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

Filters: First Letter Of Last Name is W  [Clear All Filters]
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
A
A. L. Webber and Tilghman, S. M., The absence of enhancer competition between Igf2 and H19 following transfer into differentiated cells., Mol Cell Biol, vol. 18, no. 4, pp. 1903-10, 1998.
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by cell-surface receptors., Prog Biophys Mol Biol, vol. 100, no. 1-3, pp. 33-9, 2009.
R. G. Endres and Wingreen, N. S., Accuracy of direct gradient sensing by single cells., Proc Natl Acad Sci U S A, vol. 105, no. 41, pp. 15749-54, 2008.
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., Achieving optimal growth through product feedback inhibition in metabolism., PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria., Proc Natl Acad Sci U S A, vol. 107, no. 20, pp. 9182-5, 2010.
D. Swanson and Wingreen, N. S., Active biopolymers confer fast reorganization kinetics., Phys Rev Lett, vol. 107, no. 21, p. 218103, 2011.
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.
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.
H. A. Müller and Wieschaus, E., armadillo, bazooka, and stardust are critical for early stages in formation of the zonula adherens and maintenance of the polarized blastoderm epithelium in Drosophila., J Cell Biol, vol. 134, no. 1, pp. 149-63, 1996.
N. S. Tolwinski and Wieschaus, E., Armadillo nuclear import is regulated by cytoplasmic anchor Axin and nuclear anchor dTCF/Pan., Development, vol. 128, no. 11, pp. 2107-17, 2001.
N. N. Pavlova, Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., and Zhang, J., As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid., Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
E. Wieschaus and Riggleman, R., Autonomous requirements for the segment polarity gene armadillo during Drosophila embryogenesis., Cell, vol. 49, no. 2, pp. 177-84, 1987.
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
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.
L. Poillet-Perez, Xie, X., Zhan, L., Yang, Y., Sharp, D. W., Hu, Z. Sherrie, Su, X., Maganti, A., Jiang, C., Lu, W., Zheng, H., Bosenberg, M. W., Mehnert, J. M., Guo, J. Yanxiang, Lattime, E., Rabinowitz, J. D., and White, E., Autophagy maintains tumour growth through circulating arginine., Nature, vol. 563, no. 7732, pp. 569-573, 2018.
J. Yanxiang Guo, Teng, X., Laddha, S. V., Ma, S., Van Nostrand, S. C., Yang, Y., Khor, S., Chan, C. S., Rabinowitz, J. D., and White, E., Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells., Genes Dev, vol. 30, no. 15, pp. 1704-17, 2016.
B
N. Wingreen and Botstein, D., Back to the future: education for systems-level biologists., Nat Rev Mol Cell Biol, vol. 7, no. 11, pp. 829-32, 2006.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., The bacterial actin MreB rotates, and rotation depends on cell-wall assembly., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., The bacterial actin MreB rotates, and rotation depends on cell-wall assembly., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
J. Mohler and Wieschaus, E. F., Bicaudal mutations of Drosophila melanogaster: alteration of blastoderm cell fate., Cold Spring Harb Symp Quant Biol, vol. 50, pp. 105-11, 1985.
O. Grimm and Wieschaus, E., The Bicoid gradient is shaped independently of nuclei., Development, vol. 137, no. 17, pp. 2857-62, 2010.
R. C. Oslund, Su, X., Haugbro, M., Kee, J. - M., Esposito, M., David, Y., Wang, B., Ge, E., Perlman, D. H., Kang, Y., Muir, T. W., and Rabinowitz, J. D., Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate., Nat Chem Biol, vol. 13, no. 10, pp. 1081-1087, 2017.
E. D. Schejter and Wieschaus, E., bottleneck acts as a regulator of the microfilament network governing cellularization of the Drosophila embryo., Cell, vol. 75, no. 2, pp. 373-85, 1993.
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.
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.
R. E. Dawes-Hoang, Zallen, J. A., and Wieschaus, E. F., Bringing classical embryology to C elegans gastrulation., Dev Cell, vol. 4, no. 1, pp. 6-8, 2003.
