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A. N. Boettiger and Levine, M., “Synchronous and stochastic patterns of gene activation in the Drosophila embryo.”, Science, vol. 325, no. 5939, pp. 471-3, 2009.
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.
E. Schneidman, Bialek, W., and Berry, M. J., “Synergy, redundancy, and independence in population codes.”, J Neurosci, vol. 23, no. 37, pp. 11539-53, 2003.
E. K. Farley, Olson, K. M., Zhang, W., Rokhsar, D. S., and Levine, M. S., “Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.”, Proc Natl Acad Sci U S A, vol. 113, no. 23, pp. 6508-13, 2016.
J. A. Drocco, Wieschaus, E. F., and Tank, D. W., “The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs.”, Phys Biol, vol. 9, no. 5, p. 055004, 2012.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.”, Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
S. R McIsaac, Oakes, B. L., Wang, X., Dummit, K. A., Botstein, D., and Noyes, M. B., “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.”, Nucleic Acids Res, vol. 41, no. 4, p. e57, 2013.
W. Wang, J Cherry, M., Botstein, D., and Li, H., “A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.”, Proc Natl Acad Sci U S A, vol. 99, no. 26, pp. 16893-8, 2002.
S. Nadimpalli Kobren and Singh, M., “Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.”, Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 2019.
J. Choi, Rajagopal, A., Xu, Y. - F., Rabinowitz, J. D., and O'Shea, E. K., “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
Y. Guan, Dunham, M., Caudy, A., and Troyanskaya, O., “Systematic planning of genome-scale experiments in poorly studied species.”, PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
E. S. Click, Stearns, T., and Botstein, D., “Systematic structure-function analysis of the small GTPase Arf1 in yeast.”, Mol Biol Cell, vol. 13, no. 5, pp. 1652-64, 2002.
A. V. Persikov, Wetzel, J. L., Rowland, E. F., Oakes, B. L., Xu, D. J., Singh, M., and Noyes, M. B., “A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.”, Nucleic Acids Res, vol. 43, no. 3, pp. 1965-84, 2015.
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.
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., “System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae.”, Genetics, vol. 187, no. 1, pp. 299-317, 2011.
P. Jumbo-Lucioni, Ayroles, J. F., Chambers, M. Moses, Jordan, K. W., Leips, J., Mackay, T. Fc, and De Luca, M., “Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster.”, BMC Genomics, vol. 11, p. 297, 2010.
J. F. Ayroles, Carbone, M. Anna, Stone, E. A., Jordan, K. W., Lyman, R. F., Magwire, M. M., Rollmann, S. M., Duncan, L. H., Lawrence, F., Anholt, R. R. H., and Mackay, T. F. C., “Systems genetics of complex traits in Drosophila melanogaster.”, Nat Genet, vol. 41, no. 3, pp. 299-307, 2009.
S. R. Hackett, Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O., Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D., and Rabinowitz, J. D., “Systems-level analysis of mechanisms regulating yeast metabolic flux.”, Science, vol. 354, no. 6311, 2016.
R. Lu, Markowetz, F., Unwin, R. D., Leek, J. T., Airoldi, E. M., MacArthur, B. D., Lachmann, A., Rozov, R., Ma'ayan, A., Boyer, L. A., Troyanskaya, O. G., Whetton, A. D., and Lemischka, I. R., “Systems-level dynamic analyses of fate change in murine embryonic stem cells.”, Nature, vol. 462, no. 7271, pp. 358-62, 2009.
D. Amador-Noguez, Feng, X. - J., Fan, J., Roquet, N., Rabitz, H., and Rabinowitz, J. D., “Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum.”, J Bacteriol, vol. 192, no. 17, pp. 4452-61, 2010.
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.
N. Ron-Harel, Ghergurovich, J. M., Notarangelo, G., LaFleur, M. W., Tsubosaka, Y., Sharpe, A. H., Rabinowitz, J. D., and Haigis, M. C., “T Cell Activation Depends on Extracellular Alanine.”, Cell Rep, vol. 28, no. 12, pp. 3011-3021.e4, 2019.
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.
A. Di Gregorio, Harland, R. M., Levine, M., and Casey, E. Silva, “Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle.”, Dev Biol, vol. 244, no. 2, pp. 385-95, 2002.
