Santos, V.J., C. D. Bustamante, and F. J. Valero-Cuevas. Improving the Fitness of High-Dimenstional Biomechanical Models via Data-driven Stochastic Exploration. IEEE Transac-tions on Biomedical Engineering.url

Bustamante, C. D. and S. Ramachandran. 2009. Evaluating genomic signatures of sex-specific processes. Nature Genetics 41(1):8-9. url

Degenhardt, J.D., P. de Candia, A. Chabot, S. Schwartz, L. Henderson, B. Ling, M. Hunter, Z. Jiang, J. Rogers, R. E. Palermo, M. Katze, E. Eichler, M. Ventura., P. Marx, Y. Gilad, and C. D. Bustamante. 2009. CCL3L copy number variation is a common host immune factor for SIV/HIV/AIDS in Humans and Macaques. PLoS-Genetics 5(1):e1000346. url

Auton, A., K. Bryc, A. Boyko, K. Lohmueller, J. Novembre, A. Reynolds, A. Indap, M. Wright, J. Degenhardt, R. Gutenkunst, K. King, M. Nelson, and C. D. Bustamante. 2009. Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Research. url

Gray, M. M, J. Granka, C. D. Bustamante, N. Sutter, A. Boyko, L. Zhu, E. A. Ostrander, R. K. Wayne. 2009. Linkage Disequilibrium and Demographic History of Wild and Domestic Canids. Genetics. url

Anderson, T.M., B. M. Vonholdt, S. I. Candille, M. Musiani, C. Greco, D. R. Stahler, D. W. Smith, B. Padhukasahasram, E. Randi, J. A. Leonard, C. D. Bustamante, E. A. Ostrander, H. Tang, R. K. Wayne, and G. S. Barsh. 2009. Molecular and Evolutionary History of Melanism in North American Gray Wolves. Science. 323:1339-43. url

Nielsen, R., M. J. Hubisz, D. Torgerson, A. M. Andres, A. Albrechtsen, R. Gutenkunst, M. Adams, M. Cargill, A. Boyko, A. Indap, C. D. Bustamante, I. G. Hellmann, and A. G. Clark. Darwinian and demographic forces affecting human protein coding genes. Genome Research. url

Lohmueller, K.E., C. D. Bustamante, and A. G. Clark. Methods for human demographic inference using haplotype patterns from genome-wide SNP data. Genetics. url

Bovine HapMap Consortium, Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24;324(5926):528-32. PubMed PMID: 19390050. url

Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch SR. Evolutionary History of GS3, a Gene Conferring Grain Size in Rice. Genetics. 2009 Jun 9. [Epub ahead of print] PubMed PMID: 19506305. url

McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-12278. Epub 2009 Jul 13. PubMed PMID: 19597147; PubMed Central PMCID: PMC2718348. url

Parker HG, Vonholdt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA. An Expressed Fgf4 Retrogene Is Associated with Breed-Defining Chondrodysplasia in Domestic Dogs. Science. 2009 Jul 16. [Epub ahead of print] PubMed PMID: 19608863. url

Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, White TJ, Sninsky JJ, Cargill M, Adams MD, Bustamante CD, Clark AG. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet. 2009 Aug;5(8):e1000592. Epub 2009 Aug 7. PubMed PMID: 19662163; PubMed Central PMCID: PMC2714078. url

Boyko AR, Boyko RH, Boyko CM, Parker HG, Castelhano M, Corey L, Degenhardt J, Auton A, Hedimbi M, Kityo R, Ostrander EA, Schoenebeck J, Todhunter RJ, Jones P, Bustamante CD. Complex population structure in African village dogs and its implications for inferring dog domestication history. Proc Natl Acad Sci U S A. 2009 Aug 3. [Epub ahead of print] PubMed PMID: 19666600. url