C
R. Kaletsky, Lakhina, V., Arey, R., Williams, A., Landis, J., Ashraf, J., and Murphy, C. T., The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators., Nature, vol. 529, no. 7584, pp. 92-6, 2016.
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.
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.
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.
R. E. Dawes-Hoang and Wieschaus, E. F., Cell and developmental biology--a shared past, an intertwined future., Dev Cell, vol. 1, no. 1, pp. 27-36, 2001.
X. Lu, Drocco, J., and Wieschaus, E. F., Cell cycle regulation via inter-nuclear communication during the early embryonic development of Drosophila melanogaster., Cell Cycle, vol. 9, no. 14, pp. 2908-10, 2010.
K. D. Irvine and Wieschaus, E., Cell intercalation during Drosophila germband extension and its regulation by pair-rule segmentation genes., Development, vol. 120, no. 4, pp. 827-41, 1994.
J. Szabad, Schupbach, T., and Wieschaus, E., Cell lineage and development in the larval epidermis of Drosophila melanogaster., Dev Biol, vol. 73, no. 2, pp. 256-71, 1979.
E. Wieschaus, Cell lineage relationships in the Drosophila embryo., Results Probl Cell Differ, vol. 9, pp. 97-118, 1978.
S. B. Zusman and Wieschaus, E., A cell marker system and mosaic patterns during early embryonic development in Drosophila melanogaster., Genetics, vol. 115, no. 4, pp. 725-36, 1987.
K. Casey Huang, Mukhopadhyay, R., Wen, B., Gitai, Z., and Wingreen, N. S., Cell shape and cell-wall organization in Gram-negative bacteria., Proc Natl Acad Sci U S A, vol. 105, no. 49, pp. 19282-7, 2008.
K. Casey Huang, Mukhopadhyay, R., Wen, B., Gitai, Z., and Wingreen, N. S., Cell shape and cell-wall organization in Gram-negative bacteria., Proc Natl Acad Sci U S A, vol. 105, no. 49, pp. 19282-7, 2008.
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.
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. Wang, Kaletsky, R., Silva, M., Williams, A., Haas, L. A., Androwski, R. J., Landis, J. N., Patrick, C., Rashid, A., Santiago-Martinez, D., Gravato-Nobre, M., Hodgkin, J., Hall, D. H., Murphy, C. T., and Barr, M. M., Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis., Curr Biol, vol. 25, no. 24, pp. 3232-8, 2015.
J. Wang, Kaletsky, R., Silva, M., Williams, A., Haas, L. A., Androwski, R. J., Landis, J. N., Patrick, C., Rashid, A., Santiago-Martinez, D., Gravato-Nobre, M., Hodgkin, J., Hall, D. H., Murphy, C. T., and Barr, M. M., Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis., Curr Biol, vol. 25, no. 24, pp. 3232-8, 2015.
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. E. Keymer, Endres, R. G., Skoge, M., Meir, Y., and Wingreen, N. S., Chemosensing in Escherichia coli: two regimes of two-state receptors., Proc Natl Acad Sci U S A, vol. 103, no. 6, pp. 1786-91, 2006.
C. H. Hansen, Endres, R. G., and Wingreen, N. S., Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation., PLoS Comput Biol, vol. 4, no. 1, p. e1, 2008.
R. G. Endres, Falke, J. J., and Wingreen, N. S., Chemotaxis receptor complexes: from signaling to assembly., PLoS Comput Biol, vol. 3, no. 7, p. e150, 2007.
M. Stadlmeier, Runtsch, L. Simon, Streshnev, F., Wühr, M., and Carell, T., A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry., Chembiochem, 2019.
E. Wieschaus and Gehring, W., Clonal analysis of primordial disc cells in the early embryo of Drosophila melanogaster., Dev Biol, vol. 50, no. 2, pp. 249-63, 1976.
E. Wieschaus, Audit, C., and Masson, M., A clonal analysis of the roles of somatic cells and germ line during oogenesis in Drosophila., Dev Biol, vol. 88, no. 1, pp. 92-103, 1981.
