List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

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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.
A. L. Wooldridge, Bischof, R. J., Liu, H., Heinemann, G. K., Hunter, D. S., Giles, L. C., Simmons, R. A., Lien, Y. - C., Lu, W., Rabinowitz, J. D., Kind, K. L., Owens, J. A., Clifton, V. L., and Gatford, K. L., “Late gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR.”, Am J Physiol Regul Integr Comp Physiol, p. ajpregu.00549.2016, 2017.
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. 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.
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. B. Wolf and Akey, J. M., “Outstanding questions in the study of archaic hominin admixture.”, PLoS Genet, vol. 14, no. 5, p. e1007349, 2018.
N. S. Wingreen, “Physics. Quantum many-body effects in a single-electron transistor.”, Science, vol. 304, no. 5675, pp. 1258-9, 2004.
N. S. Wingreen and Levin, S. A., “Cooperation among microorganisms.”, PLoS Biol, vol. 4, no. 9, p. e299, 2006.
N. S. Wingreen, Miller, J., and Cox, E. C., “Scaling of mutational effects in models for pleiotropy.”, Genetics, vol. 164, no. 3, pp. 1221-8, 2003.
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.
D. J. Wilson, Hernandez, R. D., Andolfatto, P., and Przeworski, M., “A population genetics-phylogenetics approach to inferring natural selection in coding sequences.”, PLoS Genet, vol. 7, no. 12, p. e1002395, 2011.
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.
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.
E. Wieschaus and Sweeton, D., “Requirements for X-linked zygotic gene activity during cellularization of early Drosophila embryos.”, Development, vol. 104, no. 3, pp. 483-93, 1988.
E. Wieschaus, Perrimon, N., and Finkelstein, R., “orthodenticle activity is required for the development of medial structures in the larval and adult epidermis of Drosophila.”, Development, vol. 115, no. 3, pp. 801-11, 1992.
E. Wieschaus, Nusslein-Volhard, C., and Kluding, H., “Krüppel, a gene whose activity is required early in the zygotic genome for normal embryonic segmentation.”, Dev Biol, vol. 104, no. 1, pp. 172-86, 1984.
E. Wieschaus, “Embryonic transcription and the control of developmental pathways.”, Genetics, vol. 142, no. 1, pp. 5-10, 1996.
E. Wieschaus and Nüsslein-Volhard, C., “Walter Gehring (1939–2014).”, Curr Biol, vol. 24, no. 14, pp. R632-4, 2014.
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.
E. Wieschaus, “A combined genetic and mosaic approach to the study of oogenesis in Drosophila.”, Basic Life Sci, vol. 16, pp. 85-94, 1980.
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 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, “Cell lineage relationships in the Drosophila embryo.”, Results Probl Cell Differ, vol. 9, pp. 97-118, 1978.
E. Wieschaus and Nöthiger, R., “The role of the transformer genes in the development of genitalia and analia of Drosophila melanogaster.”, Dev Biol, vol. 90, no. 2, pp. 320-34, 1982.
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.
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
J. L. Wetzel and Singh, M., “Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.”, Nucleic Acids Res, vol. 48, no. 2, p. e9, 2020.
S. Weng, Dong, Q., Balakrishnan, R., Christie, K., Costanzo, M., Dolinski, K., Dwight, S. S., Engel, S., Fisk, D. G., Hong, E., Issel-Tarver, L., Sethuraman, A., Theesfeld, C., Andrada, R., Binkley, G., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M., “Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.”, Nucleic Acids Res, vol. 31, no. 1, pp. 216-8, 2003.
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.
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.
J. S. Weitz, Benfey, P. N., and Wingreen, N. S., “Evolution, interactions, and biological networks.”, PLoS Biol, vol. 5, no. 1, p. e11, 2007.
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.
A. L. Webber, Ingram, R. S., Levorse, J. M., and Tilghman, S. M., “Location of enhancers is essential for the imprinting of H19 and Igf2 genes.”, Nature, vol. 391, no. 6668, pp. 711-5, 1998.
E. Watson, Olin-Sandoval, V., Hoy, M. J., Li, C. - H., Louisse, T., Yao, V., Mori, A., Holdorf, A. D., Troyanskaya, O. G., Ralser, M., and Walhout, A. Jm, “Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.”, Elife, vol. 5, 2016.
C. M. Waters, Lu, W., Rabinowitz, J. D., and Bassler, B. L., “Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT.”, J Bacteriol, vol. 190, no. 7, pp. 2527-36, 2008.
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.
Y. Wang, Tu, K. C., Ong, N. P., Bassler, B. L., and Wingreen, N. S., “Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit.”, Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
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.
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
L. Wang, Xing, X., Chen, L., Yang, L., Su, X., Rabitz, H., Lu, W., and Rabinowitz, J. D., “Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics.”, Anal Chem, vol. 91, no. 3, pp. 1838-1846, 2019.
S. Wang and Shaevitz, J. W., “The mechanics of shape in prokaryotes.”, Front Biosci (Schol Ed), vol. 5, pp. 564-74, 2013.
W. Wang, Ishibashi, J., Trefely, S., Shao, M., Cowan, A. J., Sakers, A., Lim, H. - W., O'Connor, S., Doan, M. T., Cohen, P., Baur, J. A., M King, T., Veech, R. L., Won, K. - J., Rabinowitz, J. D., Snyder, N. W., Gupta, R. K., and Seale, P., “A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate.”, Cell Metab, vol. 30, no. 1, pp. 174-189.e5, 2019.
S. Wang, Arellano-Santoyo, H., Combs, P. A., and Shaevitz, J. W., “Measuring the bending stiffness of bacterial cells using an optical trap.”, J Vis Exp, no. 38, 2010.
W. Wang, J Cherry, M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H., “Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.”, Proc Natl Acad Sci U S A, vol. 102, no. 6, pp. 1998-2003, 2005.
L. Wang, Xing, X., Zeng, X., S Jackson, R. E., TeSlaa, T., Al-Dalahmah, O., Samarah, L. Z., Goodwin, K., Yang, L., McReynolds, M. R., Li, X., Wolff, J. J., Rabinowitz, J. D., and Davidson, S. M., “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
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.
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., 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.
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
H. Wang, Wingreen, N. S., and Mukhopadhyay, R., “Self-organized periodicity of protein clusters in growing bacteria.”, Phys Rev Lett, vol. 101, no. 21, p. 218101, 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.
G. Wallace, Anshus, O. J., Bi, P., Chen, H., Chen, Y., Clark, D., Cook, P., Finkelstein, A., Funkhouser, T., Gupta, A., Hibbs, M., Li, K., Liu, Z., Samanta, R., Sukthankar, R., and Troyanskaya, O., “Tools and applications for large-scale display walls.”, IEEE Comput Graph Appl, vol. 25, no. 4, pp. 24-33, 2005.
J. D. Wall, Andolfatto, P., and Przeworski, M., “Testing models of selection and demography in Drosophila simulans.”, Genetics, vol. 162, no. 1, pp. 203-16, 2002.
A. M. Walczak, Tkačik, G., and Bialek, W., “Optimizing information flow in small genetic networks. II. Feed-forward interactions.”, Phys Rev E Stat Nonlin Soft Matter Phys, vol. 81, no. 4 Pt 1, p. 041905, 2010.
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.