Saurabh Sinha - Publications

Affiliations: 
Computer Science University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 

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Year Citation  Score
2018 Roy J, Dibaeinia P, Fan TM, Sinha S, Das A. Global Analysis of Osteosarcoma Lipidomes Reveal Altered Lipid Profiles in Metastatic vs. Non-Metastatic Cells. Journal of Lipid Research. PMID 30504231 DOI: 10.1194/jlr.M088559  0.64
2017 Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. Cell Reports. 21: 236-245. PMID 28978476 DOI: 10.1016/j.celrep.2017.09.033  0.68
2016 Suryamohan K, Hanson C, Andrews E, Sinha S, Scheel MD, Halfon MS. Redeployment of a conserved gene regulatory network during Aedes aegypti development. Developmental Biology. PMID 27341759 DOI: 10.1016/j.ydbio.2016.06.031  0.68
2016 Peng PC, Sinha S. Quantitative modeling of gene expression using DNA shape features of binding sites. Nucleic Acids Research. PMID 27257066 DOI: 10.1093/nar/gkw446  0.68
2016 Kwak JT, Hewitt SM, Kajdacsy-Balla AA, Sinha S, Bhargava R. Automated prostate tissue referencing for cancer detection and diagnosis. Bmc Bioinformatics. 17: 227. PMID 27247129 DOI: 10.1186/s12859-016-1086-6  0.68
2015 Sinha S, Song J, Weinshilboum R, Jongeneel V, Han J. KnowEnG: A knowledge engine for genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26205246 DOI: 10.1093/jamia/ocv090  0.68
2015 Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, Iyer R, Schatz MC, Sinha S, Robinson GE. Big Data: Astronomical or Genomical? Plos Biology. 13: e1002195. PMID 26151137 DOI: 10.1371/journal.pbio.1002195  0.68
2015 Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, ... ... Sinha S, et al. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science (New York, N.Y.). 348: 1139-43. PMID 25977371 DOI: 10.1126/science.aaa4788  0.68
2015 Blatti C, Kazemian M, Wolfe S, Brodsky M, Sinha S. Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. Nucleic Acids Research. 43: 3998-4012. PMID 25791631 DOI: 10.1093/nar/gkv195  0.68
2015 Kwak JT, Kajdacsy-Balla A, Macias V, Walsh M, Sinha S, Bhargava R. Improving prediction of prostate cancer recurrence using chemical imaging. Scientific Reports. 5: 8758. PMID 25737022 DOI: 10.1038/srep08758  0.68
2014 Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science (New York, N.Y.). 346: 1256780. PMID 25504732 DOI: 10.1126/science.1256780  0.68
2014 Rittschof CC, Bukhari SA, Sloofman LG, Troy JM, Caetano-Anollés D, Cash-Ahmed A, Kent M, Lu X, Sanogo YO, Weisner PA, Zhang H, Bell AM, Ma J, Sinha S, Robinson GE, et al. Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee. Proceedings of the National Academy of Sciences of the United States of America. 111: 17929-34. PMID 25453090 DOI: 10.1073/pnas.1420369111  0.68
2014 Kazemian M, Suryamohan K, Chen JY, Zhang Y, Samee MA, Halfon MS, Sinha S. Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. Genome Biology and Evolution. 6: 2301-20. PMID 25173756 DOI: 10.1093/gbe/evu184  0.68
2014 Samee MA, Sinha S. Quantitative modeling of a gene's expression from its intergenic sequence. Plos Computational Biology. 10: e1003467. PMID 24604095 DOI: 10.1371/journal.pcbi.1003467  0.68
2014 Duque T, Samee MA, Kazemian M, Pham HN, Brodsky MH, Sinha S. Simulations of enhancer evolution provide mechanistic insights into gene regulation. Molecular Biology and Evolution. 31: 184-200. PMID 24097306 DOI: 10.1093/molbev/mst170  0.68
2013 Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. Plos Genetics. 9: e1003571. PMID 23935523 DOI: 10.1371/journal.pgen.1003571  0.68