E. Wieschaus, A combined genetic and mosaic approach to the study of oogenesis in Drosophila., Basic Life Sci, vol. 16, pp. 85-94, 1980.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., Comprehensive single-cell transcriptome lineages of a proto-vertebrate., Nature, vol. 571, no. 7765, pp. 349-354, 2019.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., Comprehensive single-cell transcriptome lineages of a proto-vertebrate., Nature, vol. 571, no. 7765, pp. 349-354, 2019.
S. H Wiley, Shvartsman, S. Y., and Lauffenburger, D. A., Computational modeling of the EGF-receptor system: a paradigm for systems biology., Trends Cell Biol, vol. 13, no. 1, pp. 43-50, 2003.
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.
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.
C. Hunter, Sung, P., Schejter, E. D., and Wieschaus, E., Conserved domains of the Nullo protein required for cell-surface localization and formation of adherens junctions., Mol Biol Cell, vol. 13, no. 1, pp. 146-57, 2002.
J. Grosshans, H Müller, A. J., and Wieschaus, E., Control of cleavage cycles in Drosophila embryos by frühstart., Dev Cell, vol. 5, no. 2, pp. 285-94, 2003.
D. N. Keys, Levine, M., Harland, R. M., and Wallingford, J. B., Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis., Dev Biol, vol. 246, no. 2, pp. 329-40, 2002.
N. S. Wingreen and Levin, S. A., Cooperation among microorganisms., PLoS Biol, vol. 4, no. 9, p. e299, 2006.
C. Rauskolb and Wieschaus, E., Coordinate regulation of downstream genes by extradenticle and the homeotic selector proteins., EMBO J, vol. 13, no. 15, pp. 3561-9, 1994.
J. M. Goodliffe, Cole, M. D., and Wieschaus, E., Coordinated regulation of Myc trans-activation targets by Polycomb and the Trithorax group protein Ash1., BMC Mol Biol, vol. 8, p. 40, 2007.
S. P. Gross, Welte, M. A., Block, S. M., and Wieschaus, E. F., Coordination of opposite-polarity microtubule motors., J Cell Biol, vol. 156, no. 4, pp. 715-24, 2002.
S. P. Gross, Welte, M. A., Block, S. M., and Wieschaus, E. F., Coordination of opposite-polarity microtubule motors., J Cell Biol, vol. 156, no. 4, pp. 715-24, 2002.
X. Lu, Li, J. M., Elemento, O., Tavazoie, S., and Wieschaus, E. F., Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition., Development, vol. 136, no. 12, pp. 2101-10, 2009.
L. Peña-Castillo, Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. Kyu, Krumpelman, C., Tian, W., Obozinski, G., Qi, Y., Mostafavi, S., Lin, G. Ning, Berriz, G. F., Gibbons, F. D., Lanckriet, G., Qiu, J., Grant, C., Barutcuoglu, Z., Hill, D. P., Warde-Farley, D., Grouios, C., Ray, D., Blake, J. A., Deng, M., Jordan, M. I., Noble, W. S., Morris, Q., Klein-Seetharaman, J., Bar-Joseph, iv, Z., Chen, T., Sun, F., Troyanskaya, O. G., Marcotte, E. M., Xu, D., Hughes, T. R., and Roth, F. P., A critical assessment of Mus musculus gene function prediction using integrated genomic evidence., Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
R. Mukhopadhyay and Wingreen, N. S., Curvature and shape determination of growing bacteria., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 6 Pt 1, p. 062901, 2009.
K. Casey Huang, Mukhopadhyay, R., and Wingreen, N. S., A curvature-mediated mechanism for localization of lipids to bacterial poles., PLoS Comput Biol, vol. 2, no. 11, p. e151, 2006.
D
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.
E. G. Emberly, Wingreen, N. S., and Tang, C., Designability of alpha-helical proteins., Proc Natl Acad Sci U S A, vol. 99, no. 17, pp. 11163-8, 2002.
