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Journal Abstract Search

212 related items for PubMed ID: 23771147

  • 1. kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets.
    Fletez-Brant C, Lee D, McCallion AS, Beer MA.
    Nucleic Acids Res; 2013 Jul; 41(Web Server issue):W544-56. PubMed ID: 23771147
    [Abstract] [Full Text] [Related]

  • 2. BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.
    Kähärä J, Lähdesmäki H.
    Bioinformatics; 2015 Sep 01; 31(17):2852-9. PubMed ID: 25957350
    [Abstract] [Full Text] [Related]

  • 3. Predicting enhancer activity and variant impact using gkm-SVM.
    Beer MA.
    Hum Mutat; 2017 Sep 01; 38(9):1251-1258. PubMed ID: 28120510
    [Abstract] [Full Text] [Related]

  • 4. MEME-ChIP: motif analysis of large DNA datasets.
    Machanick P, Bailey TL.
    Bioinformatics; 2011 Jun 15; 27(12):1696-7. PubMed ID: 21486936
    [Abstract] [Full Text] [Related]

  • 5. Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space.
    Karnik R, Beer MA.
    PLoS One; 2015 Jun 15; 10(10):e0140557. PubMed ID: 26465884
    [Abstract] [Full Text] [Related]

  • 6. iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.
    Yang CC, Andrews EH, Chen MH, Wang WY, Chen JJ, Gerstein M, Liu CC, Cheng C.
    BMC Genomics; 2016 Aug 12; 17(1):632. PubMed ID: 27519564
    [Abstract] [Full Text] [Related]

  • 7. Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.
    Piper J, Elze MC, Cauchy P, Cockerill PN, Bonifer C, Ott S.
    Nucleic Acids Res; 2013 Nov 12; 41(21):e201. PubMed ID: 24071585
    [Abstract] [Full Text] [Related]

  • 8. PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
    Zambelli F, Pesole G, Pavesi G.
    Nucleic Acids Res; 2013 Jul 12; 41(Web Server issue):W535-43. PubMed ID: 23748563
    [Abstract] [Full Text] [Related]

  • 9. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
    Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z.
    Nucleic Acids Res; 2013 Jan 12; 41(Database issue):D171-6. PubMed ID: 23203885
    [Abstract] [Full Text] [Related]

  • 10. TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.
    Dang LT, Tondl M, Chiu MHH, Revote J, Paten B, Tano V, Tokolyi A, Besse F, Quaife-Ryan G, Cumming H, Drvodelic MJ, Eichenlaub MP, Hallab JC, Stolper JS, Rossello FJ, Bogoyevitch MA, Jans DA, Nim HT, Porrello ER, Hudson JE, Ramialison M.
    BMC Genomics; 2018 Apr 05; 19(1):238. PubMed ID: 29621972
    [Abstract] [Full Text] [Related]

  • 11. TFBScluster web server for the identification of mammalian composite regulatory elements.
    Donaldson IJ, Göttgens B.
    Nucleic Acids Res; 2006 Jul 01; 34(Web Server issue):W524-8. PubMed ID: 16845063
    [Abstract] [Full Text] [Related]

  • 12. gkmSVM: an R package for gapped-kmer SVM.
    Ghandi M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, Beer MA.
    Bioinformatics; 2016 Jul 15; 32(14):2205-7. PubMed ID: 27153639
    [Abstract] [Full Text] [Related]

  • 13. Information content differentiates enhancers from silencers in mouse photoreceptors.
    Friedman RZ, Granas DM, Myers CA, Corbo JC, Cohen BA, White MA.
    Elife; 2021 Sep 06; 10():. PubMed ID: 34486522
    [Abstract] [Full Text] [Related]

  • 14. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
    Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.
    Genome Res; 2012 Sep 06; 22(9):1798-812. PubMed ID: 22955990
    [Abstract] [Full Text] [Related]

  • 15. Discriminative prediction of mammalian enhancers from DNA sequence.
    Lee D, Karchin R, Beer MA.
    Genome Res; 2011 Dec 06; 21(12):2167-80. PubMed ID: 21875935
    [Abstract] [Full Text] [Related]

  • 16. Motif enrichment tool.
    Blatti C, Sinha S.
    Nucleic Acids Res; 2014 Jul 06; 42(Web Server issue):W20-5. PubMed ID: 24860165
    [Abstract] [Full Text] [Related]

  • 17. pDHS-SVM: A prediction method for plant DNase I hypersensitive sites based on support vector machine.
    Zhang S, Zhou Z, Chen X, Hu Y, Yang L.
    J Theor Biol; 2017 Aug 07; 426():126-133. PubMed ID: 28552554
    [Abstract] [Full Text] [Related]

  • 18. MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements.
    Link VM, Romanoski CE, Metzler D, Glass CK.
    Nucleic Acids Res; 2018 Aug 21; 46(14):7006-7021. PubMed ID: 29893919
    [Abstract] [Full Text] [Related]

  • 19. Enhanced regulatory sequence prediction using gapped k-mer features.
    Ghandi M, Lee D, Mohammad-Noori M, Beer MA.
    PLoS Comput Biol; 2014 Jul 21; 10(7):e1003711. PubMed ID: 25033408
    [Abstract] [Full Text] [Related]

  • 20. DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.
    Quach B, Furey TS.
    Bioinformatics; 2017 Apr 01; 33(7):956-963. PubMed ID: 27993786
    [Abstract] [Full Text] [Related]

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