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Results: 1 to 20 of 107

Similar articles for PubMed (Select 21803788)

1.

Efficiently identifying genome-wide changes with next-generation sequencing data.

Huang W, Umbach DM, Vincent Jordan N, Abell AN, Johnson GL, Li L.

Nucleic Acids Res. 2011 Oct;39(19):e130. doi: 10.1093/nar/gkr592. Epub 2011 Jul 29.

2.

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.

Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP.

BMC Bioinformatics. 2014 Aug 15;15:280. doi: 10.1186/1471-2105-15-280.

3.

Normalization of ChIP-seq data with control.

Liang K, Keleş S.

BMC Bioinformatics. 2012 Aug 10;13:199. doi: 10.1186/1471-2105-13-199.

4.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A.

BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

5.

Repeat-aware modeling and correction of short read errors.

Yang X, Aluru S, Dorman KS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52. doi: 10.1186/1471-2105-12-S1-S52.

6.

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B.

BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.

7.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.

8.

A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data.

Cheng L, Zhu Y.

Bioinformatics. 2014 Jan 15;30(2):172-9. doi: 10.1093/bioinformatics/btt674. Epub 2013 Nov 21.

9.

Statistical analysis of ChIP-seq data with MOSAiCS.

Sun G, Chung D, Liang K, Keleş S.

Methods Mol Biol. 2013;1038:193-212. doi: 10.1007/978-1-62703-514-9_12.

PMID:
23872977
10.

ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.

Zomer A, Burghout P, Bootsma HJ, Hermans PW, van Hijum SA.

PLoS One. 2012;7(8):e43012. doi: 10.1371/journal.pone.0043012. Epub 2012 Aug 10.

11.

EpiChIP: gene-by-gene quantification of epigenetic modification levels.

Hebenstreit D, Gu M, Haider S, Turner DJ, Liò P, Teichmann SA.

Nucleic Acids Res. 2011 Mar;39(5):e27. doi: 10.1093/nar/gkq1226. Epub 2010 Dec 3.

12.

Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization.

Taslim C, Huang K, Huang T, Lin S.

Methods Mol Biol. 2012;802:275-91. doi: 10.1007/978-1-61779-400-1_18.

PMID:
22130887
13.

Identifying ChIP-seq enrichment using MACS.

Feng J, Liu T, Qin B, Zhang Y, Liu XS.

Nat Protoc. 2012 Sep;7(9):1728-40. doi: 10.1038/nprot.2012.101. Epub 2012 Aug 30.

14.

seqMINER: an integrated ChIP-seq data interpretation platform.

Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L.

Nucleic Acids Res. 2011 Mar;39(6):e35. doi: 10.1093/nar/gkq1287. Epub 2010 Dec 21.

15.

Normalization, bias correction, and peak calling for ChIP-seq.

Diaz A, Park K, Lim DA, Song JS.

Stat Appl Genet Mol Biol. 2012 Mar 31;11(3):Article 9. doi: 10.1515/1544-6115.1750.

16.

Massively parallel sequencing technology in pathogenic microbes.

Tripathy S, Jiang RH.

Methods Mol Biol. 2012;835:271-94. doi: 10.1007/978-1-61779-501-5_17.

PMID:
22183660
17.

Masking as an effective quality control method for next-generation sequencing data analysis.

Yun S, Yun S.

BMC Bioinformatics. 2014 Dec 13;15:382. doi: 10.1186/s12859-014-0382-2.

18.

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.

Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW.

PLoS One. 2011;6(7):e22953. doi: 10.1371/journal.pone.0022953. Epub 2011 Jul 29.

19.

ReadXplorer--visualization and analysis of mapped sequences.

Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A.

Bioinformatics. 2014 Aug 15;30(16):2247-54. doi: 10.1093/bioinformatics/btu205. Epub 2014 Apr 30.

20.

Integrative analysis of ChIP-chip and ChIP-seq dataset.

Zhu LJ.

Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8.

PMID:
23975789
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