Q. Zhu, Wong, A. K., Krishnan, A., Aure, M. R., Tadych, A., Zhang, R., Corney, D. C., Greene, C. S., Bongo, L. A., Kristensen, V. N., Charikar, M., Li, K., and Troyanskaya, O. G., “Targeted exploration and analysis of large cross-platform human transcriptomic compendia.”, Nat Methods, vol. 12, no. 3, pp. 211-4, 3 p following 214, 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.
J. D. Rabinowitz and Vastag, L., “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
D. Botstein, “Technological innovation leads to fundamental understanding in cell biology.”, Mol Biol Cell, vol. 21, no. 22, pp. 3791-2, 2010.
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.
M. K. Shin, Levorse, J. M., Ingram, R. S., and Tilghman, S. M., “The temporal requirement for endothelin receptor-B signalling during neural crest development.”, Nature, vol. 402, no. 6761, pp. 496-501, 1999.
A. C. Martin and Wieschaus, E. F., “Tensions divide.”, Nat Cell Biol, vol. 12, no. 1, pp. 5-7, 2010.
G. I. Lang and Botstein, D., “A test of the coordinated expression hypothesis for the origin and maintenance of the GAL cluster in yeast.”, PLoS One, vol. 6, no. 9, p. e25290, 2011.
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.
D. A. Galbraith, Kocher, S. D., Glenn, T., Albert, I., Hunt, G. J., Strassmann, J. E., Queller, D. C., and Grozinger, C. M., “Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera).”, Proc Natl Acad Sci U S A, vol. 113, no. 4, pp. 1020-5, 2016.
S. Luo, Shaw, W. M., Ashraf, J., and Murphy, C. T., “TGF-beta Sma/Mab signaling mutations uncouple reproductive aging from somatic aging.”, PLoS Genet, vol. 5, no. 12, p. e1000789, 2009.
S. Luo, Kleemann, G. A., Ashraf, J. M., Shaw, W. M., and Murphy, C. T., “TGF-β and insulin signaling regulate reproductive aging via oocyte and germline quality maintenance.”, Cell, vol. 143, no. 2, pp. 299-312, 2010.
N. V. Rajeshkumar, Dutta, P., Yabuuchi, S., de Wilde, R. F., Martinez, G. V., Le, A., Kamphorst, J. J., Rabinowitz, J. D., Jain, S. K., Hidalgo, M., Dang, C. V., Gillies, R. J., and Maitra, A., “Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function.”, Cancer Res, vol. 75, no. 16, pp. 3355-64, 2015.
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.
M. Osterfield, Du, X. X., Schüpbach, T., Wieschaus, E., and Shvartsman, S. Y., “Three-dimensional epithelial morphogenesis in the developing Drosophila egg.”, Dev Cell, vol. 24, no. 4, pp. 400-10, 2013.
M. Coppey, Berezhkovskii, A. M., Sealfon, S. C., and Shvartsman, S. Y., “Time and length scales of autocrine signals in three dimensions.”, Biophys J, vol. 93, no. 6, pp. 1917-22, 2007.
L. C. Osborne, Bialek, W., and Lisberger, S. G., “Time course of information about motion direction in visual area MT of macaque monkeys.”, J Neurosci, vol. 24, no. 13, pp. 3210-22, 2004.
L. C. Osborne, Hohl, S. S., Bialek, W., and Lisberger, S. G., “Time course of precision in smooth-pursuit eye movements of monkeys.”, J Neurosci, vol. 27, no. 11, pp. 2987-98, 2007.
C. T. Murphy, Lee, S. - J., and Kenyon, C., “Tissue entrainment by feedback regulation of insulin gene expression in the endoderm of Caenorhabditis elegans.”, Proc Natl Acad Sci U S A, vol. 104, no. 48, pp. 19046-50, 2007.
T. O. Nielsen, Hsu, F. D., O'Connell, J. X., C Gilks, B., Sorensen, P. H. B., Linn, S., West, R. B., Liu, C. Long, Botstein, D., Brown, P. O., and van de Rijn, M., “Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.”, Am J Pathol, vol. 163, no. 4, pp. 1449-56, 2003.
C. Y. Park, Krishnan, A., Zhu, Q., Wong, A. K., Lee, Y. -suk, and Troyanskaya, O. G., “Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.”, Bioinformatics, 2014.
