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: 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

2016
P. Koivunen, Fell, S. M., Lu, W., Rabinowitz, J. D., Kung, A. L., and Schlisio, S., The 2-oxoglutarate analog 3-oxoglutarate decreases normoxic hypoxia-inducible factor-1α in cancer cells, induces cell death, and reduces tumor xenograft growth., Hypoxia (Auckl), vol. 4, pp. 15-27, 2016.
C. Jang, Oh, S. F., Wada, S., Rowe, G. C., Liu, L., Chan, M. Chun, Rhee, J., Hoshino, A., Kim, B., Ibrahim, A., Baca, L. G., Kim, E., Ghosh, C. C., Parikh, S. M., Jiang, A., Chu, Q., Forman, D. E., Lecker, S. H., Krishnaiah, S., Rabinowitz, J. D., Weljie, A. M., Baur, J. A., Kasper, D. L., and Arany, Z., A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance., Nat Med, vol. 22, no. 4, pp. 421-6, 2016.
P. M. Titchenell, Quinn, W. J., Lu, M., Chu, Q., Lu, W., Li, C., Chen, H., Monks, B. R., Chen, J., Rabinowitz, J. D., and Birnbaum, M. J., Direct Hepatocyte Insulin Signaling Is Required for Lipogenesis but Is Dispensable for the Suppression of Glucose Production., Cell Metab, 2016.
A. M. Roberts, Wong, A. K., Fisk, I., and Troyanskaya, O. G., GIANT API: an application programming interface for functional genomics., Nucleic Acids Res, 2016.
A. Bren, Park, J. O., Towbin, B. D., Dekel, E., Rabinowitz, J. D., and Alon, U., Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP., Sci Rep, vol. 6, p. 24834, 2016.
X. Teng, Emmett, M. J., Lazar, M. A., Goldberg, E., and Rabinowitz, J. D., Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis., ACS Chem Biol, 2016.
L. Liu, Shah, S., Fan, J., Park, J. O., Wellen, K. E., and Rabinowitz, J. D., Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage., Nat Chem Biol, vol. 12, no. 5, pp. 345-52, 2016.
X. Su, Wellen, K. E., and Rabinowitz, J. D., Metabolic control of methylation and acetylation., Curr Opin Chem Biol, vol. 30, pp. 52-60, 2016.
J. O. Park, Rubin, S. A., Xu, Y. - F., Amador-Noguez, D., Fan, J., Shlomi, T., and Rabinowitz, J. D., Metabolite concentrations, fluxes and free energies imply efficient enzyme usage., Nat Chem Biol, 2016.
W. - X. Zong, Rabinowitz, J. D., and White, E., Mitochondria and Cancer., Mol Cell, vol. 61, no. 5, pp. 667-76, 2016.
J. D. Rabinowitz and Coller, H. A., Partners in the Warburg effect., Elife, vol. 5, 2016.
J. Zhou and Troyanskaya, O. G., Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states., Nat Commun, vol. 7, p. 10528, 2016.
G. S. Ducker, Chen, L., Morscher, R. J., Ghergurovich, J. M., Esposito, M., Teng, X., Kang, Y., and Rabinowitz, J. D., Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway., Cell Metab, 2016.
E. El-Sherif and Levine, M., Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo., Curr Biol, vol. 26, no. 9, pp. 1164-9, 2016.
E. K. Farley, Olson, K. M., Zhang, W., Rokhsar, D. S., and Levine, M. S., Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers., Proc Natl Acad Sci U S A, 2016.
T. Ferraro, Esposito, E., Mancini, L., Ng, S., Lucas, T., Coppey, M., Dostatni, N., Walczak, A. M., Levine, M., and Lagha, M., Transcriptional Memory in the Drosophila Embryo., Curr Biol, vol. 26, no. 2, pp. 212-8, 2016.
2015
Y. - F. Xu, Lu, W., and Rabinowitz, J. D., Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics., Anal Chem, vol. 87, no. 4, pp. 2273-81, 2015.
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.
A. Ochoa, Storey, J. D., Llinás, M., and Singh, M., Beyond the E-Value: Stratified Statistics for Protein Domain Prediction., PLoS Comput Biol, vol. 11, no. 11, p. e1004509, 2015.
P. A. Gibney, Schieler, A., Chen, J. C., Rabinowitz, J. D., and Botstein, D., Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter., Proc Natl Acad Sci U S A, 2015.
B. T Gainous, Wagner, E., and Levine, M., Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate., Dev Biol, 2015.
K. Oktaba, Zhang, W., Lotz, T. Sabrina, Jun, D. Jayhyun, Lemke, S. Beatrice, Ng, S. Pak, Esposito, E., Levine, M., and Hilgers, V., ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System., Mol Cell, vol. 57, no. 2, pp. 341-8, 2015.
