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Items: 1 to 20 of 22

1.

Boiler: lossy compression of RNA-seq alignments using coverage vectors.

Pritt J, Langmead B.

Nucleic Acids Res. 2016 Jun 13. pii: gkw540. [Epub ahead of print]

2.

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B.

Bioinformatics. 2016 Aug 15;32(16):2551-3. doi: 10.1093/bioinformatics/btw177. Epub 2016 Apr 21.

3.

Alignment of Next-Generation Sequencing Reads.

Reinert K, Langmead B, Weese D, Evers DJ.

Annu Rev Genomics Hum Genet. 2015;16:133-51. doi: 10.1146/annurev-genom-090413-025358. Epub 2015 May 4. Review.

PMID:
25939052
4.

Polyester: simulating RNA-seq datasets with differential transcript expression.

Frazee AC, Jaffe AE, Langmead B, Leek JT.

Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28.

PMID:
25926345
5.

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.

Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS.

PeerJ. 2015 Mar 3;3:e808. doi: 10.7717/peerj.808. eCollection 2015.

6.

HISAT: a fast spliced aligner with low memory requirements.

Kim D, Langmead B, Salzberg SL.

Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317. Epub 2015 Mar 9.

7.

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT.

Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172. No abstract available.

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10.

Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization.

Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP.

Genome Res. 2014 Feb;24(2):177-84. doi: 10.1101/gr.157743.113. Epub 2013 Sep 25.

11.

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.

Hansen KD, Langmead B, Irizarry RA.

Genome Biol. 2012 Oct 3;13(10):R83. doi: 10.1186/gb-2012-13-10-r83.

12.

Reversible switching between epigenetic states in honeybee behavioral subcastes.

Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP.

Nat Neurosci. 2012 Oct;15(10):1371-3. doi: 10.1038/nn.3218. Epub 2012 Sep 16.

13.

Genotyping in the cloud with Crossbow.

Gurtowski J, Schatz MC, Langmead B.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 15:Unit15.3. doi: 10.1002/0471250953.bi1503s39.

14.

Fast gapped-read alignment with Bowtie 2.

Langmead B, Salzberg SL.

Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.

15.

ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.

Frazee AC, Langmead B, Leek JT.

BMC Bioinformatics. 2011 Nov 16;12:449. doi: 10.1186/1471-2105-12-449.

16.

Increased methylation variation in epigenetic domains across cancer types.

Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP.

Nat Genet. 2011 Jun 26;43(8):768-75. doi: 10.1038/ng.865.

17.

Aligning short sequencing reads with Bowtie.

Langmead B.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7. doi: 10.1002/0471250953.bi1107s32.

18.

Tackling the widespread and critical impact of batch effects in high-throughput data.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA.

Nat Rev Genet. 2010 Oct;11(10):733-9. doi: 10.1038/nrg2825. Epub 2010 Sep 14.

19.

Cloud-scale RNA-sequencing differential expression analysis with Myrna.

Langmead B, Hansen KD, Leek JT.

Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.

20.

Cloud computing and the DNA data race.

Schatz MC, Langmead B, Salzberg SL.

Nat Biotechnol. 2010 Jul;28(7):691-3. doi: 10.1038/nbt0710-691. No abstract available.

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