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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3' Untranslated Regions
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.
5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase
S. R McIsaac, Petti, A. A., Bussemaker, H. J., and Botstein, D., “Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 2993-3007, 2012.
A. A. Petti, R McIsaac, S., Ho-Shing, O., Bussemaker, H. J., and Botstein, D., “Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.”, Mol Biol Cell, vol. 23, no. 15, pp. 3008-24, 2012.
Actin Cytoskeleton
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.
M. A. Postner and Wieschaus, E. F., “The nullo protein is a component of the actin-myosin network that mediates cellularization in Drosophila melanogaster embryos.”, J Cell Sci, vol. 107 ( Pt 7), pp. 1863-73, 1994.
Actin Depolymerizing Factors
M. A. Postner, Miller, K. G., and Wieschaus, E. F., “Maternal effect mutations of the sponge locus affect actin cytoskeletal rearrangements in Drosophila melanogaster embryos.”, J Cell Biol, vol. 119, no. 5, pp. 1205-18, 1992.
Actins
W. Shi, Peyrot, S. M., Munro, E., and Levine, M., “FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.”, Development, vol. 136, no. 1, pp. 23-8, 2009.
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.
M. A. Postner and Wieschaus, E. F., “The nullo protein is a component of the actin-myosin network that mediates cellularization in Drosophila melanogaster embryos.”, J Cell Sci, vol. 107 ( Pt 7), pp. 1863-73, 1994.
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.
E. D. Schejter, Rose, L. S., Postner, M. A., and Wieschaus, E., “Role of the zygotic genome in the restructuring of the actin cytoskeleton at the cycle-14 transition during Drosophila embryogenesis.”, Cold Spring Harb Symp Quant Biol, vol. 57, pp. 653-9, 1992.
Action Potentials
E. Schneidman, Puchalla, J. L., Segev, R., Harris, R. A., Bialek, W., and Berry, M. J., “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
Adaptation, Physiological
O. Oleksiuk, Jakovljevic, V., Vladimirov, N., Carvalho, R., Paster, E., Ryu, W. S., Meir, Y., Wingreen, N. S., Kollmann, M., and Sourjik, V., “Thermal robustness of signaling in bacterial chemotaxis.”, Cell, vol. 145, no. 2, pp. 312-21, 2011.
D. Gresham, Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., DeSevo, C. G., Botstein, D., and Dunham, M. J., “The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.”, PLoS Genet, vol. 4, no. 12, p. e1000303, 2008.
T. Pilizota and Shaevitz, J. W., “Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli.”, PLoS One, vol. 7, no. 4, p. e35205, 2012.
Adaptor Proteins, Signal Transducing
W. Shi, Peyrot, S. M., Munro, E., and Levine, M., “FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.”, Development, vol. 136, no. 1, pp. 23-8, 2009.
Adenocarcinoma
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.
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.
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.
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.
Adenomatous Polyposis Coli Protein
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.
Adenosine Triphosphate
C. N. Peterson, Levchenko, I., Rabinowitz, J. D., Baker, T. A., and Silhavy, T. J., “RpoS proteolysis is controlled directly by ATP levels in Escherichia coli.”, Genes Dev, vol. 26, no. 6, pp. 548-53, 2012.
Adherens Junctions
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.
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.
Adult
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
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.
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.
K. Ranade, Hinds, D., Hsiung, C. Agnes, Chuang, L. - M., Chang, M. - S., Chen, Y. - T., Pesich, R., Hebert, J., Chen, Y. - D. I., Dzau, V., Olshen, R., Curb, D., Botstein, D., Cox, D. R., and Risch, N., “A genome scan for hypertension susceptibility loci in populations of Chinese and Japanese origins.”, Am J Hypertens, vol. 16, no. 2, pp. 158-62, 2003.
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.
Age Factors
N. Ron-Harel, Notarangelo, G., Ghergurovich, J. M., Paulo, J. A., Sage, P. T., Santos, D., F Satterstrom, K., Gygi, S. P., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., “Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice.”, Proc Natl Acad Sci U S A, vol. 115, no. 52, pp. 13347-13352, 2018.
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
Aged
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
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.
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.
Aged, 80 and over
T. Sørlie, Perou, C. M., Fan, C., Geisler, S., Aas, T., Nobel, A., Anker, G., Akslen, L. A., Botstein, D., Børresen-Dale, A. - L., and Lønning, P. Eystein, “Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer.”, Mol Cancer Ther, vol. 5, no. 11, pp. 2914-8, 2006.
