224 related articles for article (PubMed ID: 24279297)
1. Characterising ChIP-seq binding patterns by model-based peak shape deconvolution.
Mendoza-Parra MA; Nowicka M; Van Gool W; Gronemeyer H
BMC Genomics; 2013 Nov; 14(1):834. PubMed ID: 24279297
[TBL] [Abstract][Full Text] [Related]
2. Using combined evidence from replicates to evaluate ChIP-seq peaks.
Jalili V; Matteucci M; Masseroli M; Morelli MJ
Bioinformatics; 2015 Sep; 31(17):2761-9. PubMed ID: 25957351
[TBL] [Abstract][Full Text] [Related]
3. RECAP reveals the true statistical significance of ChIP-seq peak calls.
Chitpin JG; Awdeh A; Perkins TJ
Bioinformatics; 2019 Oct; 35(19):3592-3598. PubMed ID: 30824903
[TBL] [Abstract][Full Text] [Related]
4. Unified Analysis of Multiple ChIP-Seq Datasets.
Ma G; Babarinde IA; Zhuang Q; Hutchins AP
Methods Mol Biol; 2021; 2198():451-465. PubMed ID: 32822050
[TBL] [Abstract][Full Text] [Related]
5. The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.
Kornacker K; Rye MB; Håndstad T; Drabløs F
BMC Bioinformatics; 2012 Jul; 13():176. PubMed ID: 22827163
[TBL] [Abstract][Full Text] [Related]
6. An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.
Cheng CY; Chu CH; Hsu HW; Hsu FR; Tang CY; Wang WC; Kung HJ; Chang PC
BMC Genomics; 2014; 15 Suppl 1(Suppl 1):S1. PubMed ID: 24564277
[TBL] [Abstract][Full Text] [Related]
7. AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification.
Hiranuma N; Lundberg SM; Lee SI
Nucleic Acids Res; 2019 Jun; 47(10):e58. PubMed ID: 30869146
[TBL] [Abstract][Full Text] [Related]
8. Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.
Worsley Hunt R; Mathelier A; Del Peso L; Wasserman WW
BMC Genomics; 2014 Jun; 15(1):472. PubMed ID: 24927817
[TBL] [Abstract][Full Text] [Related]
9. ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates.
Newell R; Pienaar R; Balderson B; Piper M; Essebier A; Bodén M
Genomics; 2021 Jul; 113(4):1855-1866. PubMed ID: 33878366
[TBL] [Abstract][Full Text] [Related]
10. dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data.
Chung D; Park D; Myers K; Grass J; Kiley P; Landick R; Keleş S
PLoS Comput Biol; 2013; 9(10):e1003246. PubMed ID: 24146601
[TBL] [Abstract][Full Text] [Related]
11. Saturation analysis of ChIP-seq data for reproducible identification of binding peaks.
Hansen P; Hecht J; Ibrahim DM; Krannich A; Truss M; Robinson PN
Genome Res; 2015 Sep; 25(9):1391-400. PubMed ID: 26163319
[TBL] [Abstract][Full Text] [Related]
12. DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma.
Chen Y; Chen S; Lei EP
Bioinformatics; 2022 Sep; 38(17):4062-4069. PubMed ID: 35809062
[TBL] [Abstract][Full Text] [Related]
13. Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction.
Gomes AL; Abeel T; Peterson M; Azizi E; Lyubetskaya A; Carvalho L; Galagan J
Genome Res; 2014 Oct; 24(10):1686-97. PubMed ID: 25024162
[TBL] [Abstract][Full Text] [Related]
14. AREM: aligning short reads from ChIP-sequencing by expectation maximization.
Newkirk D; Biesinger J; Chon A; Yokomori K; Xie X
J Comput Biol; 2011 Nov; 18(11):1495-505. PubMed ID: 22035330
[TBL] [Abstract][Full Text] [Related]
15. Identifying ChIP-seq enrichment using MACS.
Feng J; Liu T; Qin B; Zhang Y; Liu XS
Nat Protoc; 2012 Sep; 7(9):1728-40. PubMed ID: 22936215
[TBL] [Abstract][Full Text] [Related]
16. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.
Chung D; Kuan PF; Li B; Sanalkumar R; Liang K; Bresnick EH; Dewey C; Keleş S
PLoS Comput Biol; 2011 Jul; 7(7):e1002111. PubMed ID: 21779159
[TBL] [Abstract][Full Text] [Related]
17. WACS: improving ChIP-seq peak calling by optimally weighting controls.
Awdeh A; Turcotte M; Perkins TJ
BMC Bioinformatics; 2021 Feb; 22(1):69. PubMed ID: 33588754
[TBL] [Abstract][Full Text] [Related]
18. Chromatin Immunoprecipitation-Sequencing (ChIP-seq) for Mapping of Estrogen Receptor-Chromatin Interactions in Breast Cancer.
Holmes KA; Brown GD; Carroll JS
Methods Mol Biol; 2016; 1366():79-98. PubMed ID: 26585129
[TBL] [Abstract][Full Text] [Related]
19. GeF-seq: A Simple Procedure for Base Pair Resolution ChIP-seq.
Chumsakul O; Nakamura K; Ishikawa S; Oshima T
Methods Mol Biol; 2018; 1837():33-47. PubMed ID: 30109604
[TBL] [Abstract][Full Text] [Related]
20. Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis.
Cortijo S; Charoensawan V; Roudier F; Wigge PA
Methods Mol Biol; 2018; 1761():231-248. PubMed ID: 29525962
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]