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Items: 1 to 20 of 102

1.

Predicting chromatin organization using histone marks.

Huang J, Marco E, Pinello L, Yuan GC.

Genome Biol. 2015 Aug 14;16:162. doi: 10.1186/s13059-015-0740-z.

2.

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.

3.

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.

Oluwadare O, Cheng J.

BMC Bioinformatics. 2017 Nov 14;18(1):480. doi: 10.1186/s12859-017-1931-2.

4.

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.

5.

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications.

Lu Y, Qu W, Shan G, Zhang C.

PLoS One. 2015 Jun 19;10(6):e0130622. doi: 10.1371/journal.pone.0130622. eCollection 2015.

6.

Denoising genome-wide histone ChIP-seq with convolutional neural networks.

Koh PW, Pierson E, Kundaje A.

Bioinformatics. 2017 Jul 15;33(14):i225-i233. doi: 10.1093/bioinformatics/btx243.

7.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

8.

OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks.

Li T, Jia L, Cao Y, Chen Q, Li C.

Genome Biol. 2018 Apr 24;19(1):54. doi: 10.1186/s13059-018-1430-4.

9.

A predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2015 Oct 15;43(18):8694-712. doi: 10.1093/nar/gkv865. Epub 2015 Sep 3. Erratum in: Nucleic Acids Res. 2016 Feb 29;44(4):1977-8.

10.

Sequence and chromatin determinants of cell-type-specific transcription factor binding.

Arvey A, Agius P, Noble WS, Leslie C.

Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111.

11.

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 2;15:1047. doi: 10.1186/1471-2164-15-1047.

12.
13.

A high-throughput ChIP-Seq for large-scale chromatin studies.

Chabbert CD, Adjalley SH, Klaus B, Fritsch ES, Gupta I, Pelechano V, Steinmetz LM.

Mol Syst Biol. 2015 Jan 12;11(1):777. doi: 10.15252/msb.20145776.

14.

An integrated approach to identifying cis-regulatory modules in the human genome.

Won KJ, Agarwal S, Shen L, Shoemaker R, Ren B, Wang W.

PLoS One. 2009;4(5):e5501. doi: 10.1371/journal.pone.0005501. Epub 2009 May 12.

15.

Genome-wide epigenetic analysis of human pluripotent stem cells by ChIP and ChIP-Seq.

Hitchler MJ, Rice JC.

Methods Mol Biol. 2011;767:253-67. doi: 10.1007/978-1-61779-201-4_19.

PMID:
21822881
16.

cChIP-seq: a robust small-scale method for investigation of histone modifications.

Valensisi C, Liao JL, Andrus C, Battle SL, Hawkins RD.

BMC Genomics. 2015 Dec 21;16:1083. doi: 10.1186/s12864-015-2285-7.

17.

Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.

Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T.

Epigenetics. 2014 Sep;9(9):1238-51. doi: 10.4161/epi.29920. Epub 2014 Jul 23.

18.

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 26;14:834. doi: 10.1186/1471-2164-14-834.

19.

A pipeline for the identification and characterization of chromatin modifications derived from ChIP-Seq datasets.

Kaspi A, Ziemann M, Rafehi H, Lazarus R, El-Osta A.

Biochimie. 2012 Nov;94(11):2353-9. doi: 10.1016/j.biochi.2012.06.002. Epub 2012 Jun 13.

PMID:
22705386
20.

Standardizing chromatin research: a simple and universal method for ChIP-seq.

Arrigoni L, Richter AS, Betancourt E, Bruder K, Diehl S, Manke T, Bönisch U.

Nucleic Acids Res. 2016 Apr 20;44(7):e67. doi: 10.1093/nar/gkv1495. Epub 2015 Dec 23.

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