J. P. Bothma, Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., and Levine, M., Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo., Elife, vol. 4, 2015.
J. G. Purdy, Shenk, T., and Rabinowitz, J. D., Fatty acid elongase 7 catalyzes lipidome remodeling essential for human cytomegalovirus replication., Cell Rep, vol. 10, no. 8, pp. 1375-85, 2015.
J. Goya, Wong, A. K., Yao, V., Krishnan, A., Homilius, M., and Troyanskaya, O. G., FNTM: a server for predicting functional networks of tissues in mouse., Nucleic Acids Res, 2015.
V. Lakhina and Murphy, C. T., For longevity, perception is everything., Cell, vol. 160, no. 5, pp. 807-9, 2015.
Y. Pritykin, Ghersi, D., and Singh, M., Genome-Wide Detection and Analysis of Multifunctional Genes., PLoS Comput Biol, vol. 11, no. 10, p. e1004467, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs., Neuron, vol. 85, no. 2, pp. 330-45, 2015.
J. J. Kamphorst, Nofal, M., Commisso, C., Hackett, S. R., Lu, W., Grabocka, E., Heiden, M. G. Vander, Miller, G., Drebin, J. A., Bar-Sagi, D., Thompson, C. B., and Rabinowitz, J. D., Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein., Cancer Res, vol. 75, no. 3, pp. 544-53, 2015.
A. K. Wong, Krishnan, A., Yao, V., Tadych, A., and Troyanskaya, O. G., IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks., Nucleic Acids Res, 2015.
K. Dolinski and Troyanskaya, O. G., Implications of Big Data for cell biology., Mol Biol Cell, vol. 26, no. 14, pp. 2575-8, 2015.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases., Immunity, vol. 43, no. 3, pp. 605-14, 2015.
M. Tikhonov, Leach, R. W., and Wingreen, N. S., Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution., ISME J, vol. 9, no. 1, pp. 68-80, 2015.
M. D. Chikina, Gerald, C. P., Li, X., Ge, Y., Pincas, H., Nair, V. D., Wong, A. K., Krishnan, A., Troyanskaya, O. G., Raymond, D., Saunders-Pullman, R., Bressman, S. B., Yue, Z., and Sealfon, S. C., Low-variance RNAs identify Parkinson's disease molecular signature in blood., Mov Disord, vol. 30, no. 6, pp. 813-21, 2015.
A. J. Bott, Peng, I. - C., Fan, Y., Faubert, B., Zhao, L., Li, J., Neidler, S., Sun, Y., Jaber, N., Krokowski, D., Lu, W., Pan, J. - A., Powers, S., Rabinowitz, J., Hatzoglou, M., Murphy, D. J., Jones, R., Wu, S., Girnun, G., and Zong, W. - X., Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation., Cell Metab, vol. 22, no. 6, pp. 1068-77, 2015.
S. Nadimpalli, Persikov, A. V., and Singh, M., Pervasive variation of transcription factor orthologs contributes to regulatory network evolution., PLoS Genet, vol. 11, no. 3, p. e1005011, 2015.
G. Tkačik, Dubuis, J. O., Petkova, M. D., and Gregor, T., Positional information, positional error, and readout precision in morphogenesis: a mathematical framework., Genetics, vol. 199, no. 1, pp. 39-59, 2015.
J. Zhou and Troyanskaya, O. G., Predicting effects of noncoding variants with deep learning-based sequence model., Nat Methods, 2015.
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.
W. W. K. Mok, Park, J. O., Rabinowitz, J. D., and Brynildsen, M. P., RNA Futile Cycling in Model Persisters Derived from MazF Accumulation., MBio, vol. 6, no. 6, pp. e01588-15, 2015.
J. M. Buescher, Antoniewicz, M. R., Boros, L. G., Burgess, S. C., Brunengraber, H., Clish, C. B., DeBerardinis, R. J., Feron, O., Frezza, C., Ghesquiere, B., Gottlieb, E., Hiller, K., Jones, R. G., Kamphorst, J. J., Kibbey, R. G., Kimmelman, A. C., Locasale, J. W., Lunt, S. Y., Maddocks, O. Dk, Malloy, C., Metallo, C. M., Meuillet, E. J., Munger, J., Nöh, K., Rabinowitz, J. D., Ralser, M., Sauer, U., Stephanopoulos, G., St-Pierre, J., Tennant, D. A., Wittmann, C., Heiden, M. G. Vander, Vazquez, A., Vousden, K., Young, J. D., Zamboni, N., and Fendt, S. - M., A roadmap for interpreting (13)C metabolite labeling patterns from cells., Curr Opin Biotechnol, vol. 34, pp. 189-201, 2015.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., Suboptimization of developmental enhancers., Science, vol. 350, no. 6258, pp. 325-8, 2015.
