These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

400 related articles for article (PubMed ID: 22973536)

  • 1. oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.
    Kwon AT; Arenillas DJ; Worsley Hunt R; Wasserman WW
    G3 (Bethesda); 2012 Sep; 2(9):987-1002. PubMed ID: 22973536
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.
    Worsley Hunt R; Mathelier A; Del Peso L; Wasserman WW
    BMC Genomics; 2014 Jun; 15(1):472. PubMed ID: 24927817
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Differential motif enrichment analysis of paired ChIP-seq experiments.
    Lesluyes T; Johnson J; Machanick P; Bailey TL
    BMC Genomics; 2014 Sep; 15(1):752. PubMed ID: 25179504
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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; 41(Web Server issue):W535-43. PubMed ID: 23748563
    [TBL] [Abstract][Full Text] [Related]  

  • 5. CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.
    Arenillas DJ; Forrest AR; Kawaji H; Lassmann T; ; Wasserman WW; Mathelier A
    Bioinformatics; 2016 Sep; 32(18):2858-60. PubMed ID: 27334471
    [TBL] [Abstract][Full Text] [Related]  

  • 6. SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.
    Ding J; Hu H; Li X
    Nucleic Acids Res; 2014 Mar; 42(5):e35. PubMed ID: 24322294
    [TBL] [Abstract][Full Text] [Related]  

  • 7. From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
    Kulakovskiy I; Levitsky V; Oshchepkov D; Bryzgalov L; Vorontsov I; Makeev V
    J Bioinform Comput Biol; 2013 Feb; 11(1):1340004. PubMed ID: 23427986
    [TBL] [Abstract][Full Text] [Related]  

  • 8. RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.
    Castro-Mondragon JA; Rioualen C; Contreras-Moreira B; van Helden J
    Methods Mol Biol; 2016; 1482():297-322. PubMed ID: 27557775
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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; 22(9):1798-812. PubMed ID: 22955990
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.
    Berger S; Pachkov M; Arnold P; Omidi S; Kelley N; Salatino S; van Nimwegen E
    Genome Res; 2019 Jul; 29(7):1164-1177. PubMed ID: 31138617
    [TBL] [Abstract][Full Text] [Related]  

  • 11. MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
    Xuan Lin QX; Sian S; An O; Thieffry D; Jha S; Benoukraf T
    Nucleic Acids Res; 2019 Jan; 47(D1):D145-D154. PubMed ID: 30380113
    [TBL] [Abstract][Full Text] [Related]  

  • 12. oPOSSUM: integrated tools for analysis of regulatory motif over-representation.
    Ho Sui SJ; Fulton DL; Arenillas DJ; Kwon AT; Wasserman WW
    Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W245-52. PubMed ID: 17576675
    [TBL] [Abstract][Full Text] [Related]  

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

  • 14. 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]  

  • 15. 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]  

  • 16. SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles.
    Wong KC; Li Y; Peng C; Zhang Z
    Bioinformatics; 2015 Jan; 31(1):17-24. PubMed ID: 25192742
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Analysis of Co-Associated Transcription Factors via Ordered Adjacency Differences on Motif Distribution.
    Pan G; Tang J; Guo F
    Sci Rep; 2017 Feb; 7():43597. PubMed ID: 28240320
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.
    Najafabadi HS; Albu M; Hughes TR
    Bioinformatics; 2015 Sep; 31(17):2879-81. PubMed ID: 25953800
    [TBL] [Abstract][Full Text] [Related]  

  • 19. 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]  

  • 20. ChIPulate: A comprehensive ChIP-seq simulation pipeline.
    Datta V; Hannenhalli S; Siddharthan R
    PLoS Comput Biol; 2019 Mar; 15(3):e1006921. PubMed ID: 30897079
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 20.