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Items: 1 to 20 of 87

1.

A Bayesian changepoint analysis of ChIP-Seq data of Lamin B.

Herrmann S, Schwender H, Ickstadt K, Müller P.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):138-44. doi: 10.1016/j.bbapap.2013.09.001. Epub 2013 Sep 10.

PMID:
24036208
2.

BayesPeak: Bayesian analysis of ChIP-seq data.

Spyrou C, Stark R, Lynch AG, Tavaré S.

BMC Bioinformatics. 2009 Sep 21;10:299. doi: 10.1186/1471-2105-10-299.

3.

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin.

Lund EG, Duband-Goulet I, Oldenburg A, Buendia B, Collas P.

Nucleus. 2015;6(1):30-9. doi: 10.4161/19491034.2014.990855.

4.

BayesPeak--an R package for analysing ChIP-seq data.

Cairns J, Spyrou C, Stark R, Smith ML, Lynch AG, Tavaré S.

Bioinformatics. 2011 Mar 1;27(5):713-4. doi: 10.1093/bioinformatics/btq685. Epub 2011 Jan 17.

5.
6.

A fully Bayesian hidden Ising model for ChIP-seq data analysis.

Mo Q.

Biostatistics. 2012 Jan;13(1):113-28. doi: 10.1093/biostatistics/kxr029. Epub 2011 Sep 13.

PMID:
21914728
7.

A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments.

Gottardo R, Li W, Johnson WE, Liu XS.

Biometrics. 2008 Jun;64(2):468-78. Epub 2007 Sep 20.

PMID:
17888037
8.

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.

Xing H, Mo Y, Liao W, Zhang MQ.

PLoS Comput Biol. 2012;8(7):e1002613. doi: 10.1371/journal.pcbi.1002613. Epub 2012 Jul 26.

9.

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 2;11:369. doi: 10.1186/1471-2105-11-369.

10.

A Bayesian hidden Markov model for motif discovery through joint modeling of genomic sequence and ChIP-chip data.

Gelfond JA, Gupta M, Ibrahim JG.

Biometrics. 2009 Dec;65(4):1087-95. doi: 10.1111/j.1541-0420.2008.01180.x.

11.

Integrative analyses for omics data: a Bayesian mixture model to assess the concordance of ChIP-chip and ChIP-seq measurements.

Schäfer M, Lkhagvasuren O, Klein HU, Elling C, Wüstefeld T, Müller-Tidow C, Zender L, Koschmieder S, Dugas M, Ickstadt K.

J Toxicol Environ Health A. 2012;75(8-10):461-70. doi: 10.1080/15287394.2012.674914.

PMID:
22686305
12.

On the detection and refinement of transcription factor binding sites using ChIP-Seq data.

Hu M, Yu J, Taylor JM, Chinnaiyan AM, Qin ZS.

Nucleic Acids Res. 2010 Apr;38(7):2154-67. doi: 10.1093/nar/gkp1180. Epub 2010 Jan 6.

13.

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 1;31(13):2066-74. doi: 10.1093/bioinformatics/btv117. Epub 2015 Feb 27.

14.

A Bayesian approach to DNA sequence segmentation.

Boys RJ, Henderson DA.

Biometrics. 2004 Sep;60(3):573-81; discussion 581-8.

PMID:
15339274
15.

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.

Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M.

BMC Bioinformatics. 2007 Aug 3;8:283.

16.

A transdimensional Bayesian model for pattern recognition in DNA sequences.

Li SM, Wakefield J, Self S.

Biostatistics. 2008 Oct;9(4):668-85. doi: 10.1093/biostatistics/kxm058. Epub 2008 Mar 18.

PMID:
18349034
17.

Using R and Bioconductor for proteomics data analysis.

Gatto L, Christoforou A.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):42-51. doi: 10.1016/j.bbapap.2013.04.032. Epub 2013 May 18. Review.

PMID:
23692960
18.

Bayesian modeling of ChIP-chip data using latent variables.

Wu M, Liang F, Tian Y.

BMC Bioinformatics. 2009 Oct 26;10:352. doi: 10.1186/1471-2105-10-352.

19.

Mapping Nuclear Lamin-Genome Interactions by Chromatin Immunoprecipitation of Nuclear Lamins.

Oldenburg AR, Collas P.

Methods Mol Biol. 2016;1411:315-24. doi: 10.1007/978-1-4939-3530-7_20.

PMID:
27147051
20.

Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

Lund E, Oldenburg AR, Collas P.

Nucleic Acids Res. 2014 Jun;42(11):e92. doi: 10.1093/nar/gku324. Epub 2014 Apr 29.

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