Publications

65 Publications
Applied Filters: First Letter Of Title: I Reset

I

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Abitua PB, Wagner E, Navarrete IA, Levine M. Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature. 2012;492(7427):104–7.
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Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KCQ, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D. Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A. 2006;103(52):19848–53.
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Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 2002;13(6):1977–2000.
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Chen L, Wolf A, Fu W, Li L, Akey J. Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals. Cell. 2020;180(4):677–687.e16. PMID: 32004458
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Marstrand TT, Storey JD. Identifying and mapping cell-type-specific chromatin programming of gene expression. Proc Natl Acad Sci U S A. 2014;111(6):E645–54.
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Kimball E, Rabinowitz JD. Identifying decomposition products in extracts of cellular metabolites. Anal Biochem. 2006;358(2):273–80.
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Emberly EG, Miller J, Zeng C, Wingreen NS, Tang C. Identifying proteins of high designability via surface-exposure patterns. Proteins. 2002;47(3):295–304.
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Nirschl CJ, Suárez-Fariñas M, Izar B, Prakadan S, Dannenfelser R, Tirosh I, Liu Y, Zhu Q, Devi SP, Carroll SL, Chau D, Rezaee M, Kim T-G, Huang R, Fuentes-Duculan J, Song-Zhao GX, Gulati N, Lowes MA, King SL, Quintana FJ, Lee Y- suk, Krueger JG, Sarin KY, Yoon CH, Garraway L, Regev A, Shalek AK, Troyanskaya OG, Anandasabapathy N. IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment. Cell. 2017;170(1):127–141.e15. PMCID: PMC5569303
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Jones BK, Levorse JM, Tilghman SM. Igf2 imprinting does not require its own DNA methylation or H19 RNA. Genes Dev. 1998;12(14):2200–7.
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van Teeffelen S, Shaevitz JW, Gitai Z. Image analysis in fluorescence microscopy: bacterial dynamics as a case study. Bioessays. 2012;34(5):427–36.
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Senger K, Armstrong GW, Rowell WJ, Kwan JM, Markstein M, Levine M. Immunity regulatory DNAs share common organizational features in Drosophila. Mol Cell. 2004;13(1):19–32.
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Mulholland J, Botstein D. Immunoelectron microscopy of aldehyde-fixed yeast cells. Methods Enzymol. 2002;351:50–81.
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Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 2012;40(Web Server issue):W484–90.
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Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics. 2009;25(18):2404–10.
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Dolinski K, Troyanskaya OG. Implications of Big Data for cell biology. Mol Biol Cell. 2015;26(14):2575–8.
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Saad-Roy C, Arinaminpathy N, Wingreen N, Levin S, Akey J, Grenfell B. Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans. PLoS computational biology. 2020;16(6):e1007892. PMCID: PMC7316228
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Neumann S, Vladimirov N, Krembel AK, Wingreen NS, Sourjik V. Imprecision of adaptation in Escherichia coli chemotaxis. PLoS One. 2014;9(1):e84904.
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Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics (Oxford, England). 2021;37(Suppl_1):i133-i141. PMCID: PMC8275333
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Vizcarra CL, Zhang N, Marshall SA, Wingreen NS, Zeng C, Mayo SL. An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. J Comput Chem. 2008;29(7):1153–62.
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Zee BM, Levin RS, Xu B, LeRoy G, Wingreen NS, Garcia BA. In vivo residue-specific histone methylation dynamics. J Biol Chem. 2010;285(5):3341–50.
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Aure MR, Leivonen S-K, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T, Louhimo R, Alnæs GIG, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale A-L, Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN. Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biol. 2013;14(11):R126.
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Wang W, Cherry M, Nochomovitz Y, Jolly E, Botstein D, Li H. Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc Natl Acad Sci U S A. 2005;102(6):1998–2003.
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Huelsenbeck JP, Andolfatto P. Inference of population structure under a Dirichlet process model. Genetics. 2007;175(4):1787–802.
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Straile D, Eckmann R, Jüngling T, Thomas G, Löffler H. Influence of climate variability on whitefish (Coregonus lavaretus) year-class strength in a deep, warm monomictic lake. Oecologia. 2007;151(3):521–9.
