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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Trans-Activators
M. Ronen and Botstein, D., Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source., Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
J. S. Kanodia, Rikhy, R., Kim, Y., Lund, V. K., DeLotto, R., Lippincott-Schwartz, J., and Shvartsman, S. Y., Dynamics of the Dorsal morphogen gradient., Proc Natl Acad Sci U S A, vol. 106, no. 51, pp. 21707-12, 2009.
B. Riggleman, Schedl, P., and Wieschaus, E., Spatial expression of the Drosophila segment polarity gene armadillo is posttranscriptionally regulated by wingless., Cell, vol. 63, no. 3, pp. 549-60, 1990.
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity., Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
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.
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.
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.
B. Riggleman, Wieschaus, E., and Schedl, P., Molecular analysis of the armadillo locus: uniformly distributed transcripts and a protein with novel internal repeats are associated with a Drosophila segment polarity gene., Genes Dev, vol. 3, no. 1, pp. 96-113, 1989.
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.
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.
Transcription Factors
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.
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.
M. Ronen and Botstein, D., Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source., Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
J. S. Kanodia, Rikhy, R., Kim, Y., Lund, V. K., DeLotto, R., Lippincott-Schwartz, J., and Shvartsman, S. Y., Dynamics of the Dorsal morphogen gradient., Proc Natl Acad Sci U S A, vol. 106, no. 51, pp. 21707-12, 2009.
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.
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome., Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
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.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets., Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.
B. Riggleman, Schedl, P., and Wieschaus, E., Spatial expression of the Drosophila segment polarity gene armadillo is posttranscriptionally regulated by wingless., Cell, vol. 63, no. 3, pp. 549-60, 1990.
N. S. Tolwinski, Wehrli, M., Rives, A., Erdeniz, N., DiNardo, S., and Wieschaus, E., Wg/Wnt signal can be transmitted through arrow/LRP5,6 and Axin independently of Zw3/Gsk3beta activity., Dev Cell, vol. 4, no. 3, pp. 407-18, 2003.
J. S. Kanodia, Liang, H. - L., Kim, Y., Lim, B., Zhan, M., Lu, H., Rushlow, C. A., and Shvartsman, S. Y., Pattern formation by graded and uniform signals in the early Drosophila embryo., Biophys J, vol. 102, no. 3, pp. 427-33, 2012.
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.
M. Shakoury-Elizeh, Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., and Philpott, C. C., Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae., Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO., PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
C. A. Rushlow and Shvartsman, S. Y., Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient., Curr Opin Genet Dev, vol. 22, no. 6, pp. 542-6, 2012.
K. Senger, Armstrong, G. W., Rowell, W. J., Kwan, J. M., Markstein, M., and Levine, M., Immunity regulatory DNAs share common organizational features in Drosophila., Mol Cell, vol. 13, no. 1, pp. 19-32, 2004.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O., Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation., Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
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.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
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.
F. Biemar, Zinzen, R., Ronshaugen, M., Sementchenko, V., J Manak, R., and Levine, M. S., Spatial regulation of microRNA gene expression in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 102, no. 44, pp. 15907-11, 2005.
B. Riggleman, Wieschaus, E., and Schedl, P., Molecular analysis of the armadillo locus: uniformly distributed transcripts and a protein with novel internal repeats are associated with a Drosophila segment polarity gene., Genes Dev, vol. 3, no. 1, pp. 96-113, 1989.
M. Shakoury-Elizeh, Tiedeman, J., Rashford, J., Ferea, T., Demeter, J., Garcia, E., Rolfes, R., Brown, P. O., Botstein, D., and Philpott, C. C., Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae., Mol Biol Cell, vol. 15, no. 3, pp. 1233-43, 2004.
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.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO., PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
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.
Transcription, Genetic
B. P. Berman, Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B., Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome., Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 757-62, 2002.
W. Bailis, Shyer, J. A., Zhao, J., Canaveras, J. Carlos Gar, Khazal, F. J. Al, Qu, R., Steach, H. R., Bielecki, P., Khan, O., Jackson, R., Kluger, Y., Maher, L. J., Rabinowitz, J., Craft, J., and Flavell, R. A., Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function., Nature, vol. 571, no. 7765, pp. 403-407, 2019.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP., Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
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.
B. Riggleman, Schedl, P., and Wieschaus, E., Spatial expression of the Drosophila segment polarity gene armadillo is posttranscriptionally regulated by wingless., Cell, vol. 63, no. 3, pp. 549-60, 1990.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A., T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression., PLoS Biol, vol. 1, no. 2, p. E53, 2003.
P. H. Bradley, Brauer, M. J., Rabinowitz, J. D., and Troyanskaya, O. G., Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
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.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO., PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
J. R. Pollack, Sørlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lonning, P. E., Tibshirani, R., Botstein, D., Børresen-Dale, A. - L., and Brown, P. O., Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors., Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12963-8, 2002.