Aging
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
Alcohol Drinking
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
K. Ranade, Jorgenson, E., Sheu, W. H. - H., Pei, D., Hsiung, C. Agnes, Chiang, F. -tien, Chen, Y. - D. I., Pratt, R., Olshen, R. A., Curb, D., Cox, D. R., Botstein, D., and Risch, N., “A polymorphism in the beta1 adrenergic receptor is associated with resting heart rate.”, Am J Hum Genet, vol. 70, no. 4, pp. 935-42, 2002.
Algorithms
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
L. C. Osborne, Palmer, S. E., Lisberger, S. G., and Bialek, W., “The neural basis for combinatorial coding in a cortical population response.”, J Neurosci, vol. 28, no. 50, pp. 13522-31, 2008.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
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.
E. Banks, Nabieva, E., Peterson, R., and Singh, M., “NetGrep: fast network schema searches in interactomes.”, Genome Biol, vol. 9, no. 9, p. R138, 2008.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., “Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.”, Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
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.
S. R McIsaac, Silverman, S. J., Parsons, L., Xu, P., Briehof, R., McClean, M. N., and Botstein, D., “Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.”, J Vis Exp, no. 76, p. e50382, 2013.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
E. Segal, Shapira, M., Regev, iv, A., Pe'er, D., Botstein, D., Koller, D., and Friedman, N., “Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.”, Nat Genet, vol. 34, no. 2, pp. 166-76, 2003.
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.
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., “Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.”, PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
Alleles
Z. Khan, Bloom, J. S., Amini, S., Singh, M., Perlman, D. H., Caudy, A. A., and Kruglyak, L., “Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.”, Mol Syst Biol, vol. 8, p. 602, 2012.
M. Peifer and Wieschaus, E., “The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin.”, Cell, vol. 63, no. 6, pp. 1167-76, 1990.
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.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
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.
S. M. Tilghman, Bartolomei, M. S., Webber, A. L., Brunkow, M. E., Saam, J., Leighton, P. A., Pfeifer, K., and Zemel, S., “Parental imprinting of the H19 and Igf2 genes in the mouse.”, Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
M. O. Press, McCoy, R. C., Hall, A. N., Akey, J. M., and Queitsch, C., “Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.”, Genome Res, vol. 28, no. 8, pp. 1169-1178, 2018.
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. Pfeifer and Tilghman, S. M., “Allele-specific gene expression in mammals: the curious case of the imprinted RNAs.”, Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
Allografts
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.
Allosteric Regulation
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.
alpha-Fetoproteins
H. Yoo-Warren, Pachnis, V., Ingram, R. S., and Tilghman, S. M., “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
Ambystoma
E. Schneidman, Puchalla, J. L., Segev, R., Harris, R. A., Bialek, W., and Berry, M. J., “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
Amino Acid Sequence
A. V. Persikov, Osada, R., and Singh, M., “Predicting DNA recognition by Cys2His2 zinc finger proteins.”, Bioinformatics, vol. 25, no. 1, pp. 22-9, 2009.
M. Peifer and Wieschaus, E., “The product of the Drosophila melanogaster segment polarity gene armadillo is highly conserved in sequence and expression in the housefly Musca domestica.”, J Mol Evol, vol. 36, no. 3, pp. 224-33, 1993.
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. Peifer, McCrea, P. D., Green, K. J., Wieschaus, E., and Gumbiner, B. M., “The vertebrate adhesive junction proteins beta-catenin and plakoglobin and the Drosophila segment polarity gene armadillo form a multigene family with similar properties.”, J Cell Biol, vol. 118, no. 3, pp. 681-91, 1992.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
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.
M. Peifer and Wieschaus, E., “The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin.”, Cell, vol. 63, no. 6, pp. 1167-76, 1990.
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.
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., “Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.”, Genome Biol, vol. 12, no. 12, p. R122, 2011.
Amino Acid Substitution
W. - L. Ng, Wei, Y., Perez, L. J., Cong, J., Long, T., Koch, M., Semmelhack, M. F., Wingreen, N. S., and Bassler, B. L., “Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules.”, Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5575-80, 2010.
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.
