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Items: 38


Analyzing whole genome bisulfite sequencing data from highly divergent genotypes.

Wulfridge P, Langmead B, Feinberg AP, Hansen KD.

Nucleic Acids Res. 2019 Aug 8. pii: gkz674. doi: 10.1093/nar/gkz674. [Epub ahead of print]


Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads.

Darby CA, Fitch JR, Brennan PJ, Kelly BJ, Bir N, Magrini V, Leonard J, Cottrell CE, Gastier-Foster JM, Wilson RK, Mardis ER, White P, Langmead B, Schatz MC.

iScience. 2019 Aug 30;18:1-10. doi: 10.1016/j.isci.2019.05.037. Epub 2019 May 29.


Prefix-free parsing for building big BWTs.

Boucher C, Gagie T, Kuhnle A, Langmead B, Manzini G, Mun T.

Algorithms Mol Biol. 2019 May 24;14:13. doi: 10.1186/s13015-019-0148-5. eCollection 2019.


Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells.

Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim MS, Pandey A.

Proteomics. 2019 Aug;19(15):e1800315. doi: 10.1002/pmic.201800315. Epub 2019 Jun 26.


How bioinformatics and open data can boost basic science in countries and universities with limited resources.

Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E.

Nat Biotechnol. 2019 Mar;37(3):324-326. doi: 10.1038/s41587-019-0053-y. No abstract available.


FORGe: prioritizing variants for graph genomes.

Pritt J, Chen NC, Langmead B.

Genome Biol. 2018 Dec 17;19(1):220. doi: 10.1186/s13059-018-1595-x.


Scaling read aligners to hundreds of threads on general-purpose processors.

Langmead B, Wilks C, Antonescu V, Charles R.

Bioinformatics. 2019 Feb 1;35(3):421-432. doi: 10.1093/bioinformatics/bty648.


Cloud computing for genomic data analysis and collaboration.

Langmead B, Nellore A.

Nat Rev Genet. 2018 May;19(5):325. doi: 10.1038/nrg.2018.8. Epub 2018 Feb 12.


Cloud computing for genomic data analysis and collaboration.

Langmead B, Nellore A.

Nat Rev Genet. 2018 Apr;19(4):208-219. doi: 10.1038/nrg.2017.113. Epub 2018 Jan 30. Review. Erratum in: Nat Rev Genet. 2018 Feb 12;:.


Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.

Wilks C, Gaddipati P, Nellore A, Langmead B.

Bioinformatics. 2018 Jan 1;34(1):114-116. doi: 10.1093/bioinformatics/btx547.


A tandem simulation framework for predicting mapping quality.

Langmead B.

Genome Biol. 2017 Aug 10;18(1):152. doi: 10.1186/s13059-017-1290-3.


Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.


Widespread splicing of repetitive element loci into coding regions of gene transcripts.

Darby MM, Leek JT, Langmead B, Yolken RH, Sabunciyan S.

Hum Mol Genet. 2016 Nov 15;25(22):4962-4982. doi: 10.1093/hmg/ddw321.


Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT.

Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.


Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.


Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B.

Bioinformatics. 2017 Dec 15;33(24):4033-4040. doi: 10.1093/bioinformatics/btw575.


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

Pritt J, Langmead B.

Nucleic Acids Res. 2016 Sep 19;44(16):e133. doi: 10.1093/nar/gkw540. Epub 2016 Jun 13.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Aligning short sequencing reads with Bowtie.

Langmead B.

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


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. Review.


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.


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.


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.


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.

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