178 related articles for article (PubMed ID: 25086003)
21. A rank-based statistical test for measuring synergistic effects between two gene sets.
Shiraishi Y; Okada-Hatakeyama M; Miyano S
Bioinformatics; 2011 Sep; 27(17):2399-405. PubMed ID: 21700673
[TBL] [Abstract][Full Text] [Related]
22. An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape.
Chen H; Li H; Liu F; Zheng X; Wang S; Bo X; Shu W
Sci Rep; 2015 Feb; 5():8465. PubMed ID: 25682954
[TBL] [Abstract][Full Text] [Related]
23. Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.
Jankowski A; Tiuryn J; Prabhakar S
Bioinformatics; 2016 Aug; 32(16):2419-26. PubMed ID: 27153645
[TBL] [Abstract][Full Text] [Related]
24. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.
Xi H; Shulha HP; Lin JM; Vales TR; Fu Y; Bodine DM; McKay RD; Chenoweth JG; Tesar PJ; Furey TS; Ren B; Weng Z; Crawford GE
PLoS Genet; 2007 Aug; 3(8):e136. PubMed ID: 17708682
[TBL] [Abstract][Full Text] [Related]
25. Genome-wide in silico prediction of gene expression.
McLeay RC; Lesluyes T; Cuellar Partida G; Bailey TL
Bioinformatics; 2012 Nov; 28(21):2789-96. PubMed ID: 22954627
[TBL] [Abstract][Full Text] [Related]
26. A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors.
Ji H; Vokes SA; Wong WH
Nucleic Acids Res; 2006; 34(21):e146. PubMed ID: 17090591
[TBL] [Abstract][Full Text] [Related]
27. Sparsely correlated hidden Markov models with application to genome-wide location studies.
Choi H; Fermin D; Nesvizhskii AI; Ghosh D; Qin ZS
Bioinformatics; 2013 Mar; 29(5):533-41. PubMed ID: 23325620
[TBL] [Abstract][Full Text] [Related]
28. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.
Li W; Meyer CA; Liu XS
Bioinformatics; 2005 Jun; 21 Suppl 1():i274-82. PubMed ID: 15961467
[TBL] [Abstract][Full Text] [Related]
29. ChIP-seq for the Identification of Functional Elements in the Human Genome.
Marinov GK
Methods Mol Biol; 2017; 1543():3-18. PubMed ID: 28349419
[TBL] [Abstract][Full Text] [Related]
30. Identifying differential histone modification sites from ChIP-seq data.
Xu H; Sung WK
Methods Mol Biol; 2012; 802():293-303. PubMed ID: 22130888
[TBL] [Abstract][Full Text] [Related]
31. kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets.
Fletez-Brant C; Lee D; McCallion AS; Beer MA
Nucleic Acids Res; 2013 Jul; 41(Web Server issue):W544-56. PubMed ID: 23771147
[TBL] [Abstract][Full Text] [Related]
32. De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.
Niu M; Tabari ES; Su Z
BMC Genomics; 2014 Dec; 15():1047. PubMed ID: 25442502
[TBL] [Abstract][Full Text] [Related]
33. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).
Crawford GE; Holt IE; Whittle J; Webb BD; Tai D; Davis S; Margulies EH; Chen Y; Bernat JA; Ginsburg D; Zhou D; Luo S; Vasicek TJ; Daly MJ; Wolfsberg TG; Collins FS
Genome Res; 2006 Jan; 16(1):123-31. PubMed ID: 16344561
[TBL] [Abstract][Full Text] [Related]
34. EPIGENE: genome-wide transcription unit annotation using a multivariate probabilistic model of histone modifications.
Sahu A; Li N; Dunkel I; Chung HR
Epigenetics Chromatin; 2020 Apr; 13(1):20. PubMed ID: 32264931
[TBL] [Abstract][Full Text] [Related]
35. OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.
Drawid A; Gupta N; Nagaraj VH; Gélinas C; Sengupta AM
BMC Bioinformatics; 2009 Jul; 10():208. PubMed ID: 19583839
[TBL] [Abstract][Full Text] [Related]
36. hiHMM: Bayesian non-parametric joint inference of chromatin state maps.
Sohn KA; Ho JW; Djordjevic D; Jeong HH; Park PJ; Kim JH
Bioinformatics; 2015 Jul; 31(13):2066-74. PubMed ID: 25725496
[TBL] [Abstract][Full Text] [Related]
37. Chromatin immunoprecipitation assays: analyzing transcription factor binding and histone modifications in vivo.
Pillai S; Dasgupta P; Chellappan SP
Methods Mol Biol; 2015; 1288():429-46. PubMed ID: 25827895
[TBL] [Abstract][Full Text] [Related]
38. A novel method to predict regulatory regions based on histone mark landscapes in macrophages.
Nagy G; Dániel B; Jónás D; Nagy L; Barta E
Immunobiology; 2013 Nov; 218(11):1416-27. PubMed ID: 23973299
[TBL] [Abstract][Full Text] [Related]
39. Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters.
Kininis M; Chen BS; Diehl AG; Isaacs GD; Zhang T; Siepel AC; Clark AG; Kraus WL
Mol Cell Biol; 2007 Jul; 27(14):5090-104. PubMed ID: 17515612
[TBL] [Abstract][Full Text] [Related]
40. Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.
Zacher B; Lidschreiber M; Cramer P; Gagneur J; Tresch A
Mol Syst Biol; 2014 Dec; 10(12):768. PubMed ID: 25527639
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]