H. Li, Tang, C., and Wingreen, N. S., Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix., Proteins, vol. 49, no. 3, pp. 403-12, 2002.
E. Wieschaus and Szabad, J., The development and function of the female germ line in Drosophila melanogaster: a cell lineage study., Dev Biol, vol. 68, no. 1, pp. 29-46, 1979.
M. A. Welte, Gross, S. P., Postner, M., Block, S. M., and Wieschaus, E. F., Developmental regulation of vesicle transport in Drosophila embryos: forces and kinetics., Cell, vol. 92, no. 4, pp. 547-57, 1998.
M. A. Welte, Gross, S. P., Postner, M., Block, S. M., and Wieschaus, E. F., Developmental regulation of vesicle transport in Drosophila embryos: forces and kinetics., Cell, vol. 92, no. 4, pp. 547-57, 1998.
S. Zhao, Jang, C., Liu, J., Uehara, K., Gilbert, M., Izzo, L., Zeng, X., Trefely, S., Fernandez, S., Carrer, A., Miller, K. D., Schug, Z. T., Snyder, N. W., Gade, T. P., Titchenell, P. M., Rabinowitz, J. D., and Wellen, K. E., Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate., Nature, vol. 579, no. 7800, pp. 586-591, 2020.
S. Neumann, Hansen, C. H., Wingreen, N. S., and Sourjik, V., Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis., EMBO J, vol. 29, no. 20, pp. 3484-95, 2010.
W. Ndifon, Wingreen, N. S., and Levin, S. A., Differential neutralization efficiency of hemagglutinin epitopes, antibody interference, and the design of influenza vaccines., Proc Natl Acad Sci U S A, vol. 106, no. 21, pp. 8701-6, 2009.
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.
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. Gregor, Bialek, W., van Steveninck, R. R. de Ruyte, Tank, D. W., and Wieschaus, E. F., Diffusion and scaling during early embryonic pattern formation., Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18403-7, 2005.
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors., Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors., Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
C. L. Myers, Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G., Discovery of biological networks from diverse functional genomic data., Genome Biol, vol. 6, no. 13, p. R114, 2005.
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.
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.
J. Isaac Murray, Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O., and Botstein, D., Diverse and specific gene expression responses to stresses in cultured human cells., Mol Biol Cell, vol. 15, no. 5, pp. 2361-74, 2004.
H. Zhao, Whitfield, M. L., Xu, T., Botstein, D., and Brooks, J. D., Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells., Mol Biol Cell, vol. 15, no. 2, pp. 506-19, 2004.
B. T Gainous, Wagner, E., and Levine, M., Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate., Dev Biol, 2015.
M. E. Garber, Troyanskaya, O. G., Schluens, K., Petersen, S., Thaesler, Z., Pacyna-Gengelbach, M., van de Rijn, M., Rosen, G. D., Perou, C. M., Whyte, R. I., Altman, R. B., Brown, P. O., Botstein, D., and Petersen, I., Diversity of gene expression in adenocarcinoma of the lung., Proc Natl Acad Sci U S A, vol. 98, no. 24, pp. 13784-9, 2001.
S. R McIsaac, Huang, K. Casey, Sengupta, A., and Wingreen, N. S., Does the potential for chaos constrain the embryonic cell-cycle oscillator?, PLoS Comput Biol, vol. 7, no. 7, p. e1002109, 2011.
J. Mohler and Wieschaus, E. F., Dominant maternal-effect mutations of Drosophila melanogaster causing the production of double-abdomen embryos., Genetics, vol. 112, no. 4, pp. 803-22, 1986.
S. De Renzis, Yu, J., Zinzen, R., and Wieschaus, E., Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway., Dev Cell, vol. 10, no. 2, pp. 257-64, 2006.
J. P. Gergen and Wieschaus, E., Dosage requirements for runt in the segmentation of Drosophila embryos., Cell, vol. 45, no. 2, pp. 289-99, 1986.
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.
L. S. Rose and Wieschaus, E., The Drosophila cellularization gene nullo produces a blastoderm-specific transcript whose levels respond to the nucleocytoplasmic ratio., Genes Dev, vol. 6, no. 7, pp. 1255-68, 1992.