Amino Acids
S. U. Bajad, Lu, W., Kimball, E. H., Yuan, J., Peterson, C., and Rabinowitz, J. D., “Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry.”, J Chromatogr A, vol. 1125, no. 1, pp. 76-88, 2006.
Amino Acids, Essential
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.
Amino-Acid N-Acetyltransferase
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.
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.
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.
Ammonia
J. Yuan, Doucette, C. D., Fowler, W. U., Feng, X. - J., Piazza, M., Rabitz, H. A., Wingreen, N. S., and Rabinowitz, J. D., “Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.”, Mol Syst Biol, vol. 5, p. 302, 2009.
Animals
D. Guan, Xiong, Y., Borck, P. C., Jang, C., Doulias, P. - T., Papazyan, R., Fang, B., Jiang, C., Zhang, Y., Briggs, E. R., Hu, W., Steger, D., Ischiropoulos, H., Rabinowitz, J. D., and Lazar, M. A., “Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes.”, Cell, vol. 174, no. 4, pp. 831-842.e12, 2018.
J. Parsch, Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P., “On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.”, Mol Biol Evol, vol. 27, no. 6, pp. 1226-34, 2010.
W. Shi, Peyrot, S. M., Munro, E., and Levine, M., “FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole.”, Development, vol. 136, no. 1, pp. 23-8, 2009.
D. Papatsenko, Levine, M., and Goltsev, Y., “Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles.”, PLoS Biol, vol. 9, no. 1, p. e1000584, 2011.
S. M. Tilghman, Bartolomei, M. S., Webber, A. L., Brunkow, M. E., Saam, J., Leighton, P. A., Pfeifer, K., and Zemel, S., “Parental imprinting of the H19 and Igf2 genes in the mouse.”, Cold Spring Harb Symp Quant Biol, vol. 58, pp. 287-95, 1993.
Y. Kim, Paroush, Z. 'ev, Nairz, K., Hafen, E., Jiménez, G., and Shvartsman, S. Y., “Substrate-dependent control of MAPK phosphorylation in vivo.”, Mol Syst Biol, vol. 7, p. 467, 2011.
Y. Pritykin and Singh, M., “Simple topological features reflect dynamics and modularity in protein interaction networks.”, PLoS Comput Biol, vol. 9, no. 10, p. e1003243, 2013.
H. Yoo-Warren, Pachnis, V., Ingram, R. S., and Tilghman, S. M., “Two regulatory domains flank the mouse H19 gene.”, Mol Cell Biol, vol. 8, no. 11, pp. 4707-15, 1988.
G. Jiménez, Shvartsman, S. Y., and Paroush, Z. 'ev, “The Capicua repressor--a general sensor of RTK signaling in development and disease.”, J Cell Sci, vol. 125, no. Pt 6, pp. 1383-91, 2012.
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.
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.
P. Engel, Kwong, W. K., McFrederick, Q., Anderson, K. E., Barribeau, S. Michael, Chandler, J. Angus, R Cornman, S., Dainat, J., de Miranda, J. R., Doublet, V., Emery, O., Evans, J. D., Farinelli, L., Flenniken, M. L., Granberg, F., Grasis, J. A., Gauthier, L., Hayer, J., Koch, H., Kocher, S., Martinson, V. G., Moran, N., Munoz-Torres, M., Newton, I., Paxton, R. J., Powell, E., Sadd, B. M., Schmid-Hempel, P., Schmid-Hempel, R., Song, S. Jin, Schwarz, R. S., vanEngelsdorp, D., and Dainat, B., “The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.”, MBio, vol. 7, no. 2, pp. e02164-15, 2016.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., “Pervasive natural selection in the Drosophila genome?”, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
M. Peifer, Orsulic, S., Sweeton, D., and Wieschaus, E., “A role for the Drosophila segment polarity gene armadillo in cell adhesion and cytoskeletal integrity during oogenesis.”, Development, vol. 118, no. 4, pp. 1191-207, 1993.
D. Papatsenko and Levine, M., “Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 102, no. 14, pp. 4966-71, 2005.
M. Peifer, Sweeton, D., Casey, M., and Wieschaus, E., “wingless signal and Zeste-white 3 kinase trigger opposing changes in the intracellular distribution of Armadillo.”, Development, vol. 120, no. 2, pp. 369-80, 1994.
W. J. Pavan, Mac, S., Cheng, M., and Tilghman, S. M., “Quantitative trait loci that modify the severity of spotting in piebald mice.”, Genome Res, vol. 5, no. 1, pp. 29-41, 1995.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
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.
