List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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Adaptation, Physiological
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
Animals
J. D. Jensen, Thornton, K. R., and Andolfatto, P., An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila., PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
P. Andolfatto, Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA., Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila., Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila., Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
P. Andolfatto, Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome., Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
M. L. Aardema, Zhen, Y., and Andolfatto, P., The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies., Mol Ecol, vol. 21, no. 2, pp. 340-9, 2012.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., Revisiting an old riddle: what determines genetic diversity levels within species?, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship., PLoS One, vol. 7, no. 8, p. e43888, 2012.
Y. Zhen and Andolfatto, P., Methods to detect selection on noncoding DNA., Methods Mol Biol, vol. 856, pp. 141-59, 2012.
A. S. Putnam, J Scriber, M., and Andolfatto, P., Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species., Evolution, vol. 61, no. 4, pp. 912-27, 2007.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes., Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
J. D. Wall, Andolfatto, P., and Przeworski, M., Testing models of selection and demography in Drosophila simulans., Genetics, vol. 162, no. 1, pp. 203-16, 2002.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., Multiplexed shotgun genotyping for rapid and efficient genetic mapping., Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., Parallel molecular evolution in an herbivore community., Science, vol. 337, no. 6102, pp. 1634-7, 2012.
P. Andolfatto and Wall, J. D., Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster., Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P., An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences., Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., Genome sequencing reveals complex speciation in the Drosophila simulans clade., Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group., Evolution, vol. 60, no. 2, pp. 292-302, 2006.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
K. Thornton and Andolfatto, P., Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster., Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
D. Bachtrog and Andolfatto, P., Selection, recombination and demographic history in Drosophila miranda., Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., Pervasive natural selection in the Drosophila genome?, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species., Cell, vol. 132, no. 5, pp. 783-93, 2008.
J. P. Huelsenbeck and Andolfatto, P., Inference of population structure under a Dirichlet process model., Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
K. Thornton, Bachtrog, D., and Andolfatto, P., X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution., Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., Correlated evolution of nearby residues in Drosophilid proteins., PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
P. Andolfatto, Wong, K. M., and Bachtrog, D., Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species., Genome Biol Evol, vol. 3, pp. 114-28, 2011.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence., Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content., Genome Biol, vol. 6, no. 8, p. R67, 2005.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
P. Andolfatto, J Scriber, M., and Charlesworth, B., No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus., Evolution, vol. 57, no. 2, pp. 305-16, 2003.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 2009.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations., Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
Drosophila
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 2009.
P. Andolfatto, Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA., Genetics, vol. 180, no. 3, pp. 1767-71, 2008.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila., Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila., Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., Revisiting an old riddle: what determines genetic diversity levels within species?, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship., PLoS One, vol. 7, no. 8, p. e43888, 2012.
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
J. D. Wall, Andolfatto, P., and Przeworski, M., Testing models of selection and demography in Drosophila simulans., Genetics, vol. 162, no. 1, pp. 203-16, 2002.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., Multiplexed shotgun genotyping for rapid and efficient genetic mapping., Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., Genome sequencing reveals complex speciation in the Drosophila simulans clade., Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group., Evolution, vol. 60, no. 2, pp. 292-302, 2006.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
D. Bachtrog and Andolfatto, P., Selection, recombination and demographic history in Drosophila miranda., Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., Pervasive natural selection in the Drosophila genome?, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species., Cell, vol. 132, no. 5, pp. 783-93, 2008.
K. Thornton, Bachtrog, D., and Andolfatto, P., X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution., Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. Andolfatto, Wong, K. M., and Bachtrog, D., Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species., Genome Biol Evol, vol. 3, pp. 114-28, 2011.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence., Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
Drosophila melanogaster
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content., Genome Biol, vol. 6, no. 8, p. R67, 2005.
P. Andolfatto, Wong, K. M., and Bachtrog, D., Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species., Genome Biol Evol, vol. 3, pp. 114-28, 2011.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila., PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations., Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila., Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
P. Andolfatto, Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome., Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
P. Andolfatto and Wall, J. D., Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster., Genetics, vol. 165, no. 3, pp. 1289-305, 2003.
K. Thornton and Andolfatto, P., Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster., Genetics, vol. 172, no. 3, pp. 1607-19, 2006.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., Correlated evolution of nearby residues in Drosophilid proteins., PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
Evolution, Molecular
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., A population genetics-phylogenetics approach to inferring natural selection in coding sequences., PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
J. D. Jensen, Thornton, K. R., and Andolfatto, P., An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila., PLoS Genet, vol. 4, no. 9, p. e1000198, 2008.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 2009.
P. Andolfatto, J Scriber, M., and Charlesworth, B., No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus., Evolution, vol. 57, no. 2, pp. 305-16, 2003.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila., Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila., Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
P. Andolfatto, Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome., Genome Res, vol. 17, no. 12, pp. 1755-62, 2007.
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., The Capsella rubella genome and the genomic consequences of rapid mating system evolution., Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
Y. Zhen and Andolfatto, P., Methods to detect selection on noncoding DNA., Methods Mol Biol, vol. 856, pp. 141-59, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship., PLoS One, vol. 7, no. 8, p. e43888, 2012.
A. S. Putnam, J Scriber, M., and Andolfatto, P., Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species., Evolution, vol. 61, no. 4, pp. 912-27, 2007.
P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila., Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
Y. Zhen, Aardema, M. L., Medina, E. M., Schumer, M., and Andolfatto, P., Parallel molecular evolution in an herbivore community., Science, vol. 337, no. 6102, pp. 1634-7, 2012.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., Genome sequencing reveals complex speciation in the Drosophila simulans clade., Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
D. Bachtrog and Andolfatto, P., Selection, recombination and demographic history in Drosophila miranda., Genetics, vol. 174, no. 4, pp. 2045-59, 2006.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., Pervasive natural selection in the Drosophila genome?, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., Correlated evolution of nearby residues in Drosophilid proteins., PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence., Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content., Genome Biol, vol. 6, no. 8, p. R67, 2005.
K. Thornton, Bachtrog, D., and Andolfatto, P., X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution., Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
Female
P. Andolfatto, J Scriber, M., and Charlesworth, B., No association between mitochondrial DNA haplotypes and a female-limited mimicry phenotype in Papilio glaucus., Evolution, vol. 57, no. 2, pp. 305-16, 2003.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship., PLoS One, vol. 7, no. 8, p. e43888, 2012.
R. Cui, Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and Rosenthal, G. G., Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes., Evolution, vol. 67, no. 8, pp. 2166-79, 2013.
P. Andolfatto, Davison, D., Erezyilmaz, D., Hu, T. T., Mast, J., Sunayama-Morita, T., and Stern, D. L., Multiplexed shotgun genotyping for rapid and efficient genetic mapping., Genome Res, vol. 21, no. 4, pp. 610-7, 2011.
D. Bachtrog, Thornton, K., Clark, A., and Andolfatto, P., Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group., Evolution, vol. 60, no. 2, pp. 292-302, 2006.
S. Jeong, Rebeiz, M., Andolfatto, P., Werner, T., True, J., and Carroll, S. B., The evolution of gene regulation underlies a morphological difference between two Drosophila sister species., Cell, vol. 132, no. 5, pp. 783-93, 2008.
K. Thornton, Bachtrog, D., and Andolfatto, P., X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution., Genome Res, vol. 16, no. 4, pp. 498-504, 2006.
P. Andolfatto, Wong, K. M., and Bachtrog, D., Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species., Genome Biol Evol, vol. 3, pp. 114-28, 2011.

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