S. Parks and Wieschaus, E., The Drosophila gastrulation gene concertina encodes a G alpha-like protein., Cell, vol. 64, no. 2, pp. 447-58, 1991.
A. Jaźwińska, Kirov, N., Wieschaus, E., Roth, S., and Rushlow, C., The Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation., Cell, vol. 96, no. 4, pp. 563-73, 1999.
S. Hayashi, Rubinfeld, B., Souza, B., Polakis, P., Wieschaus, E., and Levine, A. J., A Drosophila homolog of the tumor suppressor gene adenomatous polyposis coli down-regulates beta-catenin but its zygotic expression is not essential for the regulation of Armadillo., Proc Natl Acad Sci U S A, vol. 94, no. 1, pp. 242-7, 1997.
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.
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.
K. Casey Huang, Meir, Y., and Wingreen, N. S., Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones., Proc Natl Acad Sci U S A, vol. 100, no. 22, pp. 12724-8, 2003.
M. Skoge, Meir, Y., and Wingreen, N. S., Dynamics of cooperativity in chemical sensing among cell-surface receptors., Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
C. H. Hansen, Sourjik, V., and Wingreen, N. S., A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli., Proc Natl Acad Sci U S A, vol. 107, no. 40, pp. 17170-5, 2010.
S. P. Gross, Welte, M. A., Block, S. M., and Wieschaus, E. F., Dynein-mediated cargo transport in vivo. A switch controls travel distance., J Cell Biol, vol. 148, no. 5, pp. 945-56, 2000.
S. P. Gross, Welte, M. A., Block, S. M., and Wieschaus, E. F., Dynein-mediated cargo transport in vivo. A switch controls travel distance., J Cell Biol, vol. 148, no. 5, pp. 945-56, 2000.
E
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.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Electroporation of transgenic DNAs in the sea squirt Ciona., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5345, 2009.
E. Wieschaus, Embryonic transcription and the control of developmental pathways., Genetics, vol. 142, no. 1, pp. 5-10, 1996.
J. Miller, Zeng, C., Wingreen, N. S., and Tang, C., Emergence of highly designable protein-backbone conformations in an off-lattice model., Proteins, vol. 47, no. 4, pp. 506-12, 2002.
V. Yao, Wong, A. K., and Troyanskaya, O. G., Enabling Precision Medicine through Integrative Network Models., J Mol Biol, vol. 430, no. 18 Pt A, pp. 2913-2923, 2018.
J. - T. Chi, Chang, H. Y., Haraldsen, G., Jahnsen, F. L., Troyanskaya, O. G., Chang, D. S., Wang, Z., Rockson, S. G., van de Rijn, M., Botstein, D., and Brown, P. O., Endothelial cell diversity revealed by global expression profiling., Proc Natl Acad Sci U S A, vol. 100, no. 19, pp. 10623-8, 2003.
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina., Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
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.
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.
M. S. Bartolomei, Webber, A. L., Brunkow, M. E., and Tilghman, S. M., Epigenetic mechanisms underlying the imprinting of the mouse H19 gene., Genes Dev, vol. 7, no. 9, pp. 1663-73, 1993.
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.
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.
S. Hsin- Jung Li, Li, Z., Park, J. O., King, C. G., Rabinowitz, J. D., Wingreen, N. S., and Gitai, Z., Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions., Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.
B. Houchmandzadeh, Wieschaus, E., and Leibler, S., Establishment of developmental precision and proportions in the early Drosophila embryo., Nature, vol. 415, no. 6873, pp. 798-802, 2002.
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.
M. Wyart, Botstein, D., and Wingreen, N. S., Evaluating gene expression dynamics using pairwise RNA FISH data., PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
M. Wyart, Botstein, D., and Wingreen, N. S., Evaluating gene expression dynamics using pairwise RNA FISH data., PLoS Comput Biol, vol. 6, no. 11, p. e1000979, 2010.
