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

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
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A. Stathopoulos, Van Drenth, M., Erives, A., Markstein, M., and Levine, M., Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo., Cell, vol. 111, no. 5, pp. 687-701, 2002.
A. Stathopoulos and Levine, M., Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo., Dev Biol, vol. 280, no. 2, pp. 482-93, 2005.
A. Stathopoulos, Tam, B., Ronshaugen, M., Frasch, M., and Levine, M., pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos., Genes Dev, vol. 18, no. 6, pp. 687-99, 2004.
A. Stathopoulos and Levine, M., Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset., Development, vol. 129, no. 14, pp. 3411-9, 2002.
M. Stadlmeier, Runtsch, L. Simon, Streshnev, F., Wühr, M., and Carell, T., A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry., Chembiochem, 2019.
B. T. Spear and Tilghman, S. M., Role of alpha-fetoprotein regulatory elements in transcriptional activation in transient heterokaryons., Mol Cell Biol, vol. 10, no. 10, pp. 5047-54, 1990.
V. Sourjik and Wingreen, N. S., Turning to the cold., Nat Cell Biol, vol. 9, no. 9, pp. 1029-31, 2007.
V. Sourjik and Wingreen, N. S., Responding to chemical gradients: bacterial chemotaxis., Curr Opin Cell Biol, vol. 24, no. 2, pp. 262-8, 2012.
T. Sorlie, Tibshirani, R., Parker, J., Hastie, T., Marron, J. S., Nobel, A., Deng, S., Johnsen, H., Pesich, R., Geisler, S., Demeter, J., Perou, C. M., Lønning, P. E., Brown, P. O., Børresen-Dale, A. - L., and Botstein, D., Repeated observation of breast tumor subtypes in independent gene expression data sets., Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8418-23, 2003.
J. Song and Singh, M., From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization., PLoS Comput Biol, vol. 9, no. 2, p. e1002910, 2013.
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.
J. Song and Singh, M., How and when should interactome-derived clusters be used to predict functional modules and protein function?, Bioinformatics, vol. 25, no. 23, pp. 3143-50, 2009.
Y. Song, Park, J. O., Tanner, L., Nagano, Y., Rabinowitz, J. D., and Shvartsman, S. Y., Energy budget of Drosophila embryogenesis., Curr Biol, vol. 29, no. 12, pp. R566-R567, 2019.
H. G. Son, Seo, M., Ham, S., Hwang, W., Lee, D., An, S. Woo A., Artan, M., Seo, K., Kaletsky, R., Arey, R. N., Ryu, Y., Ha, C. Man, Kim, Y. Ki, Murphy, C. T., Roh, T. - Y., Nam, H. Gil, and Lee, S. - J. V., RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans., Nat Commun, vol. 8, p. 14749, 2017.
A. Marie Sokac and Wieschaus, E., Local actin-dependent endocytosis is zygotically controlled to initiate Drosophila cellularization., Dev Cell, vol. 14, no. 5, pp. 775-86, 2008.
A. Marie Sokac and Wieschaus, E., Zygotically controlled F-actin establishes cortical compartments to stabilize furrows during Drosophila cellularization., J Cell Sci, vol. 121, no. Pt 11, pp. 1815-24, 2008.
K. S. Smith, Chanda, S. K., Lingbeek, M., Ross, D. T., Botstein, D., van Lohuizen, M., and Cleary, M. L., Bmi-1 regulation of INK4A-ARF is a downstream requirement for transformation of hematopoietic progenitors by E2a-Pbx1., Mol Cell, vol. 12, no. 2, pp. 393-400, 2003.
T. Slotte, Hazzouri, K. M., Stern, D., Andolfatto, P., and Wright, S. I., Genetic architecture and adaptive significance of the selfing syndrome in Capsella., Evolution, vol. 66, no. 5, pp. 1360-74, 2012.
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., The Capsella rubella genome and the genomic consequences of rapid mating system evolution., Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
N. Slonim, Atwal, G. Singh, Tkačik, G., and Bialek, W., Information-based clustering., Proc Natl Acad Sci U S A, vol. 102, no. 51, pp. 18297-302, 2005.
N. Slavov and Botstein, D., Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast., Mol Biol Cell, vol. 22, no. 12, pp. 1997-2009, 2011.
N. Slavov, Macinskas, J., Caudy, A., and Botstein, D., Metabolic cycling without cell division cycling in respiring yeast., Proc Natl Acad Sci U S A, vol. 108, no. 47, pp. 19090-5, 2011.
N. Slavov, Airoldi, E. M., van Oudenaarden, A., and Botstein, D., A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes., Mol Biol Cell, vol. 23, no. 10, pp. 1986-97, 2012.
