017) Developing experimental and computational tools for sequence-census assays.
Postdoctoral Researcher, California Institute of Technology.
Brielin Brown, Ph.D. (2016) Computational approaches to understanding the genetic architecture of complex traits.
Computational Biologist, Verily Life Sciences.
Lorian Schaeffer, Ph.D. (2016) Pseudoalignment for metagenomic and metatranscriptomic read assignment.
Data Scientist, Uber.
Isaac Joseph, Ph.D. (2016) Sequencing-based computational methods for identifying impactful genomic alterations in cancers.
Computational biologist and Data Scientist, Agilent Technologies.
Shannon Hateley, Ph.D. (2016) Detection, Quantification, and Characterization of Diverse RNA Transcript Isoforms.
Computational Biologist, Ancestry.com.
Harold Pimentel, Ph.D. (2016) Fast and accurate quantification and differential analysis of transcriptomes.
Postdoctoral Researcher, Stanford University with Jonathan Pritchard.OA
Natth Bejraburnin, Ph.D. (2015) A Study on Correlations between Genes, Functions and Evolutions.
Senior Data Scientist, SCB Abacus.
Atif Rahman, Ph.D. (2015) Statistical Models for Genome Assembly and Analysis.
Assistant Professor at Bangaladesh University of Science and Technology.
Emily Berger, Ph.D. (2015) Probabilistic Methods for Single Individual Haplotype Reconstruction: HapTree and HapTree-X.
Trader, Jane Street Capital.
Nicolas Bray, Ph.D. (2014) Methods for Measurement and Interpretation of Gene Expression.
Postdoctoral Researcher at the Innovative Genomics Initiative with Jacob Corn and Jennifer Doudna, Berkeley (starting 2015).
Adam Roberts, Ph.D. (2013) Ambiguous fragment assignment for high-throughput sequencing experiments.
Senior Software Engineer, Google.
Meromit Singer, Ph.D. (2012) Statistical algorithms in the study of mammalian DNA methylation.
Postdoctoral Researcher, Broad Institute with Aviv Regev.
Aaron Kleinman, Ph.D. (2012) Combinatorial phylogenetics of reconstruction algorithms.
Computational Biologist, 23andme.
Cole Trapnell, Ph.D. (2010) Transcript Assembly And Abundance Estimation with High-throughput RNA-sequencing.
Assistant Professor of Genome Sciences, University of Washington.
Anne J. Shiu, Ph.D. (2010) Algebraic methods for biochemical reaction network theory.
Assistant Professor of Mathematics, Texas A & M University.
Peter M. Huggins, Ph.D. (2008) Polytopes in Computational Biology.
Project Scientist, University of Kentucky.
Radu H. Mihaescu, Ph.D. (2008) Distance Methods for Phylogeny Reconstruction (winner of the Bernard Friedman Memorial Prize for an outstanding thesis in applied mathematics).
Director, Knight Capital Group.
Anat Caspi, Ph.D. (2007) Comparative Genomics of Repeat Elements.
Director, The Taskar Center for Accessible Technology, Department of Computer Science & Engineering, University of Washington.
Ariel S. Schwartz, Ph.D. (2007) Posterior Decoding Methods for Optimization and Accuracy Control of Multiple Alignments.
Principal Scientist, Bioinformatics at Synthetic Genomics, San Diego.
Colin N. Dewey, Ph.D. (2006) Whole-Genome Alignments and Polytopes for Comparative Genomics.
Associate Professor, Departments of Computer Science, Biostatistics & Medical Informatics, University of Wisconsin, Madison.
Sourav Chatterji, Ph.D. (2006) Computational Analyses of Eukaryotic Gene Evolution.
Senior software engineer at Facebook.
Kevin Chen, Ph.D. (2005) Three Variations on the Theme of Comparative Genomics: Metagenomics, Mitochondrial Gene Rearrangements and MicroRNAs (co-advisor: Satish Rao).
Assistant Professor of Genetics, Rutgers.
Dan Levy, Ph.D. (2005), Applications of Graph Theory to Chromosome Rearrangements and Phylogenetics (co-advisor: Ray Sachs).
Assistant Professor, Cold Spring Harbor Laboratories.
Eric Kuo, Ph.D. (2005), Combinatorics of Viterbi Sequences.
Software Engineer, The MathWorks.
Former postdocs
Sharon Aviran
Assistant Professor, Department of Biomedical Engineerg, UC Davis.
Eliana Hechter
(1987--2014).
Mathilde Paris
Researcher, CNRS Marseille.
Valerie Hower
Instructor, Department of Mathematics, Florida Atlantic University.
Megan Owen
Assistant Professor, Department of Computer Science, Lehman college CUNY.
Alexander Schönhuth
Principal Investigator, Centrum Wiskunde & Informatica, Amsterdam.
Robert Bradley
Associate Member, Fred Hutchinson Cancer Research Center.
Radu Mihaescu
Assistant vice-president, Knight Capital Group.
Trevor Bruen
Medical student, Université de Sherbrooke.
Niko Beerenwinkel
Professor, Department of Biosystems Science and Engineering, ETH, Zurich.
Sagi Snir
Senior Lecturer, Department of Evolutionary and Environmental Biology, University of Haifa, Israel.
Mathias Drton
Professor, Department of Statistics, University of Washington.
Ruriko Yoshida
Associate Professor, Department of Operations Research, Naval Postgraduate School.
Luis David Garcia-Puente
Associate Professor of Mathematics, Sam Houston State University.
Von Bing Yap
Associate Professor of Statistics and Applied Probability, National University Singapore.
Marina Axelson-Fisk
Docent, Chalmers University of Technology, Gotheburg, Sweden.
OA