A. V. Persikov, Wetzel, J. L., Rowland, E. F., Oakes, B. L., Xu, D. J., Singh, M., and Noyes, M. B., A systematic survey of the Cys2His2 zinc finger DNA-binding landscape., Nucleic Acids Res, vol. 43, no. 3, pp. 1965-84, 2015.
Q. Zhu, Wong, A. K., Krishnan, A., Aure, M. R., Tadych, A., Zhang, R., Corney, D. C., Greene, C. S., Bongo, L. A., Kristensen, V. N., Charikar, M., Li, K., and Troyanskaya, O. G., Targeted exploration and analysis of large cross-platform human transcriptomic compendia., Nat Methods, vol. 12, no. 3, pp. 211-4, 3 p following 214, 2015.
N. V. Rajeshkumar, Dutta, P., Yabuuchi, S., de Wilde, R. F., Martinez, G. V., Le, A., Kamphorst, J. J., Rabinowitz, J. D., Jain, S. K., Hidalgo, M., Dang, C. V., Gillies, R. J., and Maitra, A., Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function., Cancer Res, vol. 75, no. 16, pp. 3355-64, 2015.
C. S. Greene, Krishnan, A., Wong, A. K., Ricciotti, E., Zelaya, R. A., Himmelstein, D. S., Zhang, R., Hartmann, B. M., Zaslavsky, E., Sealfon, S. C., Chasman, D. I., FitzGerald, G. A., Dolinski, K., Grosser, T., and Troyanskaya, O. G., Understanding multicellular function and disease with human tissue-specific networks., Nat Genet, vol. 47, no. 6, pp. 569-76, 2015.
G. S. Ducker and Rabinowitz, J. D., ZMP: a master regulator of one-carbon metabolism., Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
2014
B. He, Doubrovinski, K., Polyakov, O., and Wieschaus, E., Apical constriction drives tissue-scale hydrodynamic flow to mediate cell elongation., Nature, vol. 508, no. 7496, pp. 392-6, 2014.
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion., Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
G. Karsli-Uzunbas, Guo, J. Yanxiang, Price, S., Teng, X., Laddha, S. V., Khor, S., Kalaany, N. Y., Jacks, T., Chan, C. S., Rabinowitz, J. D., and White, E., Autophagy is required for glucose homeostasis and lung tumor maintenance., Cancer Discov, vol. 4, no. 8, pp. 914-27, 2014.
B. VanderSluis, Hess, D. C., Pesyna, C., Krumholz, E. W., Syed, T., Szappanos, B., Nislow, C., Papp, B., Troyanskaya, O. G., Myers, C. L., and Caudy, A. A., Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection., Genome Biol, vol. 15, no. 4, p. R64, 2014.
G. M. Stein and Murphy, C. T., C. elegans positive olfactory associative memory is a molecularly conserved behavioral paradigm., Neurobiol Learn Mem, vol. 115, pp. 86-94, 2014.
P. Jiang and Singh, M., CCAT: Combinatorial Code Analysis Tool for transcriptional regulation., Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
X. X. Du, Osterfield, M., and Shvartsman, S. Y., Computational analysis of three-dimensional epithelial morphogenesis using vertex models., Phys Biol, vol. 11, no. 6, p. 066007, 2014.
C. P. Broedersz, Wang, X., Meir, Y., Loparo, J. J., Rudner, D. Z., and Wingreen, N. S., Condensation and localization of the partitioning protein ParB on the bacterial chromosome., Proc Natl Acad Sci U S A, vol. 111, no. 24, pp. 8809-14, 2014.
M. Levine, The contraction of time and space in remote chromosomal interactions., Cell, vol. 158, no. 2, pp. 243-4, 2014.
R. G. Tepper, Murphy, C. T., and Bussemaker, H. J., DAF-16 and PQM-1: partners in longevity., Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
A. V. Persikov and Singh, M., De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins., Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets., Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., Design and analysis of Bar-seq experiments., G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
J. P. Bothma, Garcia, H. G., Esposito, E., Schlissel, G., Gregor, T., and Levine, M., Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos., Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
T. Gregor, Garcia, H. G., and Little, S. C., The embryo as a laboratory: quantifying transcription in Drosophila., Trends Genet, vol. 30, no. 8, pp. 364-75, 2014.
M. Castellana, Wilson, M. Z., Xu, Y., Joshi, P., Cristea, I. M., Rabinowitz, J. D., Gitai, Z., and Wingreen, N. S., Enzyme clustering accelerates processing of intermediates through metabolic channeling., Nat Biotechnol, vol. 32, no. 10, pp. 1011-8, 2014.
