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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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.
C. A. Crutchfield, Lu, W., Melamud, E., and Rabinowitz, J. D., Mass spectrometry-based metabolomics of yeast., Methods Enzymol, vol. 470, pp. 393-426, 2010.
J. Cowden and Levine, M., Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo., Dev Biol, vol. 262, no. 2, pp. 335-49, 2003.
J. Cowden and Levine, M., The Snail repressor positions Notch signaling in the Drosophila embryo., Development, vol. 129, no. 7, pp. 1785-93, 2002.
D. E. Coulter, Swaykus, E. A., Beran-Koehn, M. A., Goldberg, D., Wieschaus, E., and Schedl, P., Molecular analysis of odd-skipped, a zinc finger encoding segmentation gene with a novel pair-rule expression pattern., EMBO J, vol. 9, no. 11, pp. 3795-804, 1990.
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.
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.
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. Costa, Wilson, E. T., and Wieschaus, E., A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation., Cell, vol. 76, no. 6, pp. 1075-89, 1994.
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.
M. Coppey, Boettiger, A. N., Berezhkovskii, A. M., and Shvartsman, S. Y., Nuclear trapping shapes the terminal gradient in the Drosophila embryo., Curr Biol, vol. 18, no. 12, pp. 915-9, 2008.
M. Coppey, Berezhkovskii, A. M., Kim, Y., Boettiger, A. N., and Shvartsman, S. Y., Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein., Dev Biol, vol. 312, no. 2, pp. 623-30, 2007.
M. Coppey, Berezhkovskii, A. M., Sealfon, S. C., and Shvartsman, S. Y., Time and length scales of autocrine signals in three dimensions., Biophys J, vol. 93, no. 6, pp. 1917-22, 2007.
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.
S. E. Cole, Levorse, J. M., Tilghman, S. M., and Vogt, T. F., Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis., Dev Cell, vol. 3, no. 1, pp. 75-84, 2002.
E. S. Click, Stearns, T., and Botstein, D., Systematic structure-function analysis of the small GTPase Arf1 in yeast., Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
M. A. Cleary, van Raamsdonk, C. D., Levorse, J., Zheng, B., Bradley, A., and Tilghman, S. M., Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice., Nat Genet, vol. 29, no. 1, pp. 78-82, 2001.
M. F. Clasquin, Melamud, E., and Rabinowitz, J. D., LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine., Curr Protoc Bioinformatics, vol. Chapter 14, p. Unit14.11, 2012.
M. F. Clasquin, Melamud, E., Singer, A., Gooding, J. R., Xu, X., Dong, A., Cui, H., Campagna, S. R., Savchenko, A., Yakunin, A. F., Rabinowitz, J. D., and Caudy, A. A., Riboneogenesis in yeast., Cell, vol. 145, no. 6, pp. 969-80, 2011.
T. Clancy, Dannenfelser, R., Troyanskaya, O. G., Malmberg, K. Johan, Hovig, E., and Kristensen, V., Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery., Curr Pharm Des, 2017.
K. Chung, Kim, Y., Kanodia, J. S., Gong, E., Shvartsman, S. Y., and Lu, H., A microfluidic array for large-scale ordering and orientation of embryos., Nat Methods, vol. 8, no. 2, pp. 171-6, 2011.
N. Christophe Chung and Storey, J. D., Statistical significance of variables driving systematic variation in high-dimensional data., Bioinformatics, 2014.
K. R. Christie, Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., Hong, E. L., Issel-Tarver, L., Nash, R., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Botstein, D., and J Cherry, M., Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms., Nucleic Acids Res, vol. 32, no. Database issue, pp. D311-4, 2004.
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.
L. Christiaen, Stolfi, A., and Levine, M., BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development., Dev Biol, vol. 340, no. 2, pp. 179-87, 2010.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5347, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., X-gal staining of electroporated sea squirt (Ciona) embryos., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5346, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5348, 2009.
L. Christiaen, Davidson, B., Kawashima, T., Powell, W., Nolla, H., Vranizan, K., and Levine, M., The transcription/migration interface in heart precursors of Ciona intestinalis., Science, vol. 320, no. 5881, pp. 1349-52, 2008.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Isolation of sea squirt (Ciona) gametes, fertilization, dechorionation, and development., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5344, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., Isolation of individual cells and tissues from electroporated sea squirt (Ciona) embryos by fluorescence-activated cell sorting (FACS)., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.prot5349, 2009.
L. Christiaen, Stolfi, A., Davidson, B., and Levine, M., Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp., Dev Biol, vol. 328, no. 2, pp. 552-60, 2009.
L. Christiaen, Wagner, E., Shi, W., and Levine, M., The sea squirt Ciona intestinalis., Cold Spring Harb Protoc, vol. 2009, no. 12, p. pdb.emo138, 2009.
V. S. Chopra, Hendrix, D. A., Core, L. J., Tsui, C., Lis, J. T., and Levine, M., The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo., Mol Cell, vol. 42, no. 6, pp. 837-44, 2011.
V. S. Chopra, Kong, N., and Levine, M., Transcriptional repression via antilooping in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
V. S. Chopra, Cande, J., Hong, J. - W., and Levine, M., Stalled Hox promoters as chromosomal boundaries., Genes Dev, vol. 23, no. 13, pp. 1505-9, 2009.