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Boer VM, Amini S, Botstein D. Influence of genotype and nutrition on survival and metabolism of starving yeast. Proc Natl Acad Sci U S A. 2008;105(19):6930–5.
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Tkačik G, Callan CG, Bialek W. Information capacity of genetic regulatory elements. Phys Rev E Stat Nonlin Soft Matter Phys. 2008;78(1 Pt 1):011910.
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Adelman TL, Bialek W, Olberg RM. The information content of receptive fields. Neuron. 2003;40(4):823–33.
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Tkačik G, Callan CG, Bialek W. Information flow and optimization in transcriptional regulation. Proc Natl Acad Sci U S A. 2008;105(34):12265–70.
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Mehta P, Goyal S, Long T, Bassler BL, Wingreen NS. Information processing and signal integration in bacterial quorum sensing. Mol Syst Biol. 2009;5:325.
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Slonim N, Atwal GS, Tkačik G, Bialek W. Information-based clustering. Proc Natl Acad Sci U S A. 2005;102(51):18297–302.
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Olszewski K, Barsotti A, Feng X-J, Momcilovic M, Liu KG, Kim J-I, Morris K, Lamarque C, Gaffney J, Yu X, Patel JP, Rabinowitz JD, Shackelford DB, Poyurovsky M V. Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors. Cell Chem Biol. 2022;29(3):423–435.e10. PMID: 34715056
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Dejean A, Solano PJ, Ayroles J, Corbara B, Orivel J. Insect behaviour: arboreal ants build traps to capture prey. Nature. 2005;434(7036):973.
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Kauffman AL, Ashraf JM, Corces-Zimmerman R, Landis JN, Murphy CT. Insulin signaling and dietary restriction differentially influence the decline of learning and memory with age. PLoS Biol. 2010;8(5):e1000372.
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de Abreu DAF, Caballero A, Fardel P, Stroustrup N, Chen Z, Lee K, Keyes WD, Nash ZM, López-Moyado IF, Vaggi F, Cornils A, Regenass M, Neagu A, Ostojic I, Liu C, Cho Y, Sifoglu D, Shen Y, Fontana W, Lu H, Csikasz-Nagy A, Murphy CT, Antebi A, Blanc E, Apfeld J, Zhang Y, Alcedo J, Ch’ng Q. An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology. PLoS Genet. 2014;10(3):e1004225.
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Murphy CT, Hu PJ. Insulin/insulin-like growth factor signaling in C. elegans. WormBook. 2013;:1–43.
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Troyanskaya OG. Integrated analysis of microarray results. Methods Mol Biol. 2007;382:429–37.
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Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst Biol. 2010;4:180.
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Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Åslaug, Naume B, Perou CM, Haussler D, Troyanskaya OG, 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. 2012;109(8):2802–7.
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Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, Damle M, Fang B, Wang CC, Qian J, Lie N, Lanzillotta C, Rabinowitz JD, Sun Z. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol. 2017;. PMID: 28554803
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Martin AC, Gelbart M, Fernandez-Gonzalez R, Kaschube M, Wieschaus EF. Integration of contractile forces during tissue invagination. J Cell Biol. 2010;188(5):735–49.
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Vincent A, Blankenship JT, Wieschaus E. Integration of the head and trunk segmentation systems controls cephalic furrow formation in Drosophila. Development. 1997;124(19):3747–54.
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Pritykin Y, Brito T, Schüpbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA. 2017;23(7):1097–1109. PMCID: PMC5473144
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Greene CS, Troyanskaya OG. Integrative systems biology for data-driven knowledge discovery. Semin Nephrol. 2010;30(5):443–54.
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Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG. An integrative tissue-network approach to identify and test human disease genes. Nat Biotechnol. 2018;. PMID: 30346941
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Ghersi D, Singh M. Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res. 2014;42(3):e18.
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Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, Hartmann BM, Albrecht RA, García-Sastre A, Kleinstein SH, Troyanskaya OG, Sealfon SC. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015;43(3):605–14.
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Zhang X, Schwarz KN, Zhang L, Fassioli F, Fu B, Nguyen LQ, Knowles RR, Scholes GD. Interference of nuclear wavepackets in a pair of proton transfer reactions. Proceedings of the National Academy of Sciences [Internet]. Proceedings of the National Academy of Sciences; 2022;119. Referenced from doi.org: Interference of nuclear wavepackets in a pair of proton transfer reactions