N. Haupaix, Abitua, P. B., Sirour, C., Yasuo, H., Levine, M., and Hudson, C., Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS., Dev Biol, vol. 394, no. 1, pp. 170-80, 2014.
J. Hwang, Purdy, J. G., Wu, K., Rabinowitz, J. D., and Shenk, T., Estrogen-related receptor α is required for efficient human cytomegalovirus replication., Proc Natl Acad Sci U S A, vol. 111, no. 52, pp. E5706-15, 2014.
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.
R. Mathew, Khor, S., Hackett, S. R., Rabinowitz, J. D., Perlman, D. H., and White, E., Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity., Mol Cell, vol. 55, no. 6, pp. 916-30, 2014.
J. Kim, Ghasemzadeh, N., Eapen, D. J., Chung, N. Christophe, Storey, J. D., Quyyumi, A. A., and Gibson, G., Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death., Genome Med, vol. 6, no. 5, p. 40, 2014.
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.
A. M. Berezhkovskii and Shvartsman, S. Y., On the GFP-based analysis of dynamic concentration profiles., Biophys J, vol. 106, no. 3, pp. L13-5, 2014.
J. Zhou and Troyanskaya, O. G., Global quantitative modeling of chromatin factor interactions., PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
L. Aristilde, Lewis, I. A., Park, J. O., and Rabinowitz, J. D., Hierarchy in Pentose Sugar Metabolism in Clostridium Acetobutylicum., Appl Environ Microbiol, 2014.
M. Schumer, Cui, R., Powell, D. L., Dresner, R., Rosenthal, G. G., and Andolfatto, P., High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species., Elife, vol. 3, 2014.
M. Schumer, Rosenthal, G. G., and Andolfatto, P., How common is homoploid hybrid speciation?, Evolution, vol. 68, no. 6, pp. 1553-60, 2014.
J. Fan, Teng, X., Liu, L., Mattaini, K. R., Looper, R. E., Heiden, M. G. Vander, and Rabinowitz, J. D., Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate., ACS Chem Biol, 2014.
T. T. Marstrand and Storey, J. D., Identifying and mapping cell-type-specific chromatin programming of gene expression., Proc Natl Acad Sci U S A, vol. 111, no. 6, pp. E645-54, 2014.
S. Neumann, Vladimirov, N., Krembel, A. K., Wingreen, N. S., and Sourjik, V., Imprecision of adaptation in Escherichia coli chemotaxis., PLoS One, vol. 9, no. 1, p. e84904, 2014.
D. Andrea Fer de Abreu, Caballero, A., Fardel, P., Stroustrup, N., Chen, Z., Lee, K., Keyes, W. D., Nash, Z. M., López-Moyado, I. F., Vaggi, F., Cornils, A., Regenass, M., Neagu, A., Ostojic, I., Liu, C., Cho, Y., Sifoglu, D., Shen, Y., Fontana, W., Lu, H., Csikasz-Nagy, A., Murphy, C. T., Antebi, A., Blanc, E., Apfeld, J., Zhang, Y., Alcedo, J., and Ch'ng, Q., An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology., PLoS Genet, vol. 10, no. 3, p. e1004225, 2014.
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
M. Castellana and Bialek, W., Inverse spin glass and related maximum entropy problems., Phys Rev Lett, vol. 113, no. 11, p. 117204, 2014.
R. L. Rogers, Cridland, J. M., Shao, L., Hu, T. T., Andolfatto, P., and Thornton, K. R., Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans., Mol Biol Evol, vol. 31, no. 7, pp. 1750-66, 2014.
R. M. Barry, Bitbol, A. - F., Lorestani, A., Charles, E. J., Habrian, C. H., Hansen, J. M., Li, H. - J., Baldwin, E. P., Wingreen, N. S., Kollman, J. M., and Gitai, Z., Large-scale filament formation inhibits the activity of CTP synthetase., Elife, vol. 3, p. e03638, 2014.
D. Botstein, Lasker∼Koshland to genetics pioneer., Cell, vol. 158, no. 6, pp. 1230-2, 2014.
M. Levine, Cattoglio, C., and Tjian, R., Looping back to leap forward: transcription enters a new era., Cell, vol. 157, no. 1, pp. 13-25, 2014.
D. Quigley, Silwal-Pandit, L., Dannenfelser, R., Langerod, A., Vollan, H. Kristian M., Vaske, C., Ursini-Siegel, J., Troyanskaya, O., Chin, S. - F., Caldas, C., Balmain, A., Borresen-Dale, A. - L., and Kristensen, V., Lymphocyte invasion in IC10/Basal-like breast tumors is associated with wild-type TP53., Mol Cancer Res, 2014.
