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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Journal Article
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi., Mol Syst Biol, vol. 7, p. 491, 2011.
L. R. Swem, Swem, D. L., Wingreen, N. S., and Bassler, B. L., Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi., Cell, vol. 134, no. 3, pp. 461-73, 2008.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk., Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
S. R. McAllister, Feng, X. - J., DiMaggio, P. A., Floudas, C. A., Rabinowitz, J. D., and Rabitz, H., Descriptor-free molecular discovery in large libraries by adaptive substituent reordering., Bioorg Med Chem Lett, vol. 18, no. 22, pp. 5967-70, 2008.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., Epistasis dominates the genetic architecture of Drosophila quantitative traits., Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 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. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., Genetic architecture and adaptive significance of the selfing syndrome in Capsella., Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
J. S. Breunig, Hackett, S. R., Rabinowitz, J. D., and Kruglyak, L., Genetic basis of metabolome variation in yeast., PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
T. F. C. Mackay, Stone, E. A., and Ayroles, J. F., The genetics of quantitative traits: challenges and prospects., Nat Rev Genet, vol. 10, no. 8, pp. 565-77, 2009.
A. Massouras, Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C., and Deplancke, B., Genomic variation and its impact on gene expression in Drosophila melanogaster., PLoS Genet, vol. 8, no. 11, p. e1003055, 2012.
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations., Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
P. Mehta, Goyal, S., Long, T., Bassler, B. L., and Wingreen, N. S., Information processing and signal integration in bacterial quorum sensing., Mol Syst Biol, vol. 5, p. 325, 2009.
S. - W. Teng, Wang, Y., Tu, K. C., Long, T., Mehta, P., Wingreen, N. S., Bassler, B. L., and Ong, N. P., Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell., Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
J. Yuan, Doucette, C. D., Fowler, W. U., Feng, X. - J., Piazza, M., Rabitz, H. A., Wingreen, N. S., and Rabinowitz, J. D., Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli., Mol Syst Biol, vol. 5, p. 302, 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.
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.
K. C. Tu, Long, T., Svenningsen, S. L., Wingreen, N. S., and Bassler, B. L., Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response., Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
T. Gregor, Fujimoto, K., Masaki, N., and Sawai, S., The onset of collective behavior in social amoebae., Science, vol. 328, no. 5981, pp. 1021-5, 2010.
J. M. Goodliffe, Wieschaus, E., and Cole, M. D., Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila., Genes Dev, vol. 19, no. 24, pp. 2941-6, 2005.
W. - L. Ng, Wei, Y., Perez, L. J., Cong, J., Long, T., Koch, M., Semmelhack, M. F., Wingreen, N. S., and Bassler, B. L., Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules., Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5575-80, 2010.
Y. Wang, Tu, K. C., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit., Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
T. Long, Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Quantifying the integration of quorum-sensing signals with single-cell resolution., PLoS Biol, vol. 7, no. 3, p. e68, 2009.
C. M. Waters, Lu, W., Rabinowitz, J. D., and Bassler, B. L., Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT., J Bacteriol, vol. 190, no. 7, pp. 2527-36, 2008.
O. G. Troyanskaya, Arbell, O., Koren, Y., Landau, G. M., and Bolshoy, A., Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity., Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
J. Gollub, Ball, C. A., Binkley, G., Demeter, J., Finkelstein, D. B., Hebert, J. M., Hernandez-Boussard, T., Jin, H., Kaloper, M., Matese, J. C., Schroeder, M., Brown, P. O., Botstein, D., and Sherlock, G., The Stanford Microarray Database: data access and quality assessment tools., Nucleic Acids Res, vol. 31, no. 1, pp. 94-6, 2003.
S. T. H. Liu, Sharon-Friling, R., Ivanova, P., Milne, S. B., Myers, D. S., Rabinowitz, J. D., H Brown, A., and Shenk, T., Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress., Proc Natl Acad Sci U S A, vol. 108, no. 31, pp. 12869-74, 2011.
S. T. H. Liu, Sharon-Friling, R., Ivanova, P., Milne, S. B., Myers, D. S., Rabinowitz, J. D., H Brown, A., and Shenk, T., Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress., Proc Natl Acad Sci U S A, vol. 108, no. 31, pp. 12869-74, 2011.
P. Jumbo-Lucioni, Ayroles, J. F., Chambers, M. Moses, Jordan, K. W., Leips, J., Mackay, T. Fc, and De Luca, M., Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster., BMC Genomics, vol. 11, p. 297, 2010.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., Systems genetics of complex traits in Drosophila melanogaster., Nat Genet, vol. 41, no. 3, pp. 299-307, 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.
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.
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA., Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
A. J. Pompeani, Irgon, J. J., Berger, M. F., Bulyk, M. L., Wingreen, N. S., and Bassler, B. L., The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters., Mol Microbiol, vol. 70, no. 1, pp. 76-88, 2008.