- A. S. Schwartz and L. Pachter, "Multiple alignment by sequence annealing," in Proc. European Conf. on Computational Biology, 2007.
- C. Dewey, P. Huggins, K. Woods, B. Sturmfels, and L. Pachter, "Parametric alignment of Drosophila genomes," PLoS Computational Biology, vol. 2, no. 6, pp. 0606-0614, June 2006.
- L. Pachter and B. Sturmfels, Eds., Algebraic Statistics for Computational Biology, New York, NY: Cambridge University Press, 2005.
- K. Chen and L. Pachter, "Bioinformatics for whole-genome shotgun sequencing of microbial communities," PLoS Computational Biology, vol. 1, no. 2, pp. 0106-0112, July 2005.
- J. D. McAuliffe, M. Jordan, and L. Pachter, "Subtree power analysis finds optimal species for comparative genomics," Proc. National Academy of Sciences, vol. 102, no. 22, pp. 7900-7905, May 2005.
- L. Pachter and B. Sturmfels, "Tropical geometry of statistical models," Proc. National Acad. Sciences, vol. 101, no. 46, pp. 16132-137, Nov. 2004.
- L. Pachter, "Genome sequence of the Brown Norway rat yields insights into mammalian evolution," Nature, vol. 428, no. 6982, pp. 493-521, April 2004.
- N. Bray and L. Pachter, "MAVID: Constrained ancestral alignment of multiple sequences," Genome Research, vol. 14, no. 4, pp. 693-699, April 2004.
- D. Boffelli, J. McAuliffe, D. Ovcharenko, K. D. Lewis, I. Ovcharenko, L. Pachter, and E. M. Rubin, "Phylogenetic shadowing of primate sequences to find functional regions of the human genome," Science, vol. 299, no. 5611, pp. 1391-1394, Feb. 2003.
- C. Mayor, M. Brudno, J. R. Schwartz, A. Poliakov, E. M. Rubin, K. A. Frazer, L. Pachter, and I. Dubchak, "VISTA: Visualizing global DNA sequence alignments of arbitrary length," Bioinformatics, vol. 16, no. 11, pp. 1046-1047, Aug. 2000.