G. J. Berman, Choi, D. M., Bialek, W., and Shaevitz, J. W., Mapping the stereotyped behaviour of freely moving fruit flies., J R Soc Interface, vol. 11, no. 99, 2014.
M. D. Petkova, Little, S. C., Liu, F., and Gregor, T., Maternal origins of developmental reproducibility., Curr Biol, vol. 24, no. 11, pp. 1283-8, 2014.
C. Shi and Murphy, C. T., Mating induces shrinking and death in Caenorhabditis mothers., Science, vol. 343, no. 6170, pp. 536-40, 2014.
S. Li, Stone, H. A., and Murphy, C. T., A microfluidic device and automatic counting system for the study of C. elegans reproductive aging., Lab Chip, 2014.
D. Ghersi and Singh, M., molBLOCKS: decomposing small molecule sets and uncovering enriched fragments., Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., Morphogenesis at criticality., Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
R. Balagam, Litwin, D. B., Czerwinski, F., Sun, M., Kaplan, H. B., Shaevitz, J. W., and Igoshin, O. A., Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility., PLoS Comput Biol, vol. 10, no. 5, p. e1003619, 2014.
T. Pilizota and Shaevitz, J. W., Origins of Escherichia coli Growth Rate and Cell Shape Changes at High External Osmolality., Biophys J, vol. 107, no. 8, pp. 1962-9, 2014.
O. Polyakov, He, B., Swan, M., Shaevitz, J. W., Kaschube, M., and Wieschaus, E., Passive mechanical forces control cell-shape change during Drosophila ventral furrow formation., Biophys J, vol. 107, no. 4, pp. 998-1010, 2014.
Z. Khan, Wang, Y. - C., Wieschaus, E. F., and Kaschube, M., Quantitative 4D analyses of epithelial folding during Drosophila gastrulation., Development, vol. 141, no. 14, pp. 2895-900, 2014.
J. J. Kamphorst, Chung, M. K., Fan, J., and Rabinowitz, J. D., Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate., Cancer Metab, vol. 2, p. 23, 2014.
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., Quantitative flux analysis reveals folate-dependent NADPH production., Nature, vol. 510, no. 7504, pp. 298-302, 2014.
M. Levine, Retrospective. Walter Gehring (1939-2014)., Science, vol. 345, no. 6194, p. 277, 2014.
R. L. Rogers, Shao, L., Sanjak, J. S., Andolfatto, P., and Thornton, K. R., Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group., G3 (Bethesda), vol. 4, no. 12, pp. 2345-51, 2014.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization., Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
C. A. Haselwandter and Wingreen, N. S., The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices., PLoS Comput Biol, vol. 10, no. 12, p. e1003932, 2014.
G. Tkačik, Marre, O., Amodei, D., Schneidman, E., Bialek, W., and Berry, M. J., Searching for collective behavior in a large network of sensory neurons., PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
J. Ye, Fan, J., Venneti, S., Wan, Y. - W., Pawel, B. R., Zhang, J., Finley, L. W. S., Lu, C., Lindsten, T., Cross, J. R., Qing, G., Liu, Z., M Simon, C., Rabinowitz, J. D., and Thompson, C. B., Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia., Cancer Discov, vol. 4, no. 12, pp. 1406-17, 2014.
S. Di Talia and Wieschaus, E. F., Simple biochemical pathways far from steady state can provide switchlike and integrated responses., Biophys J, vol. 107, no. 3, pp. L1-4, 2014.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Pohl, O., Silvestri, E., Viale, M., and Walczak, A. M., Social interactions dominate speed control in poising natural flocks near criticality., Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
K. Drescher, Nadell, C. D., Stone, H. A., Wingreen, N. S., and Bassler, B. L., Solutions to the public goods dilemma in bacterial biofilms., Curr Biol, vol. 24, no. 1, pp. 50-5, 2014.
Y. Deng, Sun, M., Lin, P. - H., Ma, J., and Shaevitz, J. W., Spatial covariance reconstructive (SCORE) super-resolution fluorescence microscopy., PLoS One, vol. 9, no. 4, p. e94807, 2014.
N. Christophe Chung and Storey, J. D., Statistical significance of variables driving systematic variation in high-dimensional data., Bioinformatics, 2014.
D. G. Robinson and Storey, J. D., subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling., Bioinformatics, vol. 30, no. 23, pp. 3424-6, 2014.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae., Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
C. Y. Park, Krishnan, A., Zhu, Q., Wong, A. K., Lee, Y. -suk, and Troyanskaya, O. G., Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms., Bioinformatics, 2014.
S. M. Tilghman, Twists and turns: a scientific journey., Annu Rev Cell Dev Biol, vol. 30, pp. 1-21, 2014.
A. G. Fletcher, Osterfield, M., Baker, R. E., and Shvartsman, S. Y., Vertex models of epithelial morphogenesis., Biophys J, vol. 106, no. 11, pp. 2291-304, 2014.