N. Slavov and Botstein, D., Decoupling nutrient signaling from growth rate causes aerobic glycolysis and deregulation of cell size and gene expression., Mol Biol Cell, vol. 24, no. 2, pp. 157-68, 2013.
M. Skoge, Meir, Y., and Wingreen, N. S., Dynamics of cooperativity in chemical sensing among cell-surface receptors., Phys Rev Lett, vol. 107, no. 17, p. 178101, 2011.
M. Skoge, Naqvi, S., Meir, Y., and Wingreen, N. S., Chemical sensing by nonequilibrium cooperative receptors., Phys Rev Lett, vol. 110, no. 24, p. 248102, 2013.
M. Skoge, Naqvi, S., Meir, Y., and Wingreen, N. S., Chemical Sensing by Nonequilibrium Cooperative Receptors., Phys Rev Lett, vol. 110, no. 24, 2013.
M. L. Skoge, Endres, R. G., and Wingreen, N. S., Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters., Biophys J, vol. 90, no. 12, pp. 4317-26, 2006.
L. Simpson and Wieschaus, E., Zygotic activity of the nullo locus is required to stabilize the actin-myosin network during cellularization in Drosophila., Development, vol. 110, no. 3, pp. 851-63, 1990.
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.
S. J. Silverman, Petti, A. A., Slavov, N., Parsons, L., Briehof, R., Thiberge, S. Y., Zenklusen, D., Gandhi, S. J., Larson, D. R., Singer, R. H., and Botstein, D., Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate., Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
R. Shyamsundar, Kim, Y. H., Higgins, J. P., Montgomery, K., Jorden, M., Sethuraman, A., van de Rijn, M., Botstein, D., Brown, P. O., and Pollack, J. R., A DNA microarray survey of gene expression in normal human tissues., Genome Biol, vol. 6, no. 3, p. R22, 2005.
S. Y. Shvartsman, Muratov, C. B., and Lauffenburger, D. A., Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis., Development, vol. 129, no. 11, pp. 2577-89, 2002.
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., MAPK signaling in equations and embryos., Fly (Austin), vol. 3, no. 1, pp. 62-7, 2009.
S. Y. Shvartsman, Coppey, M., and Berezhkovskii, A. M., Dynamics of maternal morphogen gradients in Drosophila., Curr Opin Genet Dev, vol. 18, no. 4, pp. 342-7, 2008.
S. Y. Shvartsman, Shooting from the hip: spatial control of signal release by intracellular waves., Proc Natl Acad Sci U S A, vol. 99, no. 14, pp. 9087-9, 2002.
S. Y. Shvartsman and Baker, R. E., Mathematical models of morphogen gradients and their effects on gene expression., Wiley Interdiscip Rev Dev Biol, vol. 1, no. 5, pp. 715-30, 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.
M. K. Shin, Russell, L. B., and Tilghman, S. M., Molecular characterization of four induced alleles at the Ednrb locus., Proc Natl Acad Sci U S A, vol. 94, no. 24, pp. 13105-10, 1997.
C. Shi, Runnels, A. M., and Murphy, C. T., Mating and male pheromone kill Caenorhabditis males through distinct mechanisms., Elife, vol. 6, 2017.
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.
C. Shi and Murphy, C. T., Mating induces shrinking and death in Caenorhabditis mothers., Science, vol. 343, no. 6170, pp. 536-40, 2014.
C. Shi and Murphy, C. T., Feeding the germline., Genes Dev, vol. 30, no. 3, pp. 249-50, 2016.
W. Shi, Levine, M., and Davidson, B., Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis., Genome Res, vol. 15, no. 12, pp. 1668-74, 2005.
W. M. Shaw, Luo, S., Landis, J., Ashraf, J., and Murphy, C. T., The C. elegans TGF-beta Dauer pathway regulates longevity via insulin signaling., Curr Biol, vol. 17, no. 19, pp. 1635-45, 2007.
T. Sharpee, Rust, N. C., and Bialek, W., Analyzing neural responses to natural signals: maximally informative dimensions., Neural Comput, vol. 16, no. 2, pp. 223-50, 2004.
T. Sharpee and Bialek, W., Neural decision boundaries for maximal information transmission., PLoS One, vol. 2, no. 7, p. e646, 2007.
M. Shapira, Segal, E., and Botstein, D., Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress., Mol Biol Cell, vol. 15, no. 12, pp. 5659-69, 2004.
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.
J. W. Shaevitz and Fletcher, D. A., Curvature and torsion in growing actin networks., Phys Biol, vol. 5, no. 2, p. 026006, 2008.