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. S. Weitz, Benfey, P. N., and Wingreen, N. S., Evolution, interactions, and biological networks., PLoS Biol, vol. 5, no. 1, p. e11, 2007.
J. S. Weitz, Benfey, P. N., and Wingreen, N. S., Evolution, interactions, and biological networks., PLoS Biol, vol. 5, no. 1, p. e11, 2007.
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.
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.
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.
R. Nash, Weng, S., Hitz, B., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Livstone, M. S., Oughtred, R., Park, J., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Dolinski, K., Botstein, D., and J Cherry, M., Expanded protein information at SGD: new pages and proteome browser., Nucleic Acids Res, vol. 35, no. Database issue, pp. D468-71, 2007.
P. Mehta, Mukhopadhyay, R., and Wingreen, N. S., Exponential sensitivity of noise-driven switching in genetic networks., Phys Biol, vol. 5, no. 2, p. 026005, 2008.
J. J. Zartman, Kanodia, J. S., Yakoby, N., Schafer, X., Watson, C., Schlichting, K., Dahmann, C., and Shvartsman, S. Y., Expression patterns of cadherin genes in Drosophila oogenesis., Gene Expr Patterns, vol. 9, no. 1, pp. 31-6, 2009.
W. Lu, Wang, L., Chen, L., Hui, S., and Rabinowitz, J. D., Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors., Antioxid Redox Signal, 2017.
C. Rauskolb, Peifer, M., and Wieschaus, E., extradenticle, a regulator of homeotic gene activity, is a homolog of the homeobox-containing human proto-oncogene pbx1., Cell, vol. 74, no. 6, pp. 1101-12, 1993.
C. Rauskolb, Smith, K. M., Peifer, M., and Wieschaus, E., extradenticle determines segmental identities throughout Drosophila development., Development, vol. 121, no. 11, pp. 3663-73, 1995.
F
N. Zhang, Zeng, C., and Wingreen, N. S., Fast accurate evaluation of protein solvent exposure., Proteins, vol. 57, no. 3, pp. 565-76, 2004.
T. Schupbach and Wieschaus, E., Female sterile mutations on the second chromosome of Drosophila melanogaster. I. Maternal effect mutations., Genetics, vol. 121, no. 1, pp. 101-17, 1989.
T. Schupbach and Wieschaus, E., Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking oogenesis or altering egg morphology., Genetics, vol. 129, no. 4, pp. 1119-36, 1991.
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.
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., Filament depolymerization can explain chromosome pulling during bacterial mitosis., PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
E. G. Emberly, Mukhopadhyay, R., Wingreen, N. S., and Tang, C., Flexibility of alpha-helices: results of a statistical analysis of database protein structures., J Mol Biol, vol. 327, no. 1, pp. 229-37, 2003.
E. G. Emberly, Mukhopadhyay, R., Tang, C., and Wingreen, N. S., Flexibility of beta-sheets: principal component analysis of database protein structures., Proteins, vol. 55, no. 1, pp. 91-8, 2004.
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.
R. E. Dawes-Hoang, Parmar, K. M., Christiansen, A. E., Phelps, C. B., Brand, A. H., and Wieschaus, E. F., folded gastrulation, cell shape change and the control of myosin localization., Development, vol. 132, no. 18, pp. 4165-78, 2005.
S. C. Little, Tkačik, G., Kneeland, T. B., Wieschaus, E. F., and Gregor, T., The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA., PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
L. Bahati Tanner, Goglia, A. G., Wei, M. H., Sehgal, T., Parsons, L. R., Park, J. O., White, E., Toettcher, J. E., and Rabinowitz, J. D., Four Key Steps Control Glycolytic Flux in Mammalian Cells., Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
L. Bahati Tanner, Goglia, A. G., Wei, M. H., Sehgal, T., Parsons, L. R., Park, J. O., White, E., Toettcher, J. E., and Rabinowitz, J. D., Four Key Steps Control Glycolytic Flux in Mammalian Cells., Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
K. D. Irvine and Wieschaus, E., fringe, a Boundary-specific signaling molecule, mediates interactions between dorsal and ventral cells during Drosophila wing development., Cell, vol. 79, no. 4, pp. 595-606, 1994.
