1088 related articles for article (PubMed ID: 25957350)
1. 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]
2. 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]
3. 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]
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. 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]
6. MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis.
Rautio S; Lähdesmäki H
BMC Bioinformatics; 2015 Dec; 16():413. PubMed ID: 26703974
[TBL] [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; 41(21):e201. PubMed ID: 24071585
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. Mapping nucleosome positions using DNase-seq.
Zhong J; Luo K; Winter PS; Crawford GE; Iversen ES; Hartemink AJ
Genome Res; 2016 Mar; 26(3):351-64. PubMed ID: 26772197
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. TICA: Transcriptional Interaction and Coregulation Analyzer.
Perna S; Pinoli P; Ceri S; Wong L
Genomics Proteomics Bioinformatics; 2018 Oct; 16(5):342-353. PubMed ID: 30578913
[TBL] [Abstract][Full Text] [Related]
12. Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.
Jankowski A; Tiuryn J; Prabhakar S
Bioinformatics; 2016 Aug; 32(16):2419-26. PubMed ID: 27153645
[TBL] [Abstract][Full Text] [Related]
13. 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]
14. 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]
15. 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]
16. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.
Kumar S; Bucher P
BMC Bioinformatics; 2016 Jan; 17 Suppl 1(Suppl 1):4. PubMed ID: 26818008
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications.
Gusmao EG; Dieterich C; Zenke M; Costa IG
Bioinformatics; 2014 Nov; 30(22):3143-51. PubMed ID: 25086003
[TBL] [Abstract][Full Text] [Related]
19. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.
Liu S; Zibetti C; Wan J; Wang G; Blackshaw S; Qian J
BMC Bioinformatics; 2017 Jul; 18(1):355. PubMed ID: 28750606
[TBL] [Abstract][Full Text] [Related]
20. Sequence and chromatin determinants of cell-type-specific transcription factor binding.
Arvey A; Agius P; Noble WS; Leslie C
Genome Res; 2012 Sep; 22(9):1723-34. PubMed ID: 22955984
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]