Faculty Research Page

Lior Pachter

Raymond and Beverly Sackler Chair and Professor of Genetics, Genomics and Development

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Research Interests

I am a computational biologist working in genomics. My career began in comparative genomics, and initially I was interested in genome alignment, annotation, and the determination of conserved regions using phylogenetic methods. I contributed to the mouse, rat, chicken and fly genome sequencing consortia, and the ENCODE project. More recently I've become focused on functional genomics, which includes answering questions about the function and interaction of DNA, RNA and protein products. I'm particularly interested in applications of high-throughput sequencing to RNA biology.

I'm also interested in algorithms, statistical methodology, and mathematical foundations for computational genomics. These interests are reflected in my appointments across different departments and colleges: Mathematics, Molecular & Cell Biology, and Electrical Engineering & Computer Science. My group includes students and postdocs from Computer Science, Mathematics, Bioengineering, Molecular and Cell Biology and Statistics.

Selected Publications


C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn and L. Pachter, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nature Biotechnology, advance online publication (2012).
S.A. Mortimer, C. Trapnell, S. Aviran, L. Pachter and J.B. Lucks, SHAPE-Seq: High throughput RNA structure analysis, Current Protocols in Chemical Biology, advance online publication.
A. Kleinman, M. Harel and L. Pachter, Affine and projective tree metric theorems, Annals of Combinatorics, advance online publication (2012).
A. Roberts and L. Pachter, Streaming fragment assignment for real-time analysis of sequencing experiments, Nature Methods, advance online publication (2012).
V. Hower, R. Starfield, A. Roberts, and L. Pachter, Quantifying uniformity in mapped reads, Bioinformatics, 28 (2012), 2680--2682.
L. Pachter, A closer look at RNA editing, Nature Biotechnology, 30 (2012), 246--247.
C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimentel, S.L. Salzberg, J.L. Rinn and L. Pachter, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, 7 (2012), 562--578.



S. Aviran, J. Lucks and L. Pachter, RNA structure characterization from chemical mapping experiments, Proceedings of the 49th Allerton Conference on Communication, Control and Computing, p 1743--1750, 2012.
A. Roberts and L. Pachter, RNA-Seq and find: entering the RNA deep field, Genome Medicine, 3 (2011), 74 [PDF].
F. Meacham, D. Boffelli, J. Dhahbi, D.I.K. Martin, M. Singer and L. Pachter, Identification and correction of systematic error in high-throughput sequence data, BMC Bioinformatics, in press.
M. Singer, A. Engstrom, A. Schoenhuth and L. Pachter, Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains, Statistical Applications in Genetics and Molecular Biology, 10 (2011), Article 43.
D. Martin, M. Singer, J. Dhahbi, G. Mao, L. Zhang, G. Schroth, L. Pachter and D. Boffelli, Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states, Genome Research (2011), Advance publication.
A. Roberts, H. Pimentel, C. Trapnell and L. Pachter, Identification of novel transcripts in annotated genomes using RNA-Seq, Bioinformatics, 27 (2011), p 2325--2329.
S. Snir and L. Pachter, Tracing the most parsimonious indel history, Journal of Computational Biology, 8 (2011), p 1--20.
S. Aviran, C. Trapnell, J.B. Lucks, S.A. Mortimer, S. Luo, G.P. Schroth, J.A. Doudna, A.P. Arkin and L. Pachter,Modeling and automation of sequencing-based characterization of RNA structure, Proceedings of the National Academy of Sciences, (2011), early online.
J.B. Lucks, S.A. Mortimer, C. Trapnell, S. Luo, S. Aviran, G.P. Schroth, L. Pachter, J.A. Doudna and A.P. Arkin, Multiplexed RNA Secondary and Tertiary Structure Characterization with SHAPE-Seq, Proceedings of the National Academy of Sciences, (2011), early online.
A. Roberts, C. Trapnell, J. Donaghey, J.L. Rinn and L. Pachter, Improving RNA-Seq expression estimates by correcting for fragment bias, Genome Biology, 12 (2011), R22.
V. Hower, S.N. Evans and L. Pachter, Shape-based peak identification for ChIP-Seq, BMC Bioinformatics, 12 (2011), 15.


Last Updated 2013-07-27