E. Wieschaus and Nüsslein-Volhard, C., Walter Gehring (1939–2014)., Curr Biol, vol. 24, no. 14, pp. R632-4, 2014.
B. L. Bassler and Wingreen, N. S., Working together at the interface of physics and biology., Phys Biol, vol. 11, no. 5, p. 053010, 2014.
S. Melody Foo, Sun, Y., Lim, B., Ziukaite, R., O'Brien, K., Nien, C. - Y., Kirov, N., Shvartsman, S. Y., and Rushlow, C. A., Zelda potentiates morphogen activity by increasing chromatin accessibility., Curr Biol, vol. 24, no. 12, pp. 1341-6, 2014.
2013
J. O. Dubuis, Samanta, R., and Gregor, T., Accurate measurements of dynamics and reproducibility in small genetic networks., Mol Syst Biol, vol. 9, p. 639, 2013.
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection., Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
K. Dolinski and Botstein, D., Automating the construction of gene ontologies., Nat Biotechnol, vol. 31, no. 1, pp. 34-5, 2013.
A. Munivenkatappa, Devi, B. Indira, Gregor, T. Issac, Bhat, D. I., Kumarsamy, A. Deepika, and Shukla, D. P., Bicycle accident-related head injuries in India., J Neurosci Rural Pract, vol. 4, no. 3, pp. 262-6, 2013.
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.
S. Wang and Wingreen, N. S., Cell shape can mediate the spatial organization of the bacterial cytoskeleton., Biophys J, vol. 104, no. 3, pp. 541-52, 2013.
J. I. Kliegman, Fiedler, D., Ryan, C. J., Xu, Y. - F., Su, X. - Y., Thomas, D., Caccese, M. C., Cheng, A., Shales, M., Rabinowitz, J. D., Krogan, N. J., and Shokat, K. M., Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae., Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
M. Skoge, Naqvi, S., Meir, Y., and Wingreen, N. S., Chemical sensing by nonequilibrium cooperative receptors., Phys Rev Lett, vol. 110, no. 24, p. 248102, 2013.
M. Skoge, Naqvi, S., Meir, Y., and Wingreen, N. S., Chemical Sensing by Nonequilibrium Cooperative Receptors., Phys Rev Lett, vol. 110, no. 24, 2013.
J. W. Shaevitz, Combining modeling and experiment to understand bacterial growth., Biophys J, vol. 104, no. 12, p. 2573, 2013.
Y. Guan, Dunham, M. J., Troyanskaya, O. G., and Caudy, A. A., Comparative gene expression between two yeast species., BMC Genomics, vol. 14, p. 33, 2013.
P. Jiang, Singh, M., and Coller, H. A., Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay., PLoS Comput Biol, vol. 9, no. 5, p. e1003075, 2013.
M. Levine, Computing away the magic?, Elife, vol. 2, p. e01135, 2013.
Y. Kim, Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., and Shvartsman, S. Y., Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo., Chaos, vol. 23, no. 2, p. 025105, 2013.
N. Slavov and Botstein, D., Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression., Mol Biol Cell, vol. 24, no. 2, pp. 157-68, 2013.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., Defining cell-type specificity at the transcriptional level in human disease., Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
J. Bothma and Levine, M., Development: lights, camera, action--the Drosophila embryo goes live!, Curr Biol, vol. 23, no. 21, pp. R965-7, 2013.
D. Ghersi and Singh, M., Disentangling function from topology to infer the network properties of disease genes., BMC Syst Biol, vol. 7, p. 5, 2013.
Y. - C. Wang, Khan, Z., and Wieschaus, E. F., Distinct Rap1 activity states control the extent of epithelial invagination via α-catenin., Dev Cell, vol. 25, no. 3, pp. 299-309, 2013.
F. Liu, Morrison, A. H., and Gregor, T., Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network., Proc Natl Acad Sci U S A, vol. 110, no. 17, pp. 6724-9, 2013.
L. S. Cheung, Simakov, D. S. A., Fuchs, A., Pyrowolakis, G., and Shvartsman, S. Y., Dynamic model for the coordination of two enhancers of broad by EGFR signaling., Proc Natl Acad Sci U S A, vol. 110, no. 44, pp. 17939-44, 2013.
Y. Deng, Coen, P., Sun, M., and Shaevitz, J. W., Efficient multiple object tracking using mutually repulsive active membranes., PLoS One, vol. 8, no. 6, p. e65769, 2013.
A. S. Futran, A Link, J., Seger, R., and Shvartsman, S. Y., ERK as a model for systems biology of enzyme kinetics in cells., Curr Biol, vol. 23, no. 21, pp. R972-9, 2013.
