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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A
J. F. Ayroles, Hughes, K. A., Rowe, K. C., Reedy, M. M., Rodriguez-Zas, S. L., Drnevich, J. M., Cáceres, C. E., and Paige, K. N., “A genomewide assessment of inbreeding depression: gene number, function, and mode of action.”, Conserv Biol, vol. 23, no. 4, pp. 920-30, 2009.
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.
J. F. Ayroles, Buchanan, S. M., O'Leary, C., Skutt-Kakaria, K., Grenier, J. K., Clark, A. G., Hartl, D. L., and de Bivort, B. L., “Behavioral idiosyncrasy reveals genetic control of phenotypic variability.”, Proc Natl Acad Sci U S A, vol. 112, no. 21, pp. 6706-11, 2015.
J. F. Ayroles and Gibson, G., “Analysis of variance of microarray data.”, Methods Enzymol, vol. 411, pp. 214-33, 2006.
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.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., “Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.”, Genome Biol, vol. 14, no. 11, p. R126, 2013.
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W., “Nobel laureates' letter to President Bush.”, Washington Post, p. A02, 2001.
P. Armand, Knapp, A. C., Hirsch, A. J., Wieschaus, E. F., and Cole, M. D., “A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.”, Mol Cell Biol, vol. 14, no. 6, pp. 4145-54, 1994.
L. Aristilde, Lewis, I. A., Park, J. O., and Rabinowitz, J. D., “Hierarchy in Pentose Sugar Metabolism in Clostridium Acetobutylicum.”, Appl Environ Microbiol, 2014.
R. N. Arey and Murphy, C. T., “Conserved regulators of cognitive aging: From worms to humans.”, Behav Brain Res, vol. 322, no. Pt B, pp. 299-310, 2017.
P. Anikeeva, Boyden, E., Brangwynne, C., Troyanskaya, O., and al., et., “Voices in methods development.”, Nat Methods, vol. 16, no. 10, pp. 945-951, 2019.
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.
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.
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.
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, 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.
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.
P. Andolfatto, “Adaptive evolution of non-coding DNA in Drosophila.”, Nature, vol. 437, no. 7062, pp. 1149-52, 2005.
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
D. Amador-Noguez, Feng, X. - J., Fan, J., Roquet, N., Rabitz, H., and Rabinowitz, J. D., “Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum.”, J Bacteriol, vol. 192, no. 17, pp. 4452-61, 2010.
O. Alter, Brown, P. O., and Botstein, D., “Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.”, Proc Natl Acad Sci U S A, vol. 100, no. 6, pp. 3351-6, 2003.
E. M. Airoldi, Huttenhower, C., Gresham, D., Lu, C., Caudy, A. A., Dunham, M. J., Broach, J. R., Botstein, D., and Troyanskaya, O. G., “Predicting cellular growth from gene expression signatures.”, PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
Y. Ahmed, Hayashi, S., Levine, A., and Wieschaus, E., “Regulation of armadillo by a Drosophila APC inhibits neuronal apoptosis during retinal development.”, Cell, vol. 93, no. 7, pp. 1171-82, 1998.
Y. Ahmed, Nouri, A., and Wieschaus, E., “Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development.”, Development, vol. 129, no. 7, pp. 1751-62, 2002.
B. Agüera y Arcas, Fairhall, A. L., and Bialek, W., “Computation in a single neuron: Hodgkin and Huxley revisited.”, Neural Comput, vol. 15, no. 8, pp. 1715-49, 2003.
T. L. Adelman, Bialek, W., and Olberg, R. M., “The information content of receptive fields.”, Neuron, vol. 40, no. 4, pp. 823-33, 2003.
L. Abouchar, Petkova, M. D., Steinhardt, C. R., and Gregor, T., “Fly wing vein patterns have spatial reproducibility of a single cell.”, J R Soc Interface, vol. 11, no. 97, p. 20140443, 2014.
P. Barron Abitua, Wagner, E., Navarrete, I. A., and Levine, M., “Identification of a rudimentary neural crest in a non-vertebrate chordate.”, Nature, vol. 492, no. 7427, pp. 104-7, 2012.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M., “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
E. A. Abbondanzieri, Shaevitz, J. W., and Block, S. M., “Picocalorimetry of transcription by RNA polymerase.”, Biophys J, vol. 89, no. 6, pp. L61-3, 2005.
E. A. Abbondanzieri, Greenleaf, W. J., Shaevitz, J. W., Landick, R., and Block, S. M., “Direct observation of base-pair stepping by RNA polymerase.”, Nature, vol. 438, no. 7067, pp. 460-5, 2005.
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.