- Principal Investigator
- Lior Pachter
- Lab Manager
- Charlene Kim
- Graduate students
- Maria Carilli
- Vera Beilinson (co-advised by Margaret McFall-Ngai*)
- Catherine Felce
- Kayla Jackson
- Conrad Oakes
- Joseph Rich
- Nikhila Swarna
- Visitors
- Thorhallur Helgason (Summer 2022)
- Lenka Matejovicova (Spring 2016)
- Páll Melsted (Spring 2015, Fall 2019)
- 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)
- Rebekah Loving, Ph.D. (2025) Methods for Long Read RNA-seq Transcriptomics
- Meichen Fang, Ph.D. (2025) A biophysical approach to normalization and trajectory inference in single-cell RNA sequencing data analysis
- Delaney Sullivan, Ph.D. (2025) Software, tools, and methods development for single-cell transcriptomics (co-advised by Mitchell Guttman).
- Anne Yeokyoung Kil, Ph.D. (2025) Engineeringand Computational Tools for Salivary Biomedicine.
- Tara Chari, Ph.D. (2024) Perturbing the Genome: From Bench to Biophysics.
- Laura Luebbert, Ph.D. (2024) Complexity of Transcriptomic Data Analysis and Implications for Biological Discovery.
- Taleen Dilanyan, Ph.D. (2023) Open-Source Custom Beads for Single-Cell Transcriptomics.
- Gennady Gorin, Ph.D. (2023) Stochastic Foundations for Single-Cell RNA Sequencing.
- Lambda Moses, Ph.D. (2023) Computational Foundations for Spatial Transcriptomics.
- Ángel Merchán Gálvez, Ph.D. (2023) Studies of mRNA Expression and Degradation.
- Kristján Eldjarn Hjörleifsson, Ph.D. (2022) Graph modeling for genomics and epidemiology.
- Sina Booeshaghi, Ph.D. (2022) Foundations and Applications of Single-Cell RNA Sequencing.
- Lynn Yi, Ph.D. (2019) Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing.
- Jase Gehring, Ph.D. (2018) Expanding Single-Cell RNA-Sequencing in Scale and Dimension.
- Akshay Tambe, Ph.D. (2017) Developing experimental and computational tools for sequence-census assays (co-advised by Jennifer Doudna).
- Robert Tunney, Ph.D. (2017) Regression Modeling and Bias Correction of Ribosome Profiling Data (co-advised by Liana Lareau*).
- 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 (co-advised by Michael Eisen).
- Harold Pimentel, Ph.D. (2016) Fast and accurate quantification and differential analysis of transcriptomes.
- Natth Bejraburnin, Ph.D. (2015) A Study on Correlations between Genes, Functions and Evolutions.
- Atif Rahman, Ph.D. (2015) Statistical Models for Genome Assembly and Analysis.
- Emily Berger, Ph.D. (2015) Probabilistic Methods for Single Individual Haplotype Reconstruction: HapTree and HapTree-X.
- 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.
- Meromit Singer, Ph.D. (2012) Statistical algorithms in the study of mammalian DNA methylation.
- Aaron Kleinman, Ph.D. (2012) Combinatorial phylogenetics of reconstruction algorithms.
- Cole Trapnell, Ph.D. (2010) Transcript Assembly And Abundance Estimation with High-throughput RNA-sequencing (co-advised by Steven Salzberg).
- Anne J. Shiu, Ph.D. (2010) Algebraic methods for biochemical reaction network theory (co-advised by Bernd Sturmfels*).
- Peter M. Huggins, Ph.D. (2008) Polytopes in Computational Biology (co-advised by Bernd Sturmfels).
- Radu H. Mihaescu, Ph.D. (2008) Distance Methods for Phylogeny Reconstruction (co-advised by Satish Rao).
- 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 Multiple Alignments.
- Colin N. Dewey, Ph.D. (2006) Whole-Genome Alignments and Polytopes for Comparative Genomics.
- Sourav Chatterji, Ph.D. (2006) Computational Analyses of Eukaryotic Gene Evolution.
- Kevin Chen, Ph.D. (2005) Three Variations on the Theme of Comparative Genomics: Metagenomics, Mitochondrial Gene Rearrangements and MicroRNAs (co-advised by Satish Rao).
- Dan Levy, Ph.D. (2005), Applications of Graph Theory to Chromosome Rearrangements and Phylogenetics (co-advised by Rainer Sachs)
- Eric Kuo, Ph.D. (2005), Combinatorics of Viterbi Sequences.
- * primary co-advisor
- Former postdocs
- Lambda Moses (2024)
- Laura Luebbert (2024)
- Gennady Gorin (2023)
- Sina Booeshaghi (2023)
- Jase Gehring (2020)
- Valentine Svensson (2020)
- Vasilis Ntranos (2019)
- Shannon McCurdy (2017)
- Bo Li (2017)
- Sharon Aviran (2013)
- Eliana Hechter (2013)
- Mathilde Paris (2013)
- Valerie Hower (2011)
- Megan Owen (2011)
- Alexander Schönhuth (2010)
- Robert Bradley (2009)
- Radu H. Mihaescu (2009)
- Trevor Bruen (2009)
- Niko Beerenwinkel (2007)
- Sagi Snir (2006)
- Mathias Drton (2005)
- Ruriko Yoshida (2004)
- Luis David Garcia-Puente (2004)
- Von Bing Yap (2003)
- Marina Axelson-Fisk (2002)