J. W. Shaevitz, Super-resolution for a 3D world., Nat Methods, vol. 5, no. 6, pp. 471-2, 2008.
J. W. Shaevitz, Abbondanzieri, E. A., Landick, R., and Block, S. M., Backtracking by single RNA polymerase molecules observed at near-base-pair resolution., Nature, vol. 426, no. 6967, pp. 684-7, 2003.
J. W. Shaevitz and Gitai, Z., The structure and function of bacterial actin homologs., Cold Spring Harb Perspect Biol, vol. 2, no. 9, p. a000364, 2010.
J. W. Shaevitz, Combining modeling and experiment to understand bacterial growth., Biophys J, vol. 104, no. 12, p. 2573, 2013.
J. W. Shaevitz and Fletcher, D. A., Load fluctuations drive actin network growth., Proc Natl Acad Sci U S A, vol. 104, no. 40, pp. 15688-92, 2007.
J. W. Shaevitz, Block, S. M., and Schnitzer, M. J., Statistical kinetics of macromolecular dynamics., Biophys J, vol. 89, no. 4, pp. 2277-85, 2005.
J. W. Shaevitz, Lee, J. Y., and Fletcher, D. A., Spiroplasma swim by a processive change in body helicity., Cell, vol. 122, no. 6, pp. 941-5, 2005.
J. W. Shaevitz and Fletcher, D. A., Enhanced three-dimensional deconvolution microscopy using a measured depth-varying point-spread function., J Opt Soc Am A Opt Image Sci Vis, vol. 24, no. 9, pp. 2622-7, 2007.
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.
E. Semenova, Wang, X. F., Jablonski, M. M., Levorse, J., and Tilghman, S. M., An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina., Hum Mol Genet, vol. 12, no. 11, pp. 1301-12, 2003.
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.
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.
R. S. G. Sealfon, Hibbs, M. A., Huttenhower, C., Myers, C. L., and Troyanskaya, O. G., GOLEM: an interactive graph-based gene-ontology navigation and analysis tool., BMC Bioinformatics, vol. 7, p. 443, 2006.
T. Schupbach and Wieschaus, E., Germline autonomy of maternal-effect mutations altering the embryonic body pattern of Drosophila., Dev Biol, vol. 113, no. 2, pp. 443-8, 1986.
T. Schupbach and Wieschaus, E., Female sterile mutations on the second chromosome of Drosophila melanogaster. I. Maternal effect mutations., Genetics, vol. 121, no. 1, pp. 101-17, 1989.
T. Schupbach and Wieschaus, E., Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking oogenesis or altering egg morphology., Genetics, vol. 129, no. 4, pp. 1119-36, 1991.
T. Schupbach and Wieschaus, E., Probing for gene specificity in epithelial development., Int J Dev Biol, vol. 42, no. 3, pp. 249-55, 1998.
M. Schumer, Rosenthal, G. G., and Andolfatto, P., How common is homoploid hybrid speciation?, Evolution, vol. 68, no. 6, pp. 1553-60, 2014.
M. Schumer, Cui, R., Boussau, B., Walter, R., Rosenthal, G., and Andolfatto, P., An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences., Evolution, vol. 67, no. 4, pp. 1155-68, 2013.
M. Schumer, Cui, R., Powell, D. L., Dresner, R., Rosenthal, G. G., and Andolfatto, P., High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species., Elife, vol. 3, 2014.
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.
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, Still, S., Berry, M. J., and Bialek, W., Network information and connected correlations., Phys Rev Lett, vol. 91, no. 23, p. 238701, 2003.
E. Schneidman, Berry, M. J., Segev, R., and Bialek, W., Weak pairwise correlations imply strongly correlated network states in a neural population., Nature, vol. 440, no. 7087, pp. 1007-12, 2006.
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.
J. V. Schmidt, Matteson, P. G., Jones, B. K., Guan, X. J., and Tilghman, S. M., The Dlk1 and Gtl2 genes are linked and reciprocally imprinted., Genes Dev, vol. 14, no. 16, pp. 1997-2002, 2000.
J. V. Schmidt, Levorse, J. M., and Tilghman, S. M., Enhancer competition between H19 and Igf2 does not mediate their imprinting., Proc Natl Acad Sci U S A, vol. 96, no. 17, pp. 9733-8, 1999.
E. D. Schejter and Wieschaus, E., bottleneck acts as a regulator of the microfilament network governing cellularization of the Drosophila embryo., Cell, vol. 75, no. 2, pp. 373-85, 1993.
E. D. Schejter and Wieschaus, E., Functional elements of the cytoskeleton in the early Drosophila embryo., Annu Rev Cell Biol, vol. 9, pp. 67-99, 1993.