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., Yeast cells can access distinct quiescent states., Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
F. Biemar, Zinzen, R., Ronshaugen, M., Sementchenko, V., J Manak, R., and Levine, M. S., Spatial regulation of microRNA gene expression in the Drosophila embryo., Proc Natl Acad Sci U S A, vol. 102, no. 44, pp. 15907-11, 2005.
A. A. Petti, Crutchfield, C. A., Rabinowitz, J. D., and Botstein, D., Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function., Proc Natl Acad Sci U S A, vol. 108, no. 45, pp. E1089-98, 2011.
M. J. Brauer, Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., and Botstein, D., Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast., Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
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.
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.
G. Rizki, Iwata, T. Naoko, Li, J., Riedel, C. G., Picard, C. Lafontaine, Jan, M., Murphy, C. T., and Lee, S. Sylvia, The evolutionarily conserved longevity determinants HCF-1 and SIR-2.1/SIRT1 collaborate to regulate DAF-16/FOXO., PLoS Genet, vol. 7, no. 9, p. e1002235, 2011.
M. Ronen and Botstein, D., Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source., Proc Natl Acad Sci U S A, vol. 103, no. 2, pp. 389-94, 2006.
Transcriptome
C. J. Nirschl, Suárez-Fariñas, M., Izar, B., Prakadan, S., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., K Devi, S. P., Carroll, S. L., Chau, D., Rezaee, M., Kim, T. - G., Huang, R., Fuentes-Duculan, J., Song-Zhao, G. X., Gulati, N., Lowes, M. A., King, S. L., Quintana, F. J., Lee, Y. -suk, Krueger, J. G., Sarin, K. Y., Yoon, C. H., Garraway, L., Regev, iv, A., Shalek, A. K., Troyanskaya, O. G., and Anandasabapathy, N., IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment., Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
C. J. Nirschl, Suárez-Fariñas, M., Izar, B., Prakadan, S., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., K Devi, S. P., Carroll, S. L., Chau, D., Rezaee, M., Kim, T. - G., Huang, R., Fuentes-Duculan, J., Song-Zhao, G. X., Gulati, N., Lowes, M. A., King, S. L., Quintana, F. J., Lee, Y. -suk, Krueger, J. G., Sarin, K. Y., Yoon, C. H., Garraway, L., Regev, iv, A., Shalek, A. K., Troyanskaya, O. G., and Anandasabapathy, N., IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment., Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
Y. - F. Xu, Zhao, X., Glass, D. S., Absalan, F., Perlman, D. H., Broach, J. R., and Rabinowitz, J. D., Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation., Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
Tumor Cells, Cultured
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.
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.
J. R. Pollack, Sørlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lonning, P. E., Tibshirani, R., Botstein, D., Børresen-Dale, A. - L., and Brown, P. O., Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors., Proc Natl Acad Sci U S A, vol. 99, no. 20, pp. 12963-8, 2002.
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.
Tumor Microenvironment
C. J. Nirschl, Suárez-Fariñas, M., Izar, B., Prakadan, S., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., K Devi, S. P., Carroll, S. L., Chau, D., Rezaee, M., Kim, T. - G., Huang, R., Fuentes-Duculan, J., Song-Zhao, G. X., Gulati, N., Lowes, M. A., King, S. L., Quintana, F. J., Lee, Y. -suk, Krueger, J. G., Sarin, K. Y., Yoon, C. H., Garraway, L., Regev, iv, A., Shalek, A. K., Troyanskaya, O. G., and Anandasabapathy, N., IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment., Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 2017.
C. J. Nirschl, Suárez-Fariñas, M., Izar, B., Prakadan, S., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., K Devi, S. P., Carroll, S. L., Chau, D., Rezaee, M., Kim, T. - G., Huang, R., Fuentes-Duculan, J., Song-Zhao, G. X., Gulati, N., Lowes, M. A., King, S. L., Quintana, F. J., Lee, Y. -suk, Krueger, J. G., Sarin, K. Y., Yoon, C. H., Garraway, L., Regev, iv, A., Shalek, A. K., Troyanskaya, O. G., and Anandasabapathy, N., IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment., Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
Tumor Suppressor Proteins
G. S. Ducker and Rabinowitz, J. D., ZMP: a master regulator of one-carbon metabolism., Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
United States
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W., Nobel laureates' letter to President Bush., Washington Post, p. A02, 2001.
W. R. Uhlmann, Bennett, R., Botkin, J. R., Botstein, D., Boughman, J. A., Chakravarti, A., Clayton, E. Wright, Kahn, J., Koenig, B., Murray, T. H., Olson, M. V., Rowley, J., Terry, S., and Valle, D., Planning the genome institute's future., Science, vol. 299, no. 5612, p. 1515; author reply 1515, 2003.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., Overview of the Alliance for Cellular Signaling., Nature, vol. 420, no. 6916, pp. 703-6, 2002.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., Overview of the Alliance for Cellular Signaling., Nature, vol. 420, no. 6916, pp. 703-6, 2002.