E. D. Schejter and Wieschaus, E., Functional elements of the cytoskeleton in the early Drosophila embryo., Annu Rev Cell Biol, vol. 9, pp. 67-99, 1993.
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.
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.
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.
R. Balakrishnan, Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D., and J Cherry, M., Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)., Nucleic Acids Res, vol. 33, no. Database issue, pp. D374-7, 2005.
G
D. Sweeton, Parks, S., Costa, M., and Wieschaus, E., Gastrulation in Drosophila: the formation of the ventral furrow and posterior midgut invaginations., Development, vol. 112, no. 3, pp. 775-89, 1991.
D. E. Coulter and Wieschaus, E., Gene activities and segmental patterning in Drosophila: analysis of odd-skipped and pair-rule double mutants., Genes Dev, vol. 2, no. 12B, pp. 1812-23, 1988.
S. C. Linn, West, R. B., Pollack, J. R., Zhu, S., Hernandez-Boussard, T., Nielsen, T. O., Rubin, B. P., Patel, iv, R., Goldblum, J. R., Siegmund, D., Botstein, D., Brown, P. O., C Gilks, B., and van de Rijn, M., Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans., Am J Pathol, vol. 163, no. 6, pp. 2383-95, 2003.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I., Gene expression patterns in ovarian carcinomas., Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A., Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme., Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
H. Y. Chang, Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. - T., van de Rijn, M., Botstein, D., and Brown, P. O., Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds., PLoS Biol, vol. 2, no. 2, p. E7, 2004.
E. L. Hong, Balakrishnan, R., Dong, Q., Christie, K. R., Park, J., Binkley, G., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R. S., Oughtred, R., Skrzypek, M. S., Weng, S., Wong, E. D., Zhu, K. K., Dolinski, K., Botstein, D., and J Cherry, M., Gene Ontology annotations at SGD: new data sources and annotation methods., Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.
E. L. Hong, Balakrishnan, R., Dong, Q., Christie, K. R., Park, J., Binkley, G., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R. S., Oughtred, R., Skrzypek, M. S., Weng, S., Wong, E. D., Zhu, K. K., Dolinski, K., Botstein, D., and J Cherry, M., Gene Ontology annotations at SGD: new data sources and annotation methods., Nucleic Acids Res, vol. 36, no. Database issue, pp. D577-81, 2008.
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.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
J. Grosshans and Wieschaus, E., A genetic link between morphogenesis and cell division during formation of the ventral furrow in Drosophila., Cell, vol. 101, no. 5, pp. 523-31, 2000.
J. E. Hirschman, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D., and J Cherry, M., Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome., Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
J. E. Hirschman, Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D., and J Cherry, M., Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome., Nucleic Acids Res, vol. 34, no. Database issue, pp. D442-5, 2006.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder., Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
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.
J. L. Marsh, van Deusen, E. B., Wieschaus, E., and Gehring, W. J., Germ line dependence of the deep orange maternal effect in Drosophila., Dev Biol, vol. 56, no. 1, pp. 195-9, 1977.
T. Schupbach and Wieschaus, E., Germline autonomy of maternal-effect mutations altering the embryonic body pattern of Drosophila., Dev Biol, vol. 113, no. 2, pp. 443-8, 1986.
J. L. Marsh and Wieschaus, E., Germ-line dependence of the maroon-like maternal effect in Drosophila., Dev Biol, vol. 60, no. 2, pp. 396-403, 1977.
A. K. Wong, Krishnan, A., and Troyanskaya, O. G., GIANT 2.0: genome-scale integrated analysis of gene networks in tissues., Nucleic Acids Research, vol. 46, no. W1, pp. W65-W70, 2018.
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.
E. Kruus, Thumfort, P., Tang, C., and Wingreen, N. S., Gibbs sampling and helix-cap motifs., Nucleic Acids Res, vol. 33, no. 16, pp. 5343-53, 2005.