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.
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. Schacherer, Ruderfer, D. M., Gresham, D., Dolinski, K., Botstein, D., and Kruglyak, L., Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains., PLoS One, vol. 2, no. 3, p. e322, 2007.
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.
D. Sargin, Chottekalapanda, R. U., Perit, K. E., Yao, V., Chu, D., Sparks, D. W., Kalik, S., Power, S. K., Troyanskaya, O. G., Schmidt, E. F., Greengard, P., and Lambe, E. K., Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons., Mol Psychiatry, 2019.
L. L. Sandell, Guan, X. - J., Ingram, R., and Tilghman, S. M., Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta., Proc Natl Acad Sci U S A, vol. 100, no. 8, pp. 4622-7, 2003.
C. Sample and Shvartsman, S. Y., Multiscale modeling of diffusion in the early Drosophila embryo., Proc Natl Acad Sci U S A, vol. 107, no. 22, pp. 10092-6, 2010.
L. Salwinski, Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. Chatr, Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G., and Hermjakob, H., Recurated protein interaction datasets., Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.
A. J. Saldanha, Brauer, M. J., and Botstein, D., Nutritional homeostasis in batch and steady-state culture of yeast., Mol Biol Cell, vol. 15, no. 9, pp. 4089-104, 2004.
B. Sabass, Koch, M. D., Liu, G., Stone, H. A., and Shaevitz, J. W., Force generation by groups of migrating bacteria., Proc Natl Acad Sci U S A, vol. 114, no. 28, pp. 7266-7271, 2017.
R
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. C. Rowe, Singhal, S., Macmanes, M. D., Ayroles, J. F., Morelli, T. Lyn, Rubidge, E. M., Bi, K., and Moritz, C. C., Museum genomics: low-cost and high-accuracy genetic data from historical specimens., Mol Ecol Resour, vol. 11, no. 6, pp. 1082-92, 2011.
J. M. Rossi, Burke, D. T., Leung, J. C., Koos, D. S., Chen, H., and Tilghman, S. M., Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts., Proc Natl Acad Sci U S A, vol. 89, no. 6, pp. 2456-60, 1992.
J. M. Rossi, Chen, H., and Tilghman, S. M., Genetic map of the fused locus on mouse chromosome 17., Genomics, vol. 23, no. 1, pp. 178-84, 1994.
M. J. Rosenbluth, Crow, A., Shaevitz, J. W., and Fletcher, D. A., Slow stress propagation in adherent cells., Biophys J, vol. 95, no. 12, pp. 6052-9, 2008.
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.
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.
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.
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.
N. Ron-Harel, Santos, D., Ghergurovich, J. M., Sage, P. T., Reddy, A., Lovitch, S. B., Dephoure, N., F Satterstrom, K., Sheffer, M., Spinelli, J. B., Gygi, S., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation., Cell Metab, vol. 24, no. 1, pp. 104-17, 2016.
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.
R. L. Rogers, Cridland, J. M., Shao, L., Hu, T. T., Andolfatto, P., and Thornton, K. R., Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans., Mol Biol Evol, vol. 31, no. 7, pp. 1750-66, 2014.
R. L. Rogers, Shao, L., Sanjak, J. S., Andolfatto, P., and Thornton, K. R., Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group., G3 (Bethesda), vol. 4, no. 12, pp. 2345-51, 2014.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., Uncoupling neurogenic gene networks in the Drosophila embryo., Genes Dev, vol. 31, no. 7, pp. 634-638, 2017.
A. E. Rodriguez, Ducker, G. S., Billingham, L. K., Martinez, C. A., Mainolfi, N., Suri, V., Friedman, A., Manfredi, M. G., Weinberg, S. E., Rabinowitz, J. D., and Chandel, N. S., Serine Metabolism Supports Macrophage IL-1β Production., Cell Metab, vol. 29, no. 4, pp. 1003-1011.e4, 2019.
L. H. Rodan, Qi, W., Ducker, G. S., Demirbas, D., Laine, R., Yang, E., Walker, M. A., Eichler, F., Rabinowitz, J. D., Anselm, I., and Berry, G. T., 5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination., Mol Genet Metab, vol. 125, no. 1-2, pp. 118-126, 2018.
D. G. Robinson and Storey, J. D., subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling., Bioinformatics, vol. 30, no. 23, pp. 3424-6, 2014.
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., Design and analysis of Bar-seq experiments., G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
A. M. Roberts, Wong, A. K., Fisk, I., and Troyanskaya, O. G., GIANT API: an application programming interface for functional genomics., Nucleic Acids Res, 2016.
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.
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