| Year |
Citation |
Score |
| 2023 |
Wu Z, Sinha S. SPREd: A simulation-supervised neural network tool for gene regulatory network reconstruction. Biorxiv : the Preprint Server For Biology. PMID 38014297 DOI: 10.1101/2023.11.09.566399 |
0.302 |
|
| 2023 |
Bhogale S, Seward C, Stubbs L, Sinha S. SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes. Biorxiv : the Preprint Server For Biology. PMID 38014229 DOI: 10.1101/2023.11.09.565900 |
0.346 |
|
| 2023 |
Louie AY, Kim JS, Drnevich J, Dibaeinia P, Koito H, Sinha S, McKim DB, Soto-Diaz K, Nowak RA, Das A, Steelman AJ. Influenza A virus infection disrupts oligodendrocyte homeostasis and alters the myelin lipidome in the adult mouse. Journal of Neuroinflammation. 20: 190. PMID 37596606 DOI: 10.1186/s12974-023-02862-2 |
0.343 |
|
| 2023 |
Kin K, Bhogale S, Zhu L, Thomas D, Bertol J, Zheng WJ, Sinha S, Fakhouri WD. Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases. Research Square. PMID 37503250 DOI: 10.21203/rs.3.rs-3037310/v1 |
0.305 |
|
| 2023 |
Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Emerging questions in transcriptional regulation. Cell Systems. 14: 247-251. PMID 37080160 DOI: 10.1016/j.cels.2023.03.005 |
0.594 |
|
| 2022 |
Bhogale S, Sinha S. Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding. Iscience. 25: 104152. PMID 35465052 DOI: 10.1016/j.isci.2022.104152 |
0.343 |
|
| 2020 |
Dibaeinia P, Sinha S. SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks. Cell Systems. PMID 32871105 DOI: 10.1016/J.Cels.2020.08.003 |
0.403 |
|
| 2020 |
Sinha S, Jones BM, Traniello IM, Bukhari SA, Halfon MS, Hofmann HA, Huang S, Katz PS, Keagy J, Lynch VJ, Sokolowski MB, Stubbs LJ, Tabe-Bordbar S, Wolfner MF, Robinson GE. Behavior-related gene regulatory networks: A new level of organization in the brain. Proceedings of the National Academy of Sciences of the United States of America. PMID 32661177 DOI: 10.1073/Pnas.1921625117 |
0.306 |
|
| 2020 |
Blatti C, Emad A, Berry MJ, Gatzke L, Epstein M, Lanier D, Rizal P, Ge J, Liao X, Sobh O, Lambert M, Post CS, Xiao J, Groves P, Epstein AT, ... ... Sinha S, et al. Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform. Plos Biology. 18: e3000583. PMID 31971940 DOI: 10.1371/Journal.Pbio.3000583 |
0.381 |
|
| 2020 |
Huang EW, Bhope A, Lim J, Sinha S, Emad A. Tissue-guided LASSO for prediction of clinical drug response using preclinical samples. Plos Computational Biology. 16: e1007607. PMID 31967990 DOI: 10.1371/Journal.Pcbi.1007607 |
0.316 |
|
| 2020 |
Rahimi N, Carmon S, Averbukh I, Khajouei F, Sinha S, Schejter ED, Barkai N, Shilo BZ. Global shape of Toll activation is determined by enhancer properties. Proceedings of the National Academy of Sciences of the United States of America. PMID 31900360 DOI: 10.1073/Pnas.1918268117 |
0.332 |
|
| 2020 |
Ghaffari S, Hanson C, Schmidt R, Bouchonville KJ, Offer SM, Sinha S. Integrated analysis of multi-omics data to identify transcriptional regulators of cancer progression F1000research. 9. DOI: 10.7490/F1000Research.1118099.1 |
0.344 |
|
| 2019 |
Xie X, Hanson C, Sinha S. Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. Bmc Biology. 17: 62. PMID 31362726 DOI: 10.1186/S12915-019-0679-8 |
0.435 |
|
| 2019 |
Peng PC, Khoueiry P, Girardot C, Reddington JP, Garfield DA, Furlong EEM, Sinha S. The role of chromatin accessibility in cis-regulatory evolution. Genome Biology and Evolution. PMID 31114856 DOI: 10.1093/Gbe/Evz103 |
0.415 |
|
| 2019 |
Wang S, Huang E, Cairns J, Peng J, Wang L, Sinha S. Identification of pathways associated with chemosensitivity through network embedding. Plos Computational Biology. 15: e1006864. PMID 30893303 DOI: 10.1371/Journal.Pcbi.1006864 |
0.376 |
|
| 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 |
0.437 |
|
| 2018 |
Khajouei F, Sinha S. An information theoretic treatment of sequence-to-expression modeling. Plos Computational Biology. 14: e1006459. PMID 30256780 DOI: 10.1371/Journal.Pcbi.1006459 |
0.395 |
|
| 2018 |
Saul MC, Blatti C, Yang W, Bukhari SA, Shpigler HY, Troy JM, Seward CH, Sloofman L, Chandrasekaran S, Bell AM, Stubbs L, Robinson GE, Zhao SD, Sinha S. Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge. Genes, Brain, and Behavior. e12502. PMID 29968347 DOI: 10.1111/Gbb.12502 |
0.366 |
|
| 2018 |