2013 Kazemian M, Pham H, Wolfe SA, Brodsky MH, Sinha S. Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Research. 41: 8237-52. PMID 23847101 DOI: 10.1093/nar/gkt598  0.68
2013 Suleimenov Y, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DN. Global parameter estimation for thermodynamic models of transcriptional regulation. Methods (San Diego, Calif.). 62: 99-108. PMID 23726942 DOI: 10.1016/j.ymeth.2013.05.012  0.68
2013 Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, ... ... Sinha S, et al. Global analysis of Drosophila Cysâ‚‚-Hisâ‚‚ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Research. 23: 928-40. PMID 23471540 DOI: 10.1101/gr.151472.112  0.68
2012 Sanogo YO, Band M, Blatti C, Sinha S, Bell AM. Transcriptional regulation of brain gene expression in response to a territorial intrusion. Proceedings. Biological Sciences / the Royal Society. 279: 4929-38. PMID 23097509 DOI: 10.1098/rspb.2012.2087  0.68
2012 Ament SA, Blatti CA, Alaux C, Wheeler MM, Toth AL, Le Conte Y, Hunt GJ, Guzmán-Novoa E, Degrandi-Hoffman G, Uribe-Rubio JL, Amdam GV, Page RE, Rodriguez-Zas SL, Robinson GE, Sinha S. New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior. Proceedings of the National Academy of Sciences of the United States of America. 109: E1801-10. PMID 22691501 DOI: 10.1073/pnas.1205283109  0.68
2012 Ament SA, Wang Y, Chen CC, Blatti CA, Hong F, Liang ZS, Negre N, White KP, Rodriguez-Zas SL, Mizzen CA, Sinha S, Zhong S, Robinson GE. The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression. Plos Genetics. 8: e1002596. PMID 22479195 DOI: 10.1371/journal.pgen.1002596  0.68
2012 He X, Duque TS, Sinha S. Evolutionary origins of transcription factor binding site clusters. Molecular Biology and Evolution. 29: 1059-70. PMID 22075113 DOI: 10.1093/molbev/msr277  0.56
2011 Kazemian M, Zhu Q, Halfon MS, Sinha S. Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucleic Acids Research. 39: 9463-72. PMID 21821659 DOI: 10.1093/nar/gkr621  0.68
2011 Kazemian M, Brodsky MH, Sinha S. Genome Surveyor 2.0: cis-regulatory analysis in Drosophila. Nucleic Acids Research. 39: W79-85. PMID 21593125 DOI: 10.1093/nar/gkr291  0.68
2011 Zhu LJ, Christensen RG, Kazemian M, Hull CJ, Enuameh MS, Basciotta MD, Brasefield JA, Zhu C, Asriyan Y, Lapointe DS, Sinha S, Wolfe SA, Brodsky MH. FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Research. 39: D111-7. PMID 21097781 DOI: 10.1093/nar/gkq858  0.68
2010 He X, Samee MA, Blatti C, Sinha S. Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. Plos Computational Biology. 6. PMID 20862354 DOI: 10.1371/journal.pcbi.1000935  0.68
2010 He X, Sinha S. Evolution of cis-regulatory sequences in Drosophila. Methods in Molecular Biology (Clifton, N.J.). 674: 283-96. PMID 20827599 DOI: 10.1007/978-1-60761-854-6_18  0.56
2010 Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. Plos Biology. 8. PMID 20808951 DOI: 10.1371/journal.pbio.1000456  0.68
2010 Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, ... ... Sinha S, et al. The genome of a songbird. Nature. 464: 757-62. PMID 20360741 DOI: 10.1038/nature08819  0.68
2010 He X, Sinha S. ChIPs and regulatory bits. Nature Biotechnology. 28: 142-3. PMID 20139950 DOI: 10.1038/nbt0210-142  0.56
2010 Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. Plos Computational Biology. 6: e1000652. PMID 20126523 DOI: 10.1371/journal.pcbi.1000652  0.68
