BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

227 related articles for article (PubMed ID: 29893919)

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

  • 2. MEDEA: analysis of transcription factor binding motifs in accessible chromatin.
    Mariani L; Weinand K; Gisselbrecht SS; Bulyk ML
    Genome Res; 2020 May; 30(5):736-748. PubMed ID: 32424069
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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; 19(1):238. PubMed ID: 29621972
    [TBL] [Abstract][Full Text] [Related]  

  • 4. MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.
    Klepper K; Drabløs F
    BMC Bioinformatics; 2013 Jan; 14():9. PubMed ID: 23323883
    [TBL] [Abstract][Full Text] [Related]  

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

  • 6. COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.
    Ha N; Polychronidou M; Lohmann I
    PLoS One; 2012; 7(12):e52055. PubMed ID: 23272209
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
    Heinz S; Benner C; Spann N; Bertolino E; Lin YC; Laslo P; Cheng JX; Murre C; Singh H; Glass CK
    Mol Cell; 2010 May; 38(4):576-89. PubMed ID: 20513432
    [TBL] [Abstract][Full Text] [Related]  

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

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

  • 10. Inferring direct DNA binding from ChIP-seq.
    Bailey TL; Machanick P
    Nucleic Acids Res; 2012 Sep; 40(17):e128. PubMed ID: 22610855
    [TBL] [Abstract][Full Text] [Related]  

  • 11. XL-DNase-seq: improved footprinting of dynamic transcription factors.
    Oh KS; Ha J; Baek S; Sung MH
    Epigenetics Chromatin; 2019 Jun; 12(1):30. PubMed ID: 31164146
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Integrative analysis of ChIP-chip and ChIP-seq dataset.
    Zhu LJ
    Methods Mol Biol; 2013; 1067():105-24. PubMed ID: 23975789
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Genome-wide analysis of chromatin accessibility using ATAC-seq.
    Shashikant T; Ettensohn CA
    Methods Cell Biol; 2019; 151():219-235. PubMed ID: 30948010
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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
    [TBL] [Abstract][Full Text] [Related]  

  • 15. CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction.
    Guzman C; D'Orso I
    BMC Bioinformatics; 2017 Aug; 18(1):363. PubMed ID: 28789639
    [TBL] [Abstract][Full Text] [Related]  

  • 16. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
    Qin Q; Mei S; Wu Q; Sun H; Li L; Taing L; Chen S; Li F; Liu T; Zang C; Xu H; Chen Y; Meyer CA; Zhang Y; Brown M; Long HW; Liu XS
    BMC Bioinformatics; 2016 Oct; 17(1):404. PubMed ID: 27716038
    [TBL] [Abstract][Full Text] [Related]  

  • 17. RSAT 2015: Regulatory Sequence Analysis Tools.
    Medina-Rivera A; Defrance M; Sand O; Herrmann C; Castro-Mondragon JA; Delerce J; Jaeger S; Blanchet C; Vincens P; Caron C; Staines DM; Contreras-Moreira B; Artufel M; Charbonnier-Khamvongsa L; Hernandez C; Thieffry D; Thomas-Chollier M; van Helden J
    Nucleic Acids Res; 2015 Jul; 43(W1):W50-6. PubMed ID: 25904632
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells.
    Wong KC; Li Y; Peng C
    Bioinformatics; 2016 Feb; 32(3):321-4. PubMed ID: 26411866
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.
    Ng FS; Schütte J; Ruau D; Diamanti E; Hannah R; Kinston SJ; Göttgens B
    Nucleic Acids Res; 2014 Dec; 42(22):13513-24. PubMed ID: 25428352
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations.
    Ramaker RC; Hardigan AA; Goh ST; Partridge EC; Wold B; Cooper SJ; Myers RM
    Genome Res; 2020 Jul; 30(7):939-950. PubMed ID: 32616518
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.