Hanson C, Cairns J, Wang L, Sinha S. Principled multi-omic analysis reveals gene regulatory mechanisms of phenotype variation. Genome Research. PMID 29898900 DOI: 10.1101/Gr.227066.117 |
0.434 |
|
| 2018 |
Tabe-Bordbar S, Emad A, Zhao SD, Sinha S. A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models. Scientific Reports. 8: 6620. PMID 29700343 DOI: 10.1038/S41598-018-24937-4 |
0.373 |
|
| 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 |
0.409 |
|
| 2017 |
Emad A, Cairns J, Kalari KR, Wang L, Sinha S. Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance. Genome Biology. 18: 153. PMID 28800781 DOI: 10.1186/S13059-017-1282-3 |
0.325 |
|
| 2017 |
Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE. Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. Elife. 6. PMID 28792889 DOI: 10.7554/Elife.28440 |
0.407 |
|
| 2017 |
Saul M, Seward CH, Troy JM, Zhang H, Sloofman LG, Lu X, Weisner PA, Caetano-Anolles D, Sun H, Zhao SD, Chandrasekaran S, Sinha S, Stubbs L. Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice. Genome Research. PMID 28356321 DOI: 10.1101/Gr.214221.116 |
0.392 |
|
| 2017 |
Shpigler HY, Saul MC, Murdoch EE, Cash-Ahmed AC, Seward CH, Sloofman L, Chandrasekaran S, Sinha S, Stubbs LJ, Robinson GE. Behavioral, transcriptomic and epigenetic responses to social challenge in honey bees. Genes, Brain, and Behavior. PMID 28328153 DOI: 10.1111/Gbb.12379 |
0.373 |
|
| 2017 |
Khoueiry P, Girardot C, Ciglar L, Peng P, Gustafson EH, Sinha S, Furlong EE. Author response: Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity Elife. DOI: 10.7554/Elife.28440.030 |
0.342 |
|
| 2016 |
Sanogo YO, Band M, Blatti C, Sinha S, Bell AM. Correction to 'Transcriptional regulation of brain gene expression in response to a territorial intrusion in sticklebacks'. Proceedings. Biological Sciences. 283. PMID 27798313 DOI: 10.1098/Rspb.2016.2082 |
0.333 |
|
| 2016 |
Yang W, Sinha S. A novel method for predicting activity of cis-regulatory modules, based on a diverse training set. Bioinformatics (Oxford, England). PMID 27609510 DOI: 10.1093/Bioinformatics/Btw552 |
0.394 |
|
| 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 |
0.442 |
|
| 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 |
0.419 |
|
| 2016 |
Blatti C, Sinha S. Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. Bioinformatics (Oxford, England). PMID 27153592 DOI: 10.1093/Bioinformatics/Btw151 |
0.379 |
|
| 2015 |
Samee MA, Lim B, Samper N, Lu H, Rushlow CA, Jiménez G, Shvartsman SY, Sinha S. A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data. Cell Systems. 1: 396-407. PMID 27136354 DOI: 10.1016/J.Cels.2015.12.002 |
0.437 |
|
| 2015 |
Hanson C, Cairns J, Wang L, Sinha S. Computational discovery of transcription factors associated with drug response. The Pharmacogenomics Journal. PMID 26503816 DOI: 10.1038/Tpj.2015.74 |
0.417 |
|
| 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 |
0.317 |
|
| 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 |
0.333 |
|
| 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 |
0.332 |
|
| 2015 |
Duque T, Sinha S. What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation. Genome Biology and Evolution. 7: 1415-31. PMID 25956793 DOI: 10.1093/Gbe/Evv080 |
0.454 |
|
| 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 |
0.458 |
|
| 2015 |
Peng PC, Hassan Samee MA, Sinha S. Incorporating chromatin accessibility data into sequence-to-expression modeling. Biophysical Journal. 108: 1257-67. PMID 25762337 DOI: 10.1016/J.Bpj.2014.12.037 |
0.469 |
|
| 2015 |
Calvert JS, Kreig A, Sinha S, Myong S. Computational Prediction of G-Quadruplex Formation Biophysical Journal. 108: 13a. DOI: 10.1016/J.Bpj.2014.11.098 |
0.41 |
|
| 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 |
0.445 |
|
| 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 |
0.383 |
|
| 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 |
0.453 |
|
| 2014 |
Blatti C, Sinha S. Motif enrichment tool. Nucleic Acids Research. 42: W20-5. PMID 24860165 DOI: 10.1093/Nar/Gku456 |
0.463 |
|
| 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 |
0.431 |
|
| 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 |
0.435 |
|
| 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 |
0.406 |
|
