Lior Pachter

Research Interests

Research Summary

We are working on the fundamental problem of comparative genomics: the determination of the origins and evolutionary history of the nucleotides in all extant genomes. Our work incorporates various aspects of genomics, including the reconstruction of ancestral genomes (paleogenomics), the modeling of genome dynamics (phylogenomics and systems biology) and the assignment of function to genome elements (functional genomics).

In addition to working on methodology and mathematical foundations for comparative genomics, we also work with genome projects and perform large scale computational analyses. We have been members of the mouse, rat, chicken and fly genome sequencing consortia, and have participated in the ENCODE consortium.

Selected Publications

C. Dewey, P. Huggins, K, Woods, B. Sturmfels and L. Pachter, Parametric alignment of Drosophila genomes, PLoS Computational Biology, Volume 2, Number 6 (2006) p e73.

L. Pachter and B. Sturmfels, Algebraic Statistics for Computational Biology, Cambridge University Press, 2005.

J. D. McAuliffe, M. I. Jordan and L. Pachter, Subtree power analysis finds optimal species for comparative genomics, Proceedings of the National Academy of Sciences, Volume 102, Number 22 (2005), p 7900--7905.

N. Bray and L. Pachter, MAVID: Constrained ancestral alignment of multiple sequences, Genome Research 14 (2004), p 693--699.

Rat Genome Sequencing Consortium, Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol. 428, (2004), p 493--521.

D. Boffelli, J. McAuliffe, D. Ovcharenko, K. D. Lewis, I. Ovcharenko, L. Pachter, E. M. Rubin, Phylogenetic shadowing of primate sequences to find functional regions of the human genome, Science, Volume 299, Number 5611 (2003), p 1391--1394.