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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H
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.
C. Huttenhower, Hibbs, M., Myers, C., and Troyanskaya, O. G., A scalable method for integration and functional analysis of multiple microarray datasets., Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
C. Huttenhower, K Mutungu, T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., and Coller, H. A., Detailing regulatory networks through large scale data integration., Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
C. Huttenhower, Flamholz, A. I., Landis, J. N., Sahi, S., Myers, C. L., Olszewski, K. L., Hibbs, M. A., Siemers, N. O., Troyanskaya, O. G., and Coller, H. A., Nearest Neighbor Networks: clustering expression data based on gene neighborhoods., BMC Bioinformatics, vol. 8, p. 250, 2007.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
C. Huttenhower and Troyanskaya, O. G., Bayesian data integration: a functional perspective., Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
C. Huttenhower and Troyanskaya, O. G., Assessing the functional structure of genomic data., Bioinformatics, vol. 24, no. 13, pp. i330-8, 2008.
C. Huttenhower, Hibbs, M. A., Myers, C. L., Caudy, A. A., Hess, D. C., and Troyanskaya, O. G., The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction., Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
C. Huttenhower, Mehmood, S. O., and Troyanskaya, O. G., Graphle: Interactive exploration of large, dense graphs., BMC Bioinformatics, vol. 10, p. 417, 2009.
C. Huttenhower, Schroeder, M., Chikina, M. D., and Troyanskaya, O. G., The Sleipnir library for computational functional genomics., Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
C. Huttenhower, Haley, E. M., Hibbs, M. A., Dumeaux, V., Barrett, D. R., Coller, H. A., and Troyanskaya, O. G., Exploring the human genome with functional maps., Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
C. Hunter and Wieschaus, E., Regulated expression of nullo is required for the formation of distinct apical and basal adherens junctions in the Drosophila blastoderm., J Cell Biol, vol. 150, no. 2, pp. 391-401, 2000.
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.
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.
S. Hui and Rabinowitz, J. D., An unexpected trigger for calorie burning in brown fat., Nature, vol. 560, no. 7716, pp. 38-39, 2018.
K. A. Hughes, Ayroles, J. F., Reedy, M. M., Drnevich, J. M., Rowe, K. C., Ruedi, E. A., Cáceres, C. E., and Paige, K. N., Segregating variation in the transcriptome: cis regulation and additivity of effects., Genetics, vol. 173, no. 3, pp. 1347-55, 2006.
J. P. Huelsenbeck and Andolfatto, P., Inference of population structure under a Dirichlet process model., Genetics, vol. 175, no. 4, pp. 1787-802, 2007.
J. P. Huelsenbeck, Andolfatto, P., and Huelsenbeck, E. T., Structurama: bayesian inference of population structure., Evol Bioinform Online, vol. 7, pp. 55-9, 2011.
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.
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.
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.
K. Casey Huang, Ehrhardt, D. W., and Shaevitz, J. W., The molecular origins of chiral growth in walled cells., Curr Opin Microbiol, vol. 15, no. 6, pp. 707-14, 2012.
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 and Wingreen, N. S., Min-protein oscillations in round bacteria., Phys Biol, vol. 1, no. 3-4, pp. 229-35, 2004.
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.
A. - L. Hsu, Murphy, C. T., and Kenyon, C., Regulation of aging and age-related disease by DAF-16 and heat-shock factor., Science, vol. 300, no. 5622, pp. 1142-5, 2003.
B. H. Hristov and Singh, M., Network-Based Coverage of Mutational Profiles Reveals Cancer Genes., Cell Syst, vol. 5, no. 3, pp. 221-229.e4, 2017.
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.
B. Houchmandzadeh, Wieschaus, E., and Leibler, S., Precise domain specification in the developing Drosophila embryo., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 72, no. 6 Pt 1, p. 061920, 2005.
J. - W. Hong, Hendrix, D. A., Papatsenko, D., and Levine, M. S., How the Dorsal gradient works: insights from postgenome technologies., Proc Natl Acad Sci U S A, vol. 105, no. 51, pp. 20072-6, 2008.
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion., Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
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.
J. - W. Hong, Hendrix, D. A., and Levine, M. S., Shadow enhancers as a source of evolutionary novelty., Science, vol. 321, no. 5894, p. 1314, 2008.
C. Hei Ho, Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., L Y Koh, J., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M., and Boone, C., A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds., Nat Biotechnol, vol. 27, no. 4, pp. 369-77, 2009.
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.
K. Hirose, Meir, Y., and Wingreen, N. S., Local moment formation in quantum point contacts., Phys Rev Lett, vol. 90, no. 2, p. 026804, 2003.
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.
V. Hilgers, Perry, M. W., Hendrix, D., Stark, A., Levine, M., and Haley, B., Neural-specific elongation of 3' UTRs during Drosophila development., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15864-9, 2011.
M. J. Hickman, Petti, A. A., Ho-Shing, O., Silverman, S. J., R McIsaac, S., Lee, T. A., and Botstein, D., Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast., Mol Biol Cell, vol. 22, no. 21, pp. 4192-204, 2011.
M. A. Hibbs, Myers, C. L., Huttenhower, C., Hess, D. C., Li, K., Caudy, A. A., and Troyanskaya, O. G., Directing experimental biology: a case study in mitochondrial biogenesis., PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
M. A. Hibbs, Dirksen, N. C., Li, K., and Troyanskaya, O. G., Visualization methods for statistical analysis of microarray clusters., BMC Bioinformatics, vol. 6, p. 115, 2005.