V. S. Chopra, Hong, J. - W., and Levine, M., Regulation of Hox gene activity by transcriptional elongation in Drosophila., Curr Biol, vol. 19, no. 8, pp. 688-93, 2009.
J. Choi, Rajagopal, A., Xu, Y. - F., Rabinowitz, J. D., and O'Shea, E. K., A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae., PLoS One, vol. 12, no. 5, p. e0176085, 2017.
M. D. Chikina and Troyanskaya, O. G., An effective statistical evaluation of ChIPseq dataset similarity., Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
M. D. Chikina and Troyanskaya, O. G., Accurate quantification of functional analogy among close homologs., PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
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.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans., PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
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.
A. Chi, Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E. P., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., and Hunt, D. F., Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry., Proc Natl Acad Sci U S A, vol. 104, no. 7, pp. 2193-8, 2007.
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.
L. S. Cheung, Schüpbach, T., and Shvartsman, S. Y., Pattern formation by receptor tyrosine kinases: analysis of the Gurken gradient in Drosophila oogenesis., Curr Opin Genet Dev, vol. 21, no. 6, pp. 719-25, 2011.
L. S. Chen and Storey, J. D., Eigen-R2 for dissecting variation in high-dimensional studies., Bioinformatics, vol. 24, no. 19, pp. 2260-2, 2008.
X. Chen, Leung, S. Y., Yuen, S. T., Chu, K. - M., Ji, J., Li, R., S Y Chan, A., Law, S., Troyanskaya, O. G., Wong, J., So, S., Botstein, D., and Brown, P. O., Variation in gene expression patterns in human gastric cancers., Mol Biol Cell, vol. 14, no. 8, pp. 3208-15, 2003.
L. Chen, Ducker, G. S., Lu, W., Teng, X., and Rabinowitz, J. D., An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate., Anal Bioanal Chem, 2017.
L. Chen, Zhang, Z., Hoshino, A., Zheng, H. D., Morley, M., Arany, Z., and Rabinowitz, J. D., NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism., Nat Metab, vol. 1, pp. 404-415, 2019.
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., Selene: a PyTorch-based deep learning library for sequence data., Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
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.
X. Chen, Cheung, S. Tim, So, S., Fan, S. Tat, Barry, C., Higgins, J., Lai, K. - M., Ji, J., Dudoit, S., Ng, I. O. L., van de Rijn, M., Botstein, D., and Brown, P. O., Gene expression patterns in human liver cancers., Mol Biol Cell, vol. 13, no. 6, pp. 1929-39, 2002.
H. Y. Chang, Chi, J. - T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., and Brown, P. O., Diversity, topographic differentiation, and positional memory in human fibroblasts., Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12877-82, 2002.
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.
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.
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 and Bialek, W., Inverse spin glass and related maximum entropy problems., Phys Rev Lett, vol. 113, no. 11, p. 117204, 2014.
T. Caspary, Cleary, M. A., Perlman, E. J., Zhang, P., Elledge, S. J., and Tilghman, S. M., Oppositely imprinted genes p57(Kip2) and igf2 interact in a mouse model for Beckwith-Wiedemann syndrome., Genes Dev, vol. 13, no. 23, pp. 3115-24, 1999.
T. Caspary, Cleary, M. A., Baker, C. C., Guan, X. J., and Tilghman, S. M., Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster., Mol Cell Biol, vol. 18, no. 6, pp. 3466-74, 1998.
M. Anna Carbone, Ayroles, J. F., Yamamoto, A., Morozova, T. V., West, S. A., Magwire, M. M., Mackay, T. F. C., and Anholt, R. R. H., Overexpression of myocilin in the Drosophila eye activates the unfolded protein response: implications for glaucoma., PLoS One, vol. 4, no. 1, p. e4216, 2009.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure., PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
J. A. Capra and Singh, M., Predicting functionally important residues from sequence conservation., Bioinformatics, vol. 23, no. 15, pp. 1875-82, 2007.
J. A. Capra and Singh, M., Characterization and prediction of residues determining protein functional specificity., Bioinformatics, vol. 24, no. 13, pp. 1473-80, 2008.
J. A. Capra, Paeschke, K., Singh, M., and Zakian, V. A., G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 6, no. 7, p. e1000861, 2010.
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.
J. Doran Cande, Chopra, V. S., and Levine, M., Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum., Development, vol. 136, no. 18, pp. 3153-60, 2009.
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.
J. Cande, Goltsev, Y., and Levine, M. S., Conservation of enhancer location in divergent insects., Proc Natl Acad Sci U S A, vol. 106, no. 34, pp. 14414-9, 2009.
S. A. Camper and Tilghman, S. M., Postnatal repression of the alpha-fetoprotein gene is enhancer independent., Genes Dev, vol. 3, no. 4, pp. 537-46, 1989.
B. Callahan, Neher, R. A., Bachtrog, D., Andolfatto, P., and Shraiman, B. I., Correlated evolution of nearby residues in Drosophilid proteins., PLoS Genet, vol. 7, no. 2, p. e1001315, 2011.
V. C. Calhoun, Stathopoulos, A., and Levine, M., Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex., Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9243-7, 2002.
V. C. Calhoun and Levine, M., Coordinate regulation of an extended chromosome domain., Cell, vol. 113, no. 3, pp. 278-80, 2003.
V. C. Calhoun and Levine, M., Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex., Proc Natl Acad Sci U S A, vol. 100, no. 17, pp. 9878-83, 2003.