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.
J. Song and Singh, M., From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization., PLoS Comput Biol, vol. 9, no. 2, p. e1002910, 2013.
C. Y. Park, Wong, A. K., Greene, C. S., Rowland, J., Guan, Y., Bongo, L. A., Burdine, R. D., and Troyanskaya, O. G., Functional knowledge transfer for high-accuracy prediction of under-studied biological processes., PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
C. Reisser, Dick, C., Kruglyak, L., Botstein, D., Schacherer, J., and Hess, D., Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case., G3 (Bethesda), 2013.
R. B. Corbett-Detig, Zhou, J., Clark, A. G., Hartl, D. L., and Ayroles, J. F., Genetic incompatibilities are widespread within species., Nature, vol. 504, no. 7478, pp. 135-7, 2013.
J. Fan, Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., and Rabinowitz, J. D., Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia., Mol Syst Biol, vol. 9, p. 712, 2013.
J. J. Kamphorst, Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., and Rabinowitz, J. D., Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids., Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
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.
C. T. Murphy and Hu, P. J., Insulin/insulin-like growth factor signaling in C. elegans., WormBook, pp. 1-43, 2013.
B. Lim, Samper, N., Lu, H., Rushlow, C., Jiménez, G., and Shvartsman, S. Y., Kinetics of gene derepression by ERK signaling., Proc Natl Acad Sci U S A, vol. 110, no. 25, pp. 10330-5, 2013.
A. M. Berezhkovskii and Shvartsman, S. Y., Kinetics of receptor occupancy during morphogen gradient formation., J Chem Phys, vol. 138, no. 24, p. 244105, 2013.
P. V. Gordon, Muratov, C. B., and Shvartsman, S. Y., Local accumulation times for source, diffusion, and degradation models in two and three dimensions., J Chem Phys, vol. 138, no. 10, p. 104121, 2013.
K. Rajan and Bialek, W., Maximally informative "stimulus energies" in the analysis of neural responses to natural signals., PLoS One, vol. 8, no. 11, p. e71959, 2013.
S. Wang and Shaevitz, J. W., The mechanics of shape in prokaryotes., Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
T. J. Levario, Zhan, M., Lim, B., Shvartsman, S. Y., and Lu, H., Microfluidic trap array for massively parallel imaging of Drosophila embryos., Nat Protoc, vol. 8, no. 4, pp. 721-36, 2013.
A. A. Caudy, Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., J Breunig, S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. - H. Huang, Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinás, M., Botstein, D., Troyanskaya, O. G., and Dunham, M. J., A new system for comparative functional genomics of Saccharomyces yeasts., Genetics, vol. 195, no. 1, pp. 275-87, 2013.
D. Bruce Borenstein, Meir, Y., Shaevitz, J. W., and Wingreen, N. S., Non-local interaction via diffusible resource prevents coexistence of cooperators and cheaters in a lattice model., PLoS One, vol. 8, no. 5, p. e63304, 2013.
Y. - F. Xu, Létisse, F., Absalan, F., Lu, W., Kuznetsova, E., Brown, G., Caudy, A. A., Yakunin, A. F., Broach, J. R., and Rabinowitz, J. D., Nucleotide degradation and ribose salvage in yeast., Mol Syst Biol, vol. 9, p. 665, 2013.
Y. -suk Lee, Krishnan, A., Zhu, Q., and Troyanskaya, O. G., Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies., Bioinformatics, vol. 29, no. 23, pp. 3036-44, 2013.
M. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo., Cell, vol. 153, no. 5, pp. 976-87, 2013.
G. I. Lang, Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., and Desai, M. M., Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations., Nature, vol. 500, no. 7464, pp. 571-4, 2013.
P. A. Gibney, Hickman, M. J., Bradley, P. H., Matese, J. C., and Botstein, D., Phylogenetic portrait of the Saccharomyces cerevisiae functional genome., G3 (Bethesda), vol. 3, no. 8, pp. 1335-40, 2013.
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.
T. Pilizota and Shaevitz, J. W., Plasmolysis and cell shape depend on solute outer-membrane permeability during hyperosmotic shock in E. coli., Biophys J, vol. 104, no. 12, pp. 2733-42, 2013.
J. O. Dubuis, Tkačik, G., Wieschaus, E. F., Gregor, T., and Bialek, W., Positional information, in bits., Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
S. Di Talia, She, R., Blythe, S. A., Lu, X., Zhang, Q. Fan, and Wieschaus, E. F., Posttranslational control of Cdc25 degradation terminates Drosophila's early cell-cycle program., Curr Biol, vol. 23, no. 2, pp. 127-32, 2013.
