429 related articles for article (PubMed ID: 22955983)
1. Predicting cell-type-specific gene expression from regions of open chromatin.
Natarajan A; Yardimci GG; Sheffield NC; Crawford GE; Ohler U
Genome Res; 2012 Sep; 22(9):1711-22. PubMed ID: 22955983
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. The accessible chromatin landscape of the human genome.
Thurman RE; Rynes E; Humbert R; Vierstra J; Maurano MT; Haugen E; Sheffield NC; Stergachis AB; Wang H; Vernot B; Garg K; John S; Sandstrom R; Bates D; Boatman L; Canfield TK; Diegel M; Dunn D; Ebersol AK; Frum T; Giste E; Johnson AK; Johnson EM; Kutyavin T; Lajoie B; Lee BK; Lee K; London D; Lotakis D; Neph S; Neri F; Nguyen ED; Qu H; Reynolds AP; Roach V; Safi A; Sanchez ME; Sanyal A; Shafer A; Simon JM; Song L; Vong S; Weaver M; Yan Y; Zhang Z; Zhang Z; Lenhard B; Tewari M; Dorschner MO; Hansen RS; Navas PA; Stamatoyannopoulos G; Iyer VR; Lieb JD; Sunyaev SR; Akey JM; Sabo PJ; Kaul R; Furey TS; Dekker J; Crawford GE; Stamatoyannopoulos JA
Nature; 2012 Sep; 489(7414):75-82. PubMed ID: 22955617
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. 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]
6. 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]
7. 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]
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. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.
Sheffield NC; Thurman RE; Song L; Safi A; Stamatoyannopoulos JA; Lenhard B; Crawford GE; Furey TS
Genome Res; 2013 May; 23(5):777-88. PubMed ID: 23482648
[TBL] [Abstract][Full Text] [Related]
10. Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
Wang YM; Zhou P; Wang LY; Li ZH; Zhang YN; Zhang YX
PLoS One; 2012; 7(8):e42414. PubMed ID: 22900019
[TBL] [Abstract][Full Text] [Related]
11. Genome-wide mapping of DNase I hypersensitive sites in plants.
Zhang W; Jiang J
Methods Mol Biol; 2015; 1284():71-89. PubMed ID: 25757768
[TBL] [Abstract][Full Text] [Related]
12. Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions.
Benner C; Konovalov S; Mackintosh C; Hutt KR; Stunnenberg R; Garcia-Bassets I
PLoS Genet; 2013 Nov; 9(11):e1003906. PubMed ID: 24244184
[TBL] [Abstract][Full Text] [Related]
13. Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by
Chumsakul O; Anantsri DP; Quirke T; Oshima T; Nakamura K; Ishikawa S; Nakano MM
J Bacteriol; 2017 Jul; 199(13):. PubMed ID: 28439033
[TBL] [Abstract][Full Text] [Related]
14. Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses.
Han J; Wang P; Wang Q; Lin Q; Chen Z; Yu G; Miao C; Dao Y; Wu R; Schnable JC; Tang H; Wang K
Plant Cell; 2020 Aug; 32(8):2457-2473. PubMed ID: 32471863
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals.
Chen A; Chen D; Chen Y
Gene; 2018 Aug; 667():83-94. PubMed ID: 29772251
[TBL] [Abstract][Full Text] [Related]
17. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types.
Ernst J; Kellis M
Genome Res; 2013 Jul; 23(7):1142-54. PubMed ID: 23595227
[TBL] [Abstract][Full Text] [Related]
18. Genome accessibility is widely preserved and locally modulated during mitosis.
Hsiung CC; Morrissey CS; Udugama M; Frank CL; Keller CA; Baek S; Giardine B; Crawford GE; Sung MH; Hardison RC; Blobel GA
Genome Res; 2015 Feb; 25(2):213-25. PubMed ID: 25373146
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers.
van Bömmel A; Love MI; Chung HR; Vingron M
PLoS Comput Biol; 2018 Aug; 14(8):e1006372. PubMed ID: 30142147
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