M. van de Rijn, Perou, C. M., Tibshirani, R., Haas, P., Kallioniemi, O., Kononen, J., Torhorst, J., Sauter, G., Zuber, M., Köchli, O. R., Mross, F., Dieterich, H., Seitz, R., Ross, D., Botstein, D., and Brown, P., “Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.”, Am J Pathol, vol. 161, no. 6, pp. 1991-6, 2002.
K. Pfeifer and Tilghman, S. M., “Allele-specific gene expression in mammals: the curious case of the imprinted RNAs.”, Genes Dev, vol. 8, no. 16, pp. 1867-74, 1994.
S. A. McCarroll, Murphy, C. T., Zou, S., Pletcher, S. D., Chin, C. - S., Jan, Y. Nung, Kenyon, C., Bargmann, C. I., and Li, H., “Comparing genomic expression patterns across species identifies shared transcriptional profile in aging.”, Nat Genet, vol. 36, no. 2, pp. 197-204, 2004.
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.
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. Peifer, Rauskolb, C., Williams, M., Riggleman, B., and Wieschaus, E., “The segment polarity gene armadillo interacts with the wingless signaling pathway in both embryonic and adult pattern formation.”, Development, vol. 111, no. 4, pp. 1029-43, 1991.
M. A. Postner, Miller, K. G., and Wieschaus, E. F., “Maternal effect mutations of the sponge locus affect actin cytoskeletal rearrangements in Drosophila melanogaster embryos.”, J Cell Biol, vol. 119, no. 5, pp. 1205-18, 1992.
M. Peifer, McCrea, P. D., Green, K. J., Wieschaus, E., and Gumbiner, B. M., “The vertebrate adhesive junction proteins beta-catenin and plakoglobin and the Drosophila segment polarity gene armadillo form a multigene family with similar properties.”, J Cell Biol, vol. 118, no. 3, pp. 681-91, 1992.
A. S. Putnam, J Scriber, M., and Andolfatto, P., “Discordant divergence times among Z-chromosome regions between two ecologically distinct swallowtail butterfly species.”, Evolution, vol. 61, no. 4, pp. 912-27, 2007.
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.
L. C. Osborne, Palmer, S. E., Lisberger, S. G., and Bialek, W., “The neural basis for combinatorial coding in a cortical population response.”, J Neurosci, vol. 28, no. 50, pp. 13522-31, 2008.
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.
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.
G. Sella, Petrov, D. A., Przeworski, M., and Andolfatto, P., “Pervasive natural selection in the Drosophila genome?”, PLoS Genet, vol. 5, no. 6, p. e1000495, 2009.
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.
M. W. Perry, Bothma, J. P., Luu, R. D., and Levine, M., “Precision of hunchback expression in the Drosophila embryo.”, Curr Biol, vol. 22, no. 23, pp. 2247-52, 2012.
A. Davila, Liu, L., Chellappa, K., Redpath, P., Nakamaru-Ogiso, E., Paolella, L. M., Zhang, Z., Migaud, M. E., Rabinowitz, J. D., and Baur, J. A., “Nicotinamide adenine dinucleotide is transported into mammalian mitochondria.”, Elife, vol. 7, 2018.
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.
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., “Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
J. F. Ayroles, Hughes, K. A., Rowe, K. C., Reedy, M. M., Rodriguez-Zas, S. L., Drnevich, J. M., Cáceres, C. E., and Paige, K. N., “A genomewide assessment of inbreeding depression: gene number, function, and mode of action.”, Conserv Biol, vol. 23, no. 4, pp. 920-30, 2009.
Y. Kim, Iagovitina, A., Ishihara, K., Fitzgerald, K. M., Deplancke, B., Papatsenko, D., and Shvartsman, S. Y., “Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.”, Chaos, vol. 23, no. 2, p. 025105, 2013.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Pohl, O., Silvestri, E., Viale, M., and Walczak, A. M., “Social interactions dominate speed control in poising natural flocks near criticality.”, Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
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.
M. Peifer and Wieschaus, E., “The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin.”, Cell, vol. 63, no. 6, pp. 1167-76, 1990.
E. Schneidman, Puchalla, J. L., Segev, R., Harris, R. A., Bialek, W., and Berry, M. J., “Synergy from silence in a combinatorial neural code.”, J Neurosci, vol. 31, no. 44, pp. 15732-41, 2011.