J. A. Brown, Sherlock, G., Myers, C. L., Burrows, N. M., Deng, C., H Wu, I., McCann, K. E., Troyanskaya, O. G., and J Brown, M., Global analysis of gene function in yeast by quantitative phenotypic profiling., Mol Syst Biol, vol. 2, p. 2006.0001, 2006.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
S. Hui, Ghergurovich, J. M., Morscher, R. J., Jang, C., Teng, X., Lu, W., Esparza, L. A., Reya, T., Guo, J. Yanxiang, White, E., and Rabinowitz, J. D., Glucose feeds the TCA cycle via circulating lactate., Nature, vol. 551, no. 7678, pp. 115-118, 2017.
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.
E. I. Boyle, Weng, S., Gollub, J., Jin, H., Botstein, D., J Cherry, M., and Sherlock, G., GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes., Bioinformatics, vol. 20, no. 18, pp. 3710-5, 2004.
S. Goyal and Wingreen, N. S., Growth-induced instability in metabolic networks., Phys Rev Lett, vol. 98, no. 13, p. 138105, 2007.
H
S. Wang, Furchtgott, L., Huang, K. Casey, and Shaevitz, J. W., Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall., Proc Natl Acad Sci U S A, vol. 109, no. 10, pp. E595-604, 2012.
K. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., Host-parasite interactions revealed by Plasmodium falciparum metabolomics., Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
E. Emberly and Wingreen, N. S., Hourglass model for a protein-based circadian oscillator., Phys Rev Lett, vol. 96, no. 3, p. 038303, 2006.
P. L. Nara, Tobin, G. J., A Chaudhuri, R., Trujillo, J. D., Lin, G., Cho, M. W., Levin, S. A., Ndifon, W., and Wingreen, N. S., How can vaccines against influenza and other viral diseases be made more effective?, PLoS Biol, vol. 8, no. 12, p. e1000571, 2010.
J. - L. Li, Car, R., Tang, C., and Wingreen, N. S., Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water., Proc Natl Acad Sci U S A, vol. 104, no. 8, pp. 2626-30, 2007.
P. Morize, Christiansen, A. E., Costa, M., Parks, S., and Wieschaus, E., Hyperactivation of the folded gastrulation pathway induces specific cell shape changes., Development, vol. 125, no. 4, pp. 589-97, 1998.
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.
I
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.
R. J. Pelham, Rodgers, L., Hall, I., Lucito, R., Nguyen, K. C. Q., Navin, N., Hicks, J., Mu, D., Powers, S., Wigler, M., and Botstein, D., Identification of alterations in DNA copy number in host stromal cells during tumor progression., Proc Natl Acad Sci U S A, vol. 103, no. 52, pp. 19848-53, 2006.
M. L. Whitfield, Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., and Botstein, D., Identification of genes periodically expressed in the human cell cycle and their expression in tumors., Mol Biol Cell, vol. 13, no. 6, pp. 1977-2000, 2002.
L. Chen, Wolf, A. B., Fu, W., Li, L., and Akey, J. M., Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals., Cell, vol. 180, no. 4, pp. 677-687.e16, 2020.
E. G. Emberly, Miller, J., Zeng, C., Wingreen, N. S., and Tang, C., Identifying proteins of high designability via surface-exposure patterns., Proteins, vol. 47, no. 3, pp. 295-304, 2002.
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.
A. K. Wong, Park, C. Y., Greene, C. S., Bongo, L. A., Guan, Y., and Troyanskaya, O. G., IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks., Nucleic Acids Res, vol. 40, no. Web Server issue, pp. W484-90, 2012.
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.
C. L. Vizcarra, Zhang, N., Marshall, S. A., Wingreen, N. S., Zeng, C., and Mayo, S. L., An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design., J Comput Chem, vol. 29, no. 7, pp. 1153-62, 2008.
B. M. Zee, Levin, R. S., Xu, B., LeRoy, G., Wingreen, N. S., and Garcia, B. A., In vivo residue-specific histone methylation dynamics., J Biol Chem, vol. 285, no. 5, pp. 3341-50, 2010.

Pages