Publications

128 Publications
Applied Filters: First Letter Of Title: S Reset

S

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Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Cherry M, Project SGD. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast. 2006;23(12):857–65.
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Weng S, Dong Q, Balakrishnan R, Christie KR, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry M. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003;31(1):216–8.
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Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry M. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002;30(1):69–72.
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Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry M. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004;32(Database issue):D311–4.
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Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry M. Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010;38(Database issue):D433–6.
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Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry M. Saccharomyces Genome Database. Methods Enzymol. 2002;350:329–46.
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Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry M. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004;5(1):9–22.
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Koyuncu E, Purdy JG, Rabinowitz JD, Shenk T. Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny. PLoS Pathog. 2013;9(5):e1003333.
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Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics. 2006;22(23):2890–7.
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Wingreen NS, Miller J, Cox EC. Scaling of mutational effects in models for pleiotropy. Genetics. 2003;164(3):1221–8.
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Zallen JA, Cohen Y, Hudson AM, Cooley L, Wieschaus E, Schejter ED. SCAR is a primary regulator of Arp2/3-dependent morphological events in Drosophila. J Cell Biol. 2002;156(4):689–701.
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Christiaen L, Wagner E, Shi W, Levine M. The sea squirt Ciona intestinalis. Cold Spring Harb Protoc. 2009;2009(12):pdb.emo138.
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Kocher SD, Tsuruda JM, Gibson JD, Emore CM, Arechavaleta-Velasco ME, Queller DC, Strassmann JE, Grozinger CM, Gribskov MR, San Miguel P, Westerman R, Hunt GJ. A Search for Parent-of-Origin Effects on Honey Bee Gene Expression. G3 (Bethesda). 2015;5(8):1657–62. PMCID: PMC4528322
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Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ. Searching for collective behavior in a large network of sensory neurons. PLoS Comput Biol. 2014;10(1):e1003408.
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Stephens GJ, Osborne LC, Bialek W. Searching for simplicity in the analysis of neurons and behavior. Proc Natl Acad Sci U S A. 2011;108 Suppl 3:15565–71.
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Peifer M, Rauskolb C, Williams M, Riggleman B, Wieschaus E. The segment polarity gene armadillo interacts with the wingless signaling pathway in both embryonic and adult pattern formation. Development. 1991;111(4):1029–43.
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Bejsovec A, Wieschaus E. Segment polarity gene interactions modulate epidermal patterning in Drosophila embryos. Development. 1993;119(2):501–17.
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Hughes KA, Ayroles J, Reedy MM, Drnevich JM, Rowe KC, Ruedi EA, Cáceres CE, Paige KN. Segregating variation in the transcriptome: cis regulation and additivity of effects. Genetics. 2006;173(3):1347–55.
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Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O. Selected proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinformatics. 2009;10 Suppl 2:I1.
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Bachtrog D, Andolfatto P. Selection, recombination and demographic history in Drosophila miranda. Genetics. 2006;174(4):2045–59.
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Chen KM, Cofer EM, Zhou J, Troyanskaya OG. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16(4):315–318. PMID: 30923381
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Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, Betzig E, Liphardt J. Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol. 2009;7(6):e1000137.
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Wang H, Wingreen NS, Mukhopadhyay R. Self-organized periodicity of protein clusters in growing bacteria. Phys Rev Lett. 2008;101(21):218101.
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Muratov CB, Gordon P V, Shvartsman SY. Self-similar dynamics of morphogen gradients. Phys Rev E Stat Nonlin Soft Matter Phys. 2011;84(4 Pt 1):041916.
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Osborne LC, Lisberger SG, Bialek W. A sensory source for motor variation. Nature. 2005;437(7057):412–6.
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Bajad SU, Lu W, Kimball EH, Yuan J, Peterson C, Rabinowitz JD. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J Chromatogr A. 2006;1125(1):76–88.
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Troyanskaya OG, Arbell O, Koren Y, Landau GM, Bolshoy A. Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity. Bioinformatics. 2002;18(5):679–88.
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Yang L, Canaveras JCG, Chen Z, Wang L, Liang L, Jang C, Mayr JA, Zhang Z, Ghergurovich JM, Zhan L, Joshi S, Hu Z, McReynolds MR, Su X, White E, Morscher RJ, Rabinowitz JD. Serine Catabolism Feeds NADH when Respiration Is Impaired. Cell Metab. 2020;31(4):809–821.e6. PMID: 32187526
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Ye J, Fan J, Venneti S, Wan Y-W, Pawel BR, Zhang J, Finley LWS, Lu C, Lindsten T, Cross JR, Qing G, Liu Z, Simon C, Rabinowitz JD, Thompson CB. Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia. Cancer Discov. 2014;4(12):1406–17.
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Rodriguez AE, Ducker GS, Billingham LK, Martinez CA, Mainolfi N, Suri V, Friedman A, Manfredi MG, Weinberg SE, Rabinowitz JD, Chandel NS. Serine Metabolism Supports Macrophage IL-1β Production. Cell Metab. 2019;29(4):1003–1011.e4. PMCID: PMC6447453
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Jabeen S, Zucknick M, Nome M, Dannenfelser R, Fleischer T, Kumar S, Lüders T, Gythfeldt H von der L, Troyanskaya O, Kyte JA, Børresen-Dale A-L, Naume B, Tekpli X, Engebraaten O, Kristensen V. Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab. Oncoimmunology. 2018;7(11):e1457598. PMCID: PMC6205029
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Hong J-W, Hendrix DA, Levine MS. Shadow enhancers as a source of evolutionary novelty. Science. 2008;321(5894):1314.
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Perry MW, Boettiger AN, Bothma JP, Levine M. Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol. 2010;20(17):1562–7.
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Gregor T, McGregor AP, Wieschaus EF. Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Dev Biol. 2008;316(2):350–8.
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Little SC, Wieschaus EF. Shifting patterns: merging molecules, morphogens, motility, and methodology. Dev Cell. 2011;21(1):2–4.
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Shvartsman SY. Shooting from the hip: spatial control of signal release by intracellular waves. Proc Natl Acad Sci U S A. 2002;99(14):9087–9.
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Muratov CB, Shvartsman SY. Signal propagation and failure in discrete autocrine relays. Phys Rev Lett. 2004;93(11):118101.
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Berezhkovskii AM, Coppey M, Shvartsman SY. Signaling gradients in cascades of two-state reaction-diffusion systems. Proc Natl Acad Sci U S A. 2009;106(4):1087–92.
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Bratton BP, Shaevitz JW. Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System. PLoS One. 2015;10(8):e0134616. PMCID: PMC4536040
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Haley B, Hendrix D, Trang V, Levine M. A simplified miRNA-based gene silencing method for Drosophila melanogaster. Dev Biol. 2008;321(2):482–90.