140 related articles for article (PubMed ID: 35100401)
1. spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions.
Hammelman J; Krismer K; Gifford DK
Nucleic Acids Res; 2022 May; 50(9):e52. PubMed ID: 35100401
[TBL] [Abstract][Full Text] [Related]
2. Supervised learning of enhancer-promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning.
Barth D; Van R; Cardwell J; Han MV
Bioinformatics; 2024 Jun; 40(6):. PubMed ID: 38870532
[TBL] [Abstract][Full Text] [Related]
3. High resolution mapping of enhancer-promoter interactions.
Reeder C; Closser M; Poh HM; Sandhu K; Wichterle H; Gifford D
PLoS One; 2015; 10(5):e0122420. PubMed ID: 25970635
[TBL] [Abstract][Full Text] [Related]
4. Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.
Chen CY; Morris Q; Mitchell JA
BMC Genomics; 2012 Apr; 13():152. PubMed ID: 22537144
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. IDR2D identifies reproducible genomic interactions.
Krismer K; Guo Y; Gifford DK
Nucleic Acids Res; 2020 Apr; 48(6):e31. PubMed ID: 32009147
[TBL] [Abstract][Full Text] [Related]
7. Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective.
Pande A; Makalowski W; Brosius J; Raabe CA
Nucleic Acids Res; 2020 Apr; 48(7):3435-3454. PubMed ID: 32133533
[TBL] [Abstract][Full Text] [Related]
8. Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions.
Bolouri H; Ruzzo WL
J Comput Biol; 2012 Sep; 19(9):989-97. PubMed ID: 22897152
[TBL] [Abstract][Full Text] [Related]
9. Occupancy maps of 208 chromatin-associated proteins in one human cell type.
Partridge EC; Chhetri SB; Prokop JW; Ramaker RC; Jansen CS; Goh ST; Mackiewicz M; Newberry KM; Brandsmeier LA; Meadows SK; Messer CL; Hardigan AA; Coppola CJ; Dean EC; Jiang S; Savic D; Mortazavi A; Wold BJ; Myers RM; Mendenhall EM
Nature; 2020 Jul; 583(7818):720-728. PubMed ID: 32728244
[TBL] [Abstract][Full Text] [Related]
10. Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.
Wang R; Wang Y; Zhang X; Zhang Y; Du X; Fang Y; Li G
BMC Genomics; 2019 May; 20(Suppl 3):296. PubMed ID: 32039697
[TBL] [Abstract][Full Text] [Related]
11. TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.
Puente-Santamaria L; Wasserman WW; Del Peso L
Bioinformatics; 2019 Dec; 35(24):5339-5340. PubMed ID: 31347689
[TBL] [Abstract][Full Text] [Related]
12. HiCoP, a simple and robust method for detecting interactions of regulatory regions.
Zhang Y; Li Z; Bian S; Zhao H; Feng D; Chen Y; Hou Y; Liu Q; Hao B
Epigenetics Chromatin; 2020 Jul; 13(1):27. PubMed ID: 32611439
[TBL] [Abstract][Full Text] [Related]
13. MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences.
Wong KC
Bioinformatics; 2017 Oct; 33(19):3028-3035. PubMed ID: 28633280
[TBL] [Abstract][Full Text] [Related]
14. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Li G; Ruan X; Auerbach RK; Sandhu KS; Zheng M; Wang P; Poh HM; Goh Y; Lim J; Zhang J; Sim HS; Peh SQ; Mulawadi FH; Ong CT; Orlov YL; Hong S; Zhang Z; Landt S; Raha D; Euskirchen G; Wei CL; Ge W; Wang H; Davis C; Fisher-Aylor KI; Mortazavi A; Gerstein M; Gingeras T; Wold B; Sun Y; Fullwood MJ; Cheung E; Liu E; Sung WK; Snyder M; Ruan Y
Cell; 2012 Jan; 148(1-2):84-98. PubMed ID: 22265404
[TBL] [Abstract][Full Text] [Related]
15. Exploiting sequence-based features for predicting enhancer-promoter interactions.
Yang Y; Zhang R; Singh S; Ma J
Bioinformatics; 2017 Jul; 33(14):i252-i260. PubMed ID: 28881991
[TBL] [Abstract][Full Text] [Related]
16. Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.
Sahlén P; Abdullayev I; Ramsköld D; Matskova L; Rilakovic N; Lötstedt B; Albert TJ; Lundeberg J; Sandberg R
Genome Biol; 2015 Aug; 16(1):156. PubMed ID: 26313521
[TBL] [Abstract][Full Text] [Related]
17. Discovering unknown human and mouse transcription factor binding sites and their characteristics from ChIP-seq data.
Yu CP; Kuo CH; Nelson CW; Chen CA; Soh ZT; Lin JJ; Hsiao RX; Chang CY; Li WH
Proc Natl Acad Sci U S A; 2021 May; 118(20):. PubMed ID: 33975951
[TBL] [Abstract][Full Text] [Related]
18. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.
Ibn-Salem J; Andrade-Navarro MA
BMC Genomics; 2019 Oct; 20(1):777. PubMed ID: 31653198
[TBL] [Abstract][Full Text] [Related]
19. CTCF-mediated chromatin loops enclose inducible gene regulatory domains.
Oti M; Falck J; Huynen MA; Zhou H
BMC Genomics; 2016 Mar; 17():252. PubMed ID: 27004515
[TBL] [Abstract][Full Text] [Related]
20. Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.
Martinez-Ara M; Comoglio F; van Arensbergen J; van Steensel B
Mol Cell; 2022 Jul; 82(13):2519-2531.e6. PubMed ID: 35594855
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
