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Results: 15

1.

Lighter: fast and memory-efficient sequencing error correction without counting.

Song L, Florea L, Langmead B.

Genome Biol. 2014 Nov 15;15(11):509. [Epub ahead of print]

PMID:
25398208
[PubMed - as supplied by publisher]
2.

The DNA Data Deluge: Fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze.

Schatz MC, Langmead B.

IEEE Spectr. 2013 Jul;50(7):26-33. No abstract available.

PMID:
24920863
[PubMed]
Free PMC Article
3.

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.

PMID:
24068705
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
23034175
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
22983211
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22948728
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22388286
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22087737
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21706001
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Aligning short sequencing reads with Bowtie.

Langmead B.

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

PMID:
21154709
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
20838408
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
20701754
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
20622843
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Searching for SNPs with cloud computing.

Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL.

Genome Biol. 2009;10(11):R134. doi: 10.1186/gb-2009-10-11-r134. Epub 2009 Nov 20.

PMID:
19930550
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

PMID:
19261174
[PubMed - indexed for MEDLINE]
Free PMC Article

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