178 related articles for article (PubMed ID: 25086003)
1. 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]
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. 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. 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]
5. PlantDHS: a database for DNase I hypersensitive sites in plants.
Zhang T; Marand AP; Jiang J
Nucleic Acids Res; 2016 Jan; 44(D1):D1148-53. PubMed ID: 26400163
[TBL] [Abstract][Full Text] [Related]
6. Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context.
Ha M; Hong S; Li WH
Bioinformatics; 2013 May; 29(9):1199-205. PubMed ID: 23511541
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.
Shu W; Chen H; Bo X; Wang S
Nucleic Acids Res; 2011 Sep; 39(17):7428-43. PubMed ID: 21685456
[TBL] [Abstract][Full Text] [Related]
9. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica.
Du Z; Li H; Wei Q; Zhao X; Wang C; Zhu Q; Yi X; Xu W; Liu XS; Jin W; Su Z
Mol Plant; 2013 Sep; 6(5):1463-72. PubMed ID: 23355544
[TBL] [Abstract][Full Text] [Related]
10. Modeling co-occupancy of transcription factors using chromatin features.
Liu L; Zhao W; Zhou X
Nucleic Acids Res; 2016 Mar; 44(5):e49. PubMed ID: 26590261
[TBL] [Abstract][Full Text] [Related]
11. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.
Xu H; Wei CL; Lin F; Sung WK
Bioinformatics; 2008 Oct; 24(20):2344-9. PubMed ID: 18667444
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.
Lan X; Witt H; Katsumura K; Ye Z; Wang Q; Bresnick EH; Farnham PJ; Jin VX
Nucleic Acids Res; 2012 Sep; 40(16):7690-704. PubMed ID: 22675074
[TBL] [Abstract][Full Text] [Related]
14. MCAST: scanning for cis-regulatory motif clusters.
Grant CE; Johnson J; Bailey TL; Noble WS
Bioinformatics; 2016 Apr; 32(8):1217-9. PubMed ID: 26704599
[TBL] [Abstract][Full Text] [Related]
15. Differential regulation of the IL-10 gene in Th1 and Th2 T cells.
Kang KH; Im SH
Ann N Y Acad Sci; 2005 Jun; 1050():97-107. PubMed ID: 16014524
[TBL] [Abstract][Full Text] [Related]
16. A quantitative analysis of the impact on chromatin accessibility by histone modifications and binding of transcription factors in DNase I hypersensitive sites.
Cui P; Li J; Sun B; Zhang M; Lian B; Li Y; Xie L
Biomed Res Int; 2013; 2013():914971. PubMed ID: 24236298
[TBL] [Abstract][Full Text] [Related]
17. Detecting differential peaks in ChIP-seq signals with ODIN.
Allhoff M; Seré K; Chauvistré H; Lin Q; Zenke M; Costa IG
Bioinformatics; 2014 Dec; 30(24):3467-75. PubMed ID: 25371479
[TBL] [Abstract][Full Text] [Related]
18. High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.
Whitington T; Perkins AC; Bailey TL
Nucleic Acids Res; 2009 Jan; 37(1):14-25. PubMed ID: 18988630
[TBL] [Abstract][Full Text] [Related]
19. An integrated approach to identifying cis-regulatory modules in the human genome.
Won KJ; Agarwal S; Shen L; Shoemaker R; Ren B; Wang W
PLoS One; 2009; 4(5):e5501. PubMed ID: 19434238
[TBL] [Abstract][Full Text] [Related]
20. 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]
[Next] [New Search]