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 *

315 related articles for article (PubMed ID: 24071585)

  • 1. 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; 41(21):e201. PubMed ID: 24071585
    [TBL] [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; 31(17):2852-9. PubMed ID: 25957350
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks.
    Moyano TC; Gutiérrez RA; Alvarez JM
    Methods Mol Biol; 2021; 2328():25-46. PubMed ID: 34251618
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
    Yardımcı GG; Frank CL; Crawford GE; Ohler U
    Nucleic Acids Res; 2014 Oct; 42(19):11865-78. PubMed ID: 25294828
    [TBL] [Abstract][Full Text] [Related]  

  • 6. High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.
    Chumsakul O; Nakamura K; Kurata T; Sakamoto T; Hobman JL; Ogasawara N; Oshima T; Ishikawa S
    DNA Res; 2013 Aug; 20(4):325-38. PubMed ID: 23580539
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Analysis of computational footprinting methods for DNase sequencing experiments.
    Gusmao EG; Allhoff M; Zenke M; Costa IG
    Nat Methods; 2016 Apr; 13(4):303-9. PubMed ID: 26901649
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.
    Funk CC; Casella AM; Jung S; Richards MA; Rodriguez A; Shannon P; Donovan-Maiye R; Heavner B; Chard K; Xiao Y; Glusman G; Ertekin-Taner N; Golde TE; Toga A; Hood L; Van Horn JD; Kesselman C; Foster I; Madduri R; Price ND; Ament SA
    Cell Rep; 2020 Aug; 32(7):108029. PubMed ID: 32814038
    [TBL] [Abstract][Full Text] [Related]  

  • 9. TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.
    Ouyang N; Boyle AP
    Genome Res; 2020 Jul; 30(7):1040-1046. PubMed ID: 32660981
    [TBL] [Abstract][Full Text] [Related]  

  • 10. XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.
    Oh KS; Aqdas M; Sung MH
    Methods Mol Biol; 2024; 2846():243-261. PubMed ID: 39141240
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors.
    Piper J; Assi SA; Cauchy P; Ladroue C; Cockerill PN; Bonifer C; Ott S
    BMC Genomics; 2015 Nov; 16():1000. PubMed ID: 26608661
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.
    Karabacak Calviello A; Hirsekorn A; Wurmus R; Yusuf D; Ohler U
    Genome Biol; 2019 Feb; 20(1):42. PubMed ID: 30791920
    [TBL] [Abstract][Full Text] [Related]  

  • 13. The native cistrome and sequence motif families of the maize ear.
    Savadel SD; Hartwig T; Turpin ZM; Vera DL; Lung PY; Sui X; Blank M; Frommer WB; Dennis JH; Zhang J; Bass HW
    PLoS Genet; 2021 Aug; 17(8):e1009689. PubMed ID: 34383745
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Genome-wide discovery of active regulatory elements and transcription factor footprints in
    Ho MCW; Quintero-Cadena P; Sternberg PW
    Genome Res; 2017 Dec; 27(12):2108-2119. PubMed ID: 29074739
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain.
    Handel AE; Gallone G; Zameel Cader M; Ponting CP
    Hum Mol Genet; 2017 Jan; 26(1):79-89. PubMed ID: 27798116
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.
    Baek S; Sung MH
    Methods Mol Biol; 2016; 1418():225-40. PubMed ID: 27008018
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity.
    Baek S; Goldstein I; Hager GL
    Cell Rep; 2017 May; 19(8):1710-1722. PubMed ID: 28538187
    [TBL] [Abstract][Full Text] [Related]  

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

  • 19. Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.
    Wang C; Lv Y; Wang B; Yin C; Lin Y; Pan L
    Nucleic Acids Res; 2015 May; 43(9):4429-46. PubMed ID: 25883143
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Genome-wide footprinting: ready for prime time?
    Sung MH; Baek S; Hager GL
    Nat Methods; 2016 Mar; 13(3):222-228. PubMed ID: 26914206
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 16.