Y. Guan, Gorenshteyn, D., Burmeister, M., Wong, A. K., Schimenti, J. C., Handel, M. Ann, Bult, C. J., Hibbs, M. A., and Troyanskaya, O. G., “Tissue-specific functional networks for prioritizing phenotype and disease genes.”, PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
M. H. Feuerman, Godbout, R., Ingram, R. S., and Tilghman, S. M., “Tissue-specific transcription of the mouse alpha-fetoprotein gene promoter is dependent on HNF-1.”, Mol Cell Biol, vol. 9, no. 10, pp. 4204-12, 1989.
G. Wallace, Anshus, O. J., Bi, P., Chen, H., Chen, Y., Clark, D., Cook, P., Finkelstein, A., Funkhouser, T., Gupta, A., Hibbs, M., Li, K., Liu, Z., Samanta, R., Sukthankar, R., and Troyanskaya, O., “Tools and applications for large-scale display walls.”, IEEE Comput Graph Appl, vol. 25, no. 4, pp. 24-33, 2005.
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., “TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae.”, Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
O. Grimm, Zini, V. Sanchez, Kim, Y., Casanova, J., Shvartsman, S. Y., and Wieschaus, E., “Torso RTK controls Capicua degradation by changing its subcellular localization.”, Development, vol. 139, no. 21, pp. 3962-8, 2012.
R. G. Endres, Schulthess, T. C., and Wingreen, N. S., “Toward an atomistic model for predicting transcription-factor binding sites.”, Proteins, vol. 57, no. 2, pp. 262-8, 2004.
M. Levine and Tjian, R., “Transcription regulation and animal diversity.”, Nature, vol. 424, no. 6945, pp. 147-51, 2003.
A. Fuchs, Cheung, L. S., Charbonnier, E., Shvartsman, S. Y., and Pyrowolakis, G., “Transcriptional interpretation of the EGF receptor signaling gradient.”, Proc Natl Acad Sci U S A, vol. 109, no. 5, pp. 1572-7, 2012.
T. Ferraro, Esposito, E., Mancini, L., Ng, S., Lucas, T., Coppey, M., Dostatni, N., Walczak, A. M., Levine, M., and Lagha, M., “Transcriptional Memory in the Drosophila Embryo.”, Curr Biol, vol. 26, no. 2, pp. 212-8, 2016.
A. C. Edwards, Ayroles, J. F., Stone, E. A., Carbone, M. Anna, Lyman, R. F., and Mackay, T. F. C., “A transcriptional network associated with natural variation in Drosophila aggressive behavior.”, Genome Biol, vol. 10, no. 7, p. R76, 2009.
B. Lim, Levine, M., and Yamazaki, Y., “Transcriptional Pre-patterning of Drosophila Gastrulation.”, Curr Biol, vol. 27, no. 2, pp. 286-290, 2017.
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.
V. S. Chopra, Kong, N., and Levine, M., “Transcriptional repression via antilooping in the Drosophila embryo.”, Proc Natl Acad Sci U S A, vol. 109, no. 24, pp. 9460-4, 2012.
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J., “Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”, BMC Immunol, vol. 3, p. 5, 2002.
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.
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.
R. Kaletsky, Yao, V., Williams, A., Runnels, A. M., Tadych, A., Zhou, S., Troyanskaya, O. G., and Murphy, C. T., “Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.”, PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R., “Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”, Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
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.
T. Fukaya and Levine, M., “Transvection.”, Curr Biol, vol. 27, no. 19, pp. R1047-R1049, 2017.
N. V. Rajeshkumar, Yabuuchi, S., Pai, S. G., De Oliveira, E., Kamphorst, J. J., Rabinowitz, J. D., Tejero, H., Al-Shahrour, F., Hidalgo, M., Maitra, A., and Dang, C. V., “Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin.”, Clin Cancer Res, vol. 23, no. 18, pp. 5639-5647, 2017.
J. C. García-Cañaveras, Chen, L., and Rabinowitz, J. D., “The Tumor Metabolic Microenvironment: Lessons from Lactate.”, Cancer Res, vol. 79, no. 13, pp. 3155-3162, 2019.
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A. F. Schober, Mathis, A. D., Ingle, C., Park, J. O., Chen, L., Rabinowitz, J. D., Junier, I., Rivoire, O., and Reynolds, K. A., “A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism.”, Cell Rep, vol. 27, no. 11, pp. 3359-3370.e7, 2019.
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S. P. Bohen, Troyanskaya, O. G., Alter, O., Warnke, R., Botstein, D., Brown, P. O., and Levy, R., “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
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