R. A. Miller, Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cárdenas, C., Wan, M., J Foskett, K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., and Birnbaum, M. J., “Targeting hepatic glutaminase activity to ameliorate hyperglycemia.”, Nat Med, vol. 24, no. 4, pp. 518-524, 2018.
M. Piazza, Feng, X. - J., Rabinowitz, J. D., and Rabitz, H., “Diverse metabolic model parameters generate similar methionine cycle dynamics.”, J Theor Biol, vol. 251, no. 4, pp. 628-39, 2008.
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.
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.
D. Papatsenko and Levine, M. S., “Dual regulation by the Hunchback gradient in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 105, no. 8, pp. 2901-6, 2008.
M. W. Perry, Boettiger, A. N., Bothma, J. P., and Levine, M., “Shadow enhancers foster robustness of Drosophila gastrulation.”, Curr Biol, vol. 20, no. 17, pp. 1562-7, 2010.
E. Banks, Nabieva, E., Peterson, R., and Singh, M., “NetGrep: fast network schema searches in interactomes.”, Genome Biol, vol. 9, no. 9, p. R138, 2008.
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.
D. Papatsenko, Goltsev, Y., and Levine, M., “Organization of developmental enhancers in the Drosophila embryo.”, Nucleic Acids Res, vol. 37, no. 17, pp. 5665-77, 2009.
D. Papatsenko and Levine, M., “Computational identification of regulatory DNAs underlying animal development.”, Nat Methods, vol. 2, no. 7, pp. 529-34, 2005.
V. Pachnis, Brannan, C. I., and Tilghman, S. M., “The structure and expression of a novel gene activated in early mouse embryogenesis.”, EMBO J, vol. 7, no. 3, pp. 673-81, 1988.
M. A. Postner and Wieschaus, E. F., “The nullo protein is a component of the actin-myosin network that mediates cellularization in Drosophila melanogaster embryos.”, J Cell Sci, vol. 107 ( Pt 7), pp. 1863-73, 1994.
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.
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.
P. B. Vrana, Matteson, P. G., Schmidt, J. V., Ingram, R. S., Joyce, A., Prince, K. L., Dewey, M. J., and Tilghman, S. M., “Genomic imprinting of a placental lactogen gene in Peromyscus.”, Dev Genes Evol, vol. 211, no. 11, pp. 523-32, 2001.
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.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Transitions in the model of epithelial patterning.”, Dev Dyn, vol. 226, no. 1, pp. 155-9, 2003.
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.
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., “A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis.”, Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
Y. Song, Marmion, R. A., Park, J. O., Biswas, D., Rabinowitz, J. D., and Shvartsman, S. Y., “Dynamic Control of dNTP Synthesis in Early Embryos.”, Dev Cell, vol. 42, no. 3, pp. 301-308.e3, 2017.
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.
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. Pane, Jiang, P., Zhao, D. Yanling, Singh, M., and Schüpbach, T., “The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline.”, EMBO J, vol. 30, no. 22, pp. 4601-15, 2011.
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.
M. Peifer and Wieschaus, E., “Mutations in the Drosophila gene extradenticle affect the way specific homeo domain proteins regulate segmental identity.”, Genes Dev, vol. 4, no. 7, pp. 1209-23, 1990.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., “Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation.”, RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
E. M. Leffler, Bullaughey, K., Matute, D. R., Meyer, W. K., Ségurel, L., Venkat, A., Andolfatto, P., and Przeworski, M., “Revisiting an old riddle: what determines genetic diversity levels within species?”, PLoS Biol, vol. 10, no. 9, p. e1001388, 2012.
F. Biemar, Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., J Manak, R., and Levine, M. S., “Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.”, Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
W. J. Pavan and Tilghman, S. M., “Piebald lethal (sl) acts early to disrupt the development of neural crest-derived melanocytes.”, Proc Natl Acad Sci U S A, vol. 91, no. 15, pp. 7159-63, 1994.
J. P. Bothma, Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., and Levine, M., “Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.”, Elife, vol. 4, 2015.
D. S. A. Simakov, Cheung, L. S., Pismen, L. M., and Shvartsman, S. Y., “EGFR-dependent network interactions that pattern Drosophila eggshell appendages.”, Development, vol. 139, no. 15, pp. 2814-20, 2012.
