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Items: 1 to 20 of 72

1.

An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data.

Peng W, Zhao K.

Genome Biol. 2011 Jul 25;12(7):120. doi: 10.1186/gb-2011-12-7-120.

2.

Reptile: representative tiling for short read error correction.

Yang X, Dorman KS, Aluru S.

Bioinformatics. 2010 Oct 15;26(20):2526-33. doi: 10.1093/bioinformatics/btq468. Epub 2010 Aug 16.

PMID:
20834037
3.

BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.

Wang J, Lunyak VV, Jordan IK.

Bioinformatics. 2013 Feb 15;29(4):492-3. doi: 10.1093/bioinformatics/bts722. Epub 2013 Jan 7.

PMID:
23300134
4.

BamBam: genome sequence analysis tools for biologists.

Page JT, Liechty ZS, Huynh MD, Udall JA.

BMC Res Notes. 2014 Nov 24;7:829. doi: 10.1186/1756-0500-7-829.

5.

T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets.

Li Y, Umbach DM, Li L.

BMC Genomics. 2014 Jan 15;15:27. doi: 10.1186/1471-2164-15-27.

6.

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.

Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD.

Genome Biol. 2011 Jul 25;12(7):R67. doi: 10.1186/gb-2011-12-7-r67.

7.

REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data.

Shaik JS, Khan A, Beverley SM, Sibley LD.

BMC Genomics. 2015 Feb 26;16:133. doi: 10.1186/s12864-015-1309-7.

8.

Bioinformatics software for biologists in the genomics era.

Kumar S, Dudley J.

Bioinformatics. 2007 Jul 15;23(14):1713-7. Epub 2007 May 7.

PMID:
17485425
9.

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.

Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS.

Genome Biol. 2011;12(2):R11. doi: 10.1186/gb-2011-12-2-r11. Epub 2011 Feb 1.

10.

ChIPseek, a web-based analysis tool for ChIP data.

Chen TW, Li HP, Lee CC, Gan RC, Huang PJ, Wu TH, Lee CY, Chang YF, Tang P.

BMC Genomics. 2014 Jun 30;15:539. doi: 10.1186/1471-2164-15-539.

11.

Scaffolding pre-assembled contigs using SSPACE.

Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W.

Bioinformatics. 2011 Feb 15;27(4):578-9. doi: 10.1093/bioinformatics/btq683. Epub 2010 Dec 12.

PMID:
21149342
12.

Advances in plant genome sequencing.

Hamilton JP, Buell CR.

Plant J. 2012 Apr;70(1):177-90. doi: 10.1111/j.1365-313X.2012.04894.x. Review.

13.

Characterizing and interpreting genetic variation from personal genome sequencing.

Johansson AC, Feuk L.

Methods Mol Biol. 2012;838:343-67. doi: 10.1007/978-1-61779-507-7_17.

PMID:
22228021
14.

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.

15.

Strategy for genome sequencing analysis and assembly for comparative genomics of Pseudomonas genomes.

Jeukens J, Boyle B, Tucker NP, Levesque RC.

Methods Mol Biol. 2014;1149:565-77. doi: 10.1007/978-1-4939-0473-0_43.

PMID:
24818933
16.

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. doi: 10.1101/gr.189894.115. Epub 2015 Jul 10.

17.

Use of Next Generation Sequencing (NGS) technologies for the genome-wide detection of transposition.

Elbaidouri M, Chaparro C, Panaud O.

Methods Mol Biol. 2013;1057:265-74. doi: 10.1007/978-1-62703-568-2_19.

PMID:
23918435
18.

Short Read Alignment Using SOAP2.

Hurgobin B.

Methods Mol Biol. 2016;1374:241-52. doi: 10.1007/978-1-4939-3167-5_13.

PMID:
26519410
19.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyut├╝rk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

PMID:
21856737
20.

Evaluation and comparison of multiple aligners for next-generation sequencing data analysis.

Shang J, Zhu F, Vongsangnak W, Tang Y, Zhang W, Shen B.

Biomed Res Int. 2014;2014:309650. doi: 10.1155/2014/309650. Epub 2014 Mar 23.

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