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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2015
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., “Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.”, Science, vol. 348, no. 6239, pp. 1139-43, 2015.
2013
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.
2012
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.
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.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., “Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.”, PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
2011
J. F. Ayroles, Laflamme, B. A., Stone, E. A., Wolfner, M. F., and Mackay, T. F. C., “Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks.”, Genet Res (Camb), vol. 93, no. 6, pp. 387-95, 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.
2009
T. V. Morozova, Ayroles, J. F., Jordan, K. W., Duncan, L. H., Carbone, M. Anna, Lyman, R. F., Stone, E. A., Govindaraju, D. R., R Ellison, C., Mackay, T. F. C., and Anholt, R. R. H., “Alcohol sensitivity in Drosophila: translational potential of systems genetics.”, Genetics, vol. 183, no. 2, pp. 733-45, 1SI-12SI, 2009.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., “Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep.”, Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
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.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
2008
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.
2007
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.
2006
F. Biemar, Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., J Manak, R., and Levine, M. S., “Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.”, Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
D. Papatsenko, Kislyuk, A., Levine, M., and Dubchak, I., “Conservation patterns in different functional sequence categories of divergent Drosophila species.”, Genomics, vol. 88, no. 4, pp. 431-42, 2006.