2010 Kim J, Sinha S. Towards realistic benchmarks for multiple alignments of non-coding sequences. Bmc Bioinformatics. 11: 54. PMID 20102627 DOI: 10.1186/1471-2105-11-54  1
2009 He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S. A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. Plos One. 4: e8155. PMID 19956545 DOI: 10.1371/journal.pone.0008155  0.68
2009 Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B, Halfon MS, Sinha S. Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Developmental Cell. 17: 568-79. PMID 19853570 DOI: 10.1016/j.devcel.2009.09.002  0.68
2009 Alaux C, Sinha S, Hasadsri L, Hunt GJ, Guzmán-Novoa E, DeGrandi-Hoffman G, Uribe-Rubio JL, Southey BR, Rodriguez-Zas S, Robinson GE. Honey bee aggression supports a link between gene regulation and behavioral evolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 15400-5. PMID 19706434 DOI: 10.1073/pnas.0907043106  0.68
2009 He X, Ling X, Sinha S. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. Plos Computational Biology. 5: e1000299. PMID 19293946 DOI: 10.1371/journal.pcbi.1000299  0.56
2009 Kim J, He X, Sinha S. Evolution of regulatory sequences in 12 Drosophila species. Plos Genetics. 5: e1000330. PMID 19132088 DOI: 10.1371/journal.pgen.1000330  1
2008 Sinha S, Adler AS, Field Y, Chang HY, Segal E. Systematic functional characterization of cis-regulatory motifs in human core promoters. Genome Research. 18: 477-88. PMID 18256240 DOI: 10.1101/gr.6828808  0.68
2008 Ivan A, Halfon MS, Sinha S. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biology. 9: R22. PMID 18226245 DOI: 10.1186/gb-2008-9-1-r22  0.68
2007 Adler AS, Sinha S, Kawahara TL, Zhang JY, Segal E, Chang HY. Motif module map reveals enforcement of aging by continual NF-kappaB activity. Genes & Development. 21: 3244-57. PMID 18055696 DOI: 10.1101/gad.1588507  0.68
2007 Sinha S, He X. MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules. Plos Computational Biology. 3: e216. PMID 17997594 DOI: 10.1371/journal.pcbi.0030216  0.56
2007 Sinha S. PhyME: A software tool for finding motifs in sets of orthologous sequences Methods in Molecular Biology. 395: 309-317. PMID 17993682 DOI: 10.1385/1-59745-514-8:309  0.68
2007 Kantorovitz MR, Robinson GE, Sinha S. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics (Oxford, England). 23: i249-55. PMID 17646303 DOI: 10.1093/bioinformatics/btm211  0.68
2007 Li L, Zhu Q, He X, Sinha S, Halfon MS. Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biology. 8: R101. PMID 17550599 DOI: 10.1186/gb-2007-8-6-r101  0.68
2007 Kim J, Sinha S. Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics (Oxford, England). 23: 289-97. PMID 17110370 DOI: 10.1093/bioinformatics/btl578  1
2006 Sinha S, Ling X, Whitfield CW, Zhai C, Robinson GE. Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees. Proceedings of the National Academy of Sciences of the United States of America. 103: 16352-7. PMID 17065326 DOI: 10.1073/pnas.0607448103  0.68
2005 Sinha S, Siggia ED. Sequence turnover and tandem repeats in cis-regulatory modules in drosophila. Molecular Biology and Evolution. 22: 874-85. PMID 15659554 DOI: 10.1093/molbev/msi090  0.96
2004 Sinha S, Schroeder MD, Unnerstall U, Gaul U, Siggia ED. Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. Bmc Bioinformatics. 5: 129. PMID 15357878 DOI: 10.1186/1471-2105-5-129  0.68
2003 Sinha S, van Nimwegen E, Siggia ED. A probabilistic method to detect regulatory modules. Bioinformatics (Oxford, England). 19: i292-301. PMID 12855472  0.96
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