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W., Nobel laureates' letter to President Bush., Washington Post, p. A02, 2001.
A. G. Gilman, Simon, M. I., Bourne, H. R., Harris, B. A., Long, R., Ross, E. M., Stull, J. T., Taussig, R., Bourne, H. R., Arkin, A. P., Cobb, M. H., Cyster, J. G., Devreotes, P. N., Ferrell, J. E., Fruman, D., Gold, M., Weiss, A., Stull, J. T., Berridge, M. J., Cantley, L. C., Catterall, W. A., Coughlin, S. R., Olson, E. N., Smith, T. F., Brugge, J. S., Botstein, D., Dixon, J. E., Hunter, T., Lefkowitz, R. J., Pawson, A. J., Sternberg, P. W., Varmus, H., Subramaniam, S., Sinkovits, R. S., Li, J., Mock, D., Ning, Y., Saunders, B., Sternweis, P. C., Hilgemann, D., Scheuermann, R. H., DeCamp, D., Hsueh, R., Lin, K. - M., Ni, Y., Seaman, W. E., Simpson, P. C., O'Connell, T. D., Roach, T., Simon, M. I., Choi, S., Eversole-Cire, P., Fraser, I., Mumby, M. C., Zhao, Y., Brekken, D., Shu, H., Meyer, T., Chandy, G., Heo, W. Do, Liou, J., O'Rourke, N., Verghese, M., Mumby, S. M., Han, H., H Brown, A., Forrester, J. S., Ivanova, P., Milne, S. B., Casey, P. J., T Harden, K., Arkin, A. P., Doyle, J., Gray, M. L., Meyer, T., Michnick, S., Schmidt, M. A., Toner, M., Tsien, R. Y., Natarajan, M., Ranganathan, R., and Sambrano, G. R., Overview of the Alliance for Cellular Signaling., Nature, vol. 420, no. 6916, pp. 703-6, 2002.
K. J. Arrow, Axelrod, J., Benacerraf, B., Berg, P., Bishop, J. M., Bloembergen, N., Brown, H. C., Cibelli, J., Cohen, S., Cooper, L. N., Corey, E. J., Cronin, J. W., Curl, R., Dulbecco, R., Fischer, E. H., Fitch, V. L., Fogel, R., Friedman, J. I., Furchgott, R. F., Gell-Mann, M., Gilbert, W., Gilman, A., Glaser, D., Glashow, S. L., Green, R. M., Greengard, P., Guillemin, R., Hayflick, L., Hauptman, H. A., Heckman, J. J., Heeger, A., Herschbach, D., Hubel, D. H., Hulse, R., Kandel, E., Karle, J., Klein, L. R., Kohn, W., Kornberg, A., Krebs, E. G., Lanza, R. P., Laughlin, R., Lederman, L., Lee, D. M., Lewis, E., Lipscomb, W., Marcus, R. A., McFadden, D., Merrifield, R. B., Merton, R., Modigliani, F., Molina, M. J., Murad, F., Nirenberg, M. W., North, D. C., Olah, G. A., Osheroff, D., Palade, G. E., Perl, M., Ramsey, N. F., Richter, B., Roberts, R. J., Samuelson, P. A., Schwartz, M., Sharp, P. A., Smalley, R. E., Smith, H. O., Solow, R. M., Stormer, H., Taube, H., Taylor, R., Thomas, E. D., Tobin, J., Tonegawa, S., Townes, C., Watson, J. D., Weinberg, S., Weller, T. H., West, M. D., Wieschaus, E. F., Wiesel, T. N., and Wilson, R. W., Nobel laureates' letter to President Bush., Washington Post, p. A02, 2001.
Virus Replication
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection., Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
L. J. Terry, Vastag, L., Rabinowitz, J. D., and Shenk, T., Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection., Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
L. Vastag, Koyuncu, E., Grady, S. L., Shenk, T. E., and Rabinowitz, J. D., Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism., PLoS Pathog, vol. 7, no. 7, p. e1002124, 2011.
J. Munger, Bajad, S. U., Coller, H. A., Shenk, T., and Rabinowitz, J. D., Dynamics of the cellular metabolome during human cytomegalovirus infection., PLoS Pathog, vol. 2, no. 12, p. e132, 2006.
S. T. H. Liu, Sharon-Friling, R., Ivanova, P., Milne, S. B., Myers, D. S., Rabinowitz, J. D., H Brown, A., and Shenk, T., Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress., Proc Natl Acad Sci U S A, vol. 108, no. 31, pp. 12869-74, 2011.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., Interpretation of an individual functional genomics experiment guided by massive public data., Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
X Chromosome
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.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
M. 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.
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.
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.
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.

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