M. A. Hibbs, Hess, D. C., Myers, C. L., Huttenhower, C., Li, K., and Troyanskaya, O. G., Exploring the functional landscape of gene expression: directed search of large microarray compendia., Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis., PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
D. C. Hess, Lu, W., Rabinowitz, J. D., and Botstein, D., Ammonium toxicity and potassium limitation in yeast., PLoS Biol, vol. 4, no. 11, p. e351, 2006.
D. Hermans, Gautam, S., García-Cañaveras, J. C., Gromer, D., Mitra, S., Spolski, R., Li, P., Christensen, S., Nguyen, R., Lin, J. - X., Oh, J., Du, N., Veenbergen, S., Fioravanti, J., Ebina-Shibuya, R., Bleck, C., Neckers, L. M., Rabinowitz, J. D., Gattinoni, L., and Leonard, W. J., Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity., Proc Natl Acad Sci U S A, vol. 117, no. 11, pp. 6047-6055, 2020.
D. A. Hendrix, Hong, J. - W., Zeitlinger, J., Rokhsar, D. S., and Levine, M. S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 105, no. 22, pp. 7762-7, 2008.
D. Hendrix, Levine, M., and Shi, W., miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data., Genome Biol, vol. 11, no. 4, p. R39, 2010.
A. Helman, Lim, B., Andreu, M. José, Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., and Paroush, Z. 'ev, RTK signaling modulates the Dorsal gradient., Development, vol. 139, no. 16, pp. 3032-9, 2012.
T. Heist, Fukaya, T., and Levine, M., Large distances separate coregulated genes in living embryos., Proc Natl Acad Sci U S A, vol. 116, no. 30, pp. 15062-15067, 2019.
S. Heinicke, Livstone, M. S., Lu, C., Oughtred, R., Kang, F., Angiuoli, S. V., White, O., Botstein, D., and Dolinski, K., The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists., PLoS One, vol. 2, no. 8, p. e766, 2007.
J. Akiko Heck, Gresham, D., Botstein, D., and Alani, E., Accumulation of recessive lethal mutations in Saccharomyces cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements., Genetics, vol. 174, no. 1, pp. 519-23, 2006.
B. He, Caudy, A., Parsons, L., Rosebrock, A., Pane, A., Raj, S., and Wieschaus, E., Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster., Genome Res, vol. 22, no. 12, pp. 2507-19, 2012.
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.
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.
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.
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.
A. T. Hark, Schoenherr, C. J., Katz, D. J., Ingram, R. S., Levorse, J. M., and Tilghman, S. M., CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus., Nature, vol. 405, no. 6785, pp. 486-9, 2000.
A. T. Hark and Tilghman, S. M., Chromatin conformation of the H19 epigenetic mark., Hum Mol Genet, vol. 7, no. 12, pp. 1979-85, 1998.
J. L. Harder, Menon, R., Otto, E. A., Zhou, J., Eddy, S., Wys, N. L., O'Connor, C., Luo, J., Nair, V., Cebrián, C., Spence, J. R., Bitzer, M., Troyanskaya, O. G., Hodgin, J. B., Wiggins, R. C., Freedman, B. S., and Kretzler, M., Organoid single cell profiling identifies a transcriptional signature of glomerular disease., JCI Insight, vol. 4, no. 1, 2019.
S. T. Harbison, Carbone, M. Anna, Ayroles, J. F., Stone, E. A., Lyman, R. F., and Mackay, T. F. C., Co-regulated transcriptional networks contribute to natural genetic variation in Drosophila sleep., Nat Genet, vol. 41, no. 3, pp. 371-5, 2009.
N. Harafuji, Keys, D. N., and Levine, M., Genome-wide identification of tissue-specific enhancers in the Ciona tadpole., Proc Natl Acad Sci U S A, vol. 99, no. 10, pp. 6802-5, 2002.
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.
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.
D. L. Halligan, Eyre-Walker, A., Andolfatto, P., and Keightley, P. D., Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila., Genome Res, vol. 14, no. 2, pp. 273-9, 2004.
B. Haley, Foys, B., and Levine, M., Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila., Proc Natl Acad Sci U S A, vol. 107, no. 25, pp. 11435-40, 2010.
B. Haley, Hendrix, D., Trang, V., and Levine, M., A simplified miRNA-based gene silencing method for Drosophila melanogaster., Dev Biol, vol. 321, no. 2, pp. 482-90, 2008.
J. - H. Hahm, Kim, S., DiLoreto, R., Shi, C., Lee, S. - J. V., Murphy, C. T., and Nam, H. Gil, C. elegans maximum velocity correlates with healthspan and is maintained in worms with an insulin receptor mutation., Nat Commun, vol. 6, p. 8919, 2015.
P. R. Haddrill, Bachtrog, D., and Andolfatto, P., Positive and negative selection on noncoding DNA in Drosophila simulans., Mol Biol Evol, vol. 25, no. 9, pp. 1825-34, 2008.
P. R. Haddrill, Charlesworth, B., Halligan, D. L., and Andolfatto, P., Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content., Genome Biol, vol. 6, no. 8, p. R67, 2005.
P. R. Haddrill, Thornton, K. R., Charlesworth, B., and Andolfatto, P., Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations., Genome Res, vol. 15, no. 6, pp. 790-9, 2005.
S. R. Hackett, Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O., Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D., and Rabinowitz, J. D., Systems-level analysis of mechanisms regulating yeast metabolic flux., Science, vol. 354, no. 6311, 2016.
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies., Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.