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.
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.
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.
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.
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.
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.
L. Abouchar, Petkova, M. D., Steinhardt, C. R., and Gregor, T., “Fly wing vein patterns have spatial reproducibility of a single cell.”, J R Soc Interface, vol. 11, no. 97, p. 20140443, 2014.
M. Pribyl, Muratov, C. B., and Shvartsman, S. Y., “Discrete models of autocrine cell communication in epithelial layers.”, Biophys J, vol. 84, no. 6, pp. 3624-35, 2003.
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.
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.
M. Peifer and Wieschaus, E., “The product of the Drosophila melanogaster segment polarity gene armadillo is highly conserved in sequence and expression in the housefly Musca domestica.”, J Mol Evol, vol. 36, no. 3, pp. 224-33, 1993.
Y. Kim, Coppey, M., Grossman, R., Ajuria, L., Jiménez, G., Paroush, Z. 'ev, and Shvartsman, S. Y., “MAPK substrate competition integrates patterning signals in the Drosophila embryo.”, Curr Biol, vol. 20, no. 5, pp. 446-51, 2010.
N. Novoradovskaya, Whitfield, M. L., Basehore, L. S., Novoradovsky, A., Pesich, R., Usary, J., Karaca, M., Wong, W. K., Aprelikova, O., Fero, M., Perou, C. M., Botstein, D., and Braman, J., “Universal Reference RNA as a standard for microarray experiments.”, BMC Genomics, vol. 5, no. 1, p. 20, 2004.
J. M. S. Lemons, Feng, X. - J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., and Coller, H. A., “Quiescent fibroblasts exhibit high metabolic activity.”, PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
E. D. Schejter, Rose, L. S., Postner, M. A., and Wieschaus, E., “Role of the zygotic genome in the restructuring of the actin cytoskeleton at the cycle-14 transition during Drosophila embryogenesis.”, Cold Spring Harb Symp Quant Biol, vol. 57, pp. 653-9, 1992.
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.
J. Munger, Bennett, B. D., Parikh, A., Feng, X. - J., McArdle, J., Rabitz, H. A., Shenk, T., and Rabinowitz, J. D., “Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy.”, Nat Biotechnol, vol. 26, no. 10, pp. 1179-86, 2008.
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.
D. Papatsenko, Kislyuk, A., Levine, M., and Dubchak, I., “Conservation patterns in different functional sequence categories of divergent Drosophila species.”, Genomics, vol. 88, no. 4, pp. 431-42, 2006.
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.
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.
K. Pfeifer, Leighton, P. A., and Tilghman, S. M., “The structural H19 gene is required for transgene imprinting.”, Proc Natl Acad Sci U S A, vol. 93, no. 24, pp. 13876-83, 1996.
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.
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
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.
F. Biemar, Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., J Manak, R., and Levine, M. S., “Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.”, Proc Natl Acad Sci U S A, vol. 103, no. 34, pp. 12763-8, 2006.
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.
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., “Automatically tracking neurons in a moving and deforming brain.”, PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 2017.
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.
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.
R. A. Miller, Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cárdenas, C., Wan, M., J Foskett, K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., and Birnbaum, M. J., “Targeting hepatic glutaminase activity to ameliorate hyperglycemia.”, Nat Med, vol. 24, no. 4, pp. 518-524, 2018.
P. Engel, Kwong, W. K., McFrederick, Q., Anderson, K. E., Barribeau, S. Michael, Chandler, J. Angus, R Cornman, S., Dainat, J., de Miranda, J. R., Doublet, V., Emery, O., Evans, J. D., Farinelli, L., Flenniken, M. L., Granberg, F., Grasis, J. A., Gauthier, L., Hayer, J., Koch, H., Kocher, S., Martinson, V. G., Moran, N., Munoz-Torres, M., Newton, I., Paxton, R. J., Powell, E., Sadd, B. M., Schmid-Hempel, P., Schmid-Hempel, R., Song, S. Jin, Schwarz, R. S., vanEngelsdorp, D., and Dainat, B., “The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.”, MBio, vol. 7, no. 2, pp. e02164-15, 2016.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., “Genome sequencing reveals complex speciation in the Drosophila simulans clade.”, Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
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.
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.
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.
M. W. Perry, Boettiger, A. N., and Levine, M., “Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 108, no. 33, pp. 13570-5, 2011.

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