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Pachter Lab

Principal Investigator
Lior Pachter
Lab Manager
Charlene Kim
Postdoctoral researcher
Sina Booeshaghi
Graduate students
Maria Carilli
Vera Beilinson (primary advisor Margaret McFall-Ngai)
Tara Chari
Taleen Dilanyan
Meichen Fang
Catherine Felce
Ángel Merchán Gálvez
Gennady Gorin
Kayla Jackson
Anne Yeokyoung Kil
Laura Luebbert
Rebekah Loving
Lambda Moses
Delaney Sullivan
Mihir Borkar
Thorhallur Helgason
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)
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.
Robert Tunney, Ph.D. (2017) Regression Modeling and Bias Correction of Ribosome Profiling Data.
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.
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.
Anne J. Shiu, Ph.D. (2010) Algebraic methods for biochemical reaction network theory.
Peter M. Huggins, Ph.D. (2008) Polytopes in Computational Biology.
Radu H. Mihaescu, Ph.D. (2008) Distance Methods for Phylogeny Reconstruction.
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.
Dan Levy, Ph.D. (2005), Applications of Graph Theory to Chromosome Rearrangements and Phylogenetics.
Eric Kuo, Ph.D. (2005), Combinatorics of Viterbi Sequences.
Former postdocs
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)