- Graduated students (also in the Mathematics Genealogy Project)
- Brielin Brown, Ph.D. (2016) Computational approaches to understanding the genetic architecture of complex traits.
- Lorian Schaeffer, Ph.D. (2016) Pseudoalignment for metagenomic and metatranscriptomic read assignment.
- Isaac Joseph, Ph.D. (2016) Sequencing-based computational methods for identifying impactful genomic alterations in cancers.
- Shannon Hateley, Ph.D. (2016) Detection, Quantification, and Characterization of Diverse RNA Transcript Isoforms.
- 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.
Research Scientist, Facebook.
- 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.
- 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, Carnegie Mellon University.
- 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.
- Ariel S. Schwartz, Ph.D. (2007) Posterior Decoding Methods for Optimization and Accuracy Control of
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.
- Mathilde Paris
Researcher, CNRS Marseille.
- Valerie Hower
Assistant Professor, Department of Mathematics, University of Miami.
- Megan Owen
Assistant Professor, Department of Computer Science, Lehman college CUNY.
- Alexander Schönhuth
Assistant Professor, Centrum Wiskunde & Informatica, Amsterdam.
- Robert Bradley
Assistant Member, Fred Hutchinson Cancer Research Center.
- Radu Mihaescu
Assistant vice-president, Knight Capital Group.
- Trevor Bruen
Assistant Professor, Department of Mathematics, Saint Francis Xavier University.
- 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, Departments of Mathematics and Statistics, University of Kentucky.
- 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.