R. G. Tepper, Ashraf, J., Kaletsky, R., Kleemann, G., Murphy, C. T., and Bussemaker, H. J., PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity., Cell, vol. 154, no. 3, pp. 676-90, 2013.
S. C. Little, Tikhonov, M., and Gregor, T., Precise developmental gene expression arises from globally stochastic transcriptional activity., Cell, vol. 154, no. 4, pp. 789-800, 2013.
R. S. Dwyer, Ricci, D. P., Colwell, L. J., Silhavy, T. J., and Wingreen, N. S., Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis., Genetics, vol. 195, no. 2, pp. 443-55, 2013.
M. Louis Reaves, Young, B. D., Hosios, A. M., Xu, Y. - F., and Rabinowitz, J. D., Pyrimidine homeostasis is accomplished by directed overflow metabolism., Nature, vol. 500, no. 7461, pp. 237-41, 2013.
W. Bialek, QnAs with William Bialek., Proc Natl Acad Sci U S A, vol. 110, no. 41, p. 16288, 2013.
H. G. Garcia, Tikhonov, M., Lin, A., and Gregor, T., Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning., Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
S. R McIsaac, Oakes, B. L., Botstein, D., and Noyes, M. B., Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters., J Vis Exp, no. 81, p. e51153, 2013.
E. Koyuncu, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny., PLoS Pathog, vol. 9, no. 5, p. e1003333, 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.
Y. Pritykin and Singh, M., Simple topological features reflect dynamics and modularity in protein interaction networks., PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
S. C. Little and Gregor, T., Sorting sloppy Sonic., Cell, vol. 153, no. 3, pp. 509-10, 2013.
G. J. Stephens, Mora, T., Tkačik, G., and Bialek, W., Statistical thermodynamics of natural images., Phys Rev Lett, vol. 110, no. 1, p. 018701, 2013.
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast., Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
M. Osterfield, Du, X. X., Schüpbach, T., Wieschaus, E., and Shvartsman, S. Y., Three-dimensional epithelial morphogenesis in the developing Drosophila egg., Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae., Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
S. R McIsaac, Silverman, S. J., Parsons, L., Xu, P., Briehof, R., McClean, M. N., and Botstein, D., Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae., J Vis Exp, no. 76, p. e50382, 2013.
P. A. Gibney, Lu, C., Caudy, A. A., Hess, D. C., and Botstein, D., Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes., Proc Natl Acad Sci U S A, vol. 110, no. 46, pp. E4393-402, 2013.
2012
M. Louis Reaves, Sinha, S., Rabinowitz, J. D., Kruglyak, L., and Redfield, R. J., Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells., Science, vol. 337, no. 6093, pp. 470-3, 2012.
C. S. Greene and Troyanskaya, O. G., Accurate evaluation and analysis of functional genomics data and methods., Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
G. Jiménez, Shvartsman, S. Y., and Paroush, Z. 'ev, The Capicua repressor--a general sensor of RTK signaling in development and disease., J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 2012.
C. S. Greene and Troyanskaya, O. G., Chapter 2: Data-driven view of disease biology., PLoS Comput Biol, vol. 8, no. 12, p. e1002816, 2012.
A. A. Petti, R McIsaac, S., Ho-Shing, O., Bussemaker, H. J., and Botstein, D., Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway., Mol Biol Cell, vol. 23, no. 15, pp. 3008-24, 2012.
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes., Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
Y. - C. Wang, Khan, Z., Kaschube, M., and Wieschaus, E. F., Differential positioning of adherens junctions is associated with initiation of epithelial folding., Nature, vol. 484, no. 7394, pp. 390-3, 2012.
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.
M. D. Chikina and Troyanskaya, O. G., An effective statistical evaluation of ChIPseq dataset similarity., Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
D. S. A. Simakov, Cheung, L. S., Pismen, L. M., and Shvartsman, S. Y., EGFR-dependent network interactions that pattern Drosophila eggshell appendages., Development, vol. 139, no. 15, pp. 2814-20, 2012.
V. Hilgers, Lemke, S. B., and Levine, M., ELAV mediates 3' UTR extension in the Drosophila nervous system., Genes Dev, vol. 26, no. 20, pp. 2259-64, 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.
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.
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. M. Cooper, Wingreen, N. S., and Cox, E. C., An excitable cortex and memory model successfully predicts new pseudopod dynamics., PLoS One, vol. 7, no. 3, p. e33528, 2012.
T. Pilizota and Shaevitz, J. W., Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli., PLoS One, vol. 7, no. 4, p. e35205, 2012.
E. Wagner and Levine, M., FGF signaling establishes the anterior border of the Ciona neural tube., Development, vol. 139, no. 13, pp. 2351-9, 2012.
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.

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