These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
5. Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells. Liu T Methods Mol Biol; 2014; 1150():81-95. PubMed ID: 24743991 [TBL] [Abstract][Full Text] [Related]
6. An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data. Wang C; Xu J; Zhang D; Wilson ZA; Zhang D BMC Bioinformatics; 2010 Feb; 11():81. PubMed ID: 20144209 [TBL] [Abstract][Full Text] [Related]
7. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Jothi R; Cuddapah S; Barski A; Cui K; Zhao K Nucleic Acids Res; 2008 Sep; 36(16):5221-31. PubMed ID: 18684996 [TBL] [Abstract][Full Text] [Related]
8. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. Qin ZS; Yu J; Shen J; Maher CA; Hu M; Kalyana-Sundaram S; Yu J; Chinnaiyan AM BMC Bioinformatics; 2010 Jul; 11():369. PubMed ID: 20598134 [TBL] [Abstract][Full Text] [Related]
10. Genome Wide Approaches to Identify Protein-DNA Interactions. Ma T; Ye Z; Wang L Curr Med Chem; 2019; 26(42):7641-7654. PubMed ID: 29848263 [TBL] [Abstract][Full Text] [Related]
11. 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]
12. Using CisGenome to analyze ChIP-chip and ChIP-seq data. Ji H; Jiang H; Ma W; Wong WH Curr Protoc Bioinformatics; 2011 Mar; Chapter 2():Unit2.13. PubMed ID: 21400695 [TBL] [Abstract][Full Text] [Related]
13. A fully Bayesian hidden Ising model for ChIP-seq data analysis. Mo Q Biostatistics; 2012 Jan; 13(1):113-28. PubMed ID: 21914728 [TBL] [Abstract][Full Text] [Related]
14. A comparison of peak callers used for DNase-Seq data. Koohy H; Down TA; Spivakov M; Hubbard T PLoS One; 2014; 9(5):e96303. PubMed ID: 24810143 [TBL] [Abstract][Full Text] [Related]
15. A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data. Han Z; Tian L; Pécot T; Huang T; Machiraju R; Huang K BMC Bioinformatics; 2012 Mar; 13 Suppl 2(Suppl 2):S2. PubMed ID: 22536865 [TBL] [Abstract][Full Text] [Related]
16. Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information. Osmanbeyoglu HU; Hartmaier RJ; Oesterreich S; Lu X BMC Genomics; 2012; 13 Suppl 1(Suppl 1):S1. PubMed ID: 22369349 [TBL] [Abstract][Full Text] [Related]
17. Is this the right normalization? A diagnostic tool for ChIP-seq normalization. Angelini C; Heller R; Volkinshtein R; Yekutieli D BMC Bioinformatics; 2015 May; 16():150. PubMed ID: 25957089 [TBL] [Abstract][Full Text] [Related]
18. 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]
19. 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]
20. Software for rapid time dependent ChIP-sequencing analysis (TDCA). Myschyshyn M; Farren-Dai M; Chuang TJ; Vocadlo D BMC Bioinformatics; 2017 Nov; 18(1):521. PubMed ID: 29178831 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]