| 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 |
0.409 |
|
| 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 |
0.635 |
|
| 2013 |
Samee AH, Sinha S. Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data. Methods (San Diego, Calif.). 62: 79-90. PMID 23624421 DOI: 10.1016/J.Ymeth.2013.03.005 |
0.414 |
|
| 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 |
0.439 |
|
| 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 |
0.376 |
|
| 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 |
0.413 |
|
| 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 |
0.423 |
|
| 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 |
0.41 |
|
| 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 |
0.475 |
|
| 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 |
0.423 |
|
| 2011 |
Janes DE, Chapus C, Gondo Y, Clayton DF, Sinha S, Blatti CA, Organ CL, Fujita MK, Balakrishnan CN, Edwards SV. Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. Genome Biology and Evolution. 3: 102-13. PMID 21183607 DOI: 10.1093/Gbe/Evq087 |
0.44 |
|
| 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 |
0.441 |
|
| 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 |
0.449 |
|
| 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 |
0.416 |
|
| 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 |
0.47 |
|
| 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 |
0.43 |
|
| 2010 |
He X, Sinha S. ChIPs and regulatory bits. Nature Biotechnology. 28: 142-3. PMID 20139950 DOI: 10.1038/Nbt0210-142 |
0.375 |
|
| 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 |
0.481 |
|
| 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 |
0.321 |
|
| 2010 |
Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, ... ... Sinha S, et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (New York, N.Y.). 327: 343-8. PMID 20075255 DOI: 10.1126/Science.1178028 |
0.388 |
|
| 2010 |
Robinson GE, Banks JA, Padilla DK, Burggren WW, Cohen CS, Delwiche CF, Funk V, Hoekstra HE, Jarvis ED, Johnson L, Martindale MQ, Rio CMD, Medina M, Salt DE, Sinha S, et al. Empowering 21st century biology Bioscience. 60: 923-930. DOI: 10.1525/Bio.2010.60.11.8 |
0.307 |
|
| 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 |
0.451 |
|
| 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 |
0.469 |
|
| 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 |
0.386 |
|
| 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 |
0.468 |
|
| 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 |
0.451 |
|
| 2008 |
Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Research. 36: 2547-60. PMID 18332042 DOI: 10.1093/Nar/Gkn048 |
0.46 |
|
| 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 |
0.454 |
|
| 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 |
0.348 |
|
| 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 |
0.343 |
|
| 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 |
0.457 |
|
| 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 |
0.368 |
|
| 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 |
0.457 |
|
| 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 |
0.357 |
|
| 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 |
0.467 |
|
| 2006 |
Sinha S, Liang Y, Siggia E. Stubb: a program for discovery and analysis of cis-regulatory modules. Nucleic Acids Research. 34: W555-9. PMID 16845069 DOI: 10.1093/Nar/Gkl224 |
0.628 |
|
| 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 |
0.612 |
|
| 2005 |
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, ... ... Sinha S, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology. 23: 137-44. PMID 15637633 DOI: 10.1038/Nbt1053 |
0.335 |
|
| 2004 |
Sinha S, Blanchette M, Tompa M. PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. Bmc Bioinformatics. 5: 170. PMID 15511292 DOI: 10.1186/1471-2105-5-170 |
0.42 |
|
| 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 |
0.626 |
|
| 2003 |
Sinha S, van Nimwegen E, Siggia ED. A probabilistic method to detect regulatory modules. Bioinformatics (Oxford, England). 19: i292-301. PMID 12855472 DOI: 10.1093/Bioinformatics/Btg1040 |
0.602 |
|
| 2003 |
Sinha S, Tompa M. YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Research. 31: 3586-8. PMID 12824371 DOI: 10.1093/Nar/Gkg618 |
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