Publications

Includes preprints

 

2017

Langmead B. A tandem simulation framework for predicting mapping quality. bioRxiv doi: 10.1101/103952.

Wilks C, Gaddipati P, Nellore A, Langmead B. Snaptron: querying and visualizing splicing across tens of thousands of RNA-seq samples. bioRxiv doi: 10.1101/097881.

2016

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive . Genome Biology. 2016, 17:266.

Describes the Intropolis resource. Research highlight by Robert & Watson.

Collado Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek J, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Research. 2016 Sept 15. Advance access.

Describes the derfinder differential expression tool.

Wulfridge P, Langmead B, Feinberg AP, Hansen KD. Choice of reference genome can introduce massive bias in bisulfite sequencing data. bioRxiv doi: 10.1101/076844.

Darby MM, Leek JT, Langmead B, Yolken RH, Sabunciyan S. Widespread Splicing of Repetitive Element Loci into Coding Regions of Gene Transcripts. Human Molecular Genetics. 2016 Sep 20. Advance access.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. recount: A large-scale resource of analysis-ready RNA-seq expression data. bioRxiv doi: 10.1101/068478.

Describes the recount resource and Bioconductor package.

Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B. Rail-RNA: Scalable analysis of RNA-seq splicing and coverage. Bioinformatics. 2016 Sep 4. Advance access.

Describes the Rail-RNA software tool, as presented at HiTSeq 2016.

Pritt J, Langmead B. Boiler: lossy compression of RNA-seq alignments using coverage vectors. Nucleic Acids Research. 2016 Sep 19;44(16):e133.

Describes the Boiler RNA-seq alignment compression tool.

Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B. Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. Bioinformatics. 2016 Aug 15;32(16):2551-3.

Describes the Rail-dbGaP software and protocol.

The Computational Pan-Genomics Consortium (incl Langmead B). Computational pan-genomics: Status, promises and challenges. Briefing in Bioinformatics. 2016 Oct 21.

2015

Reinert K, Langmead B, Weese D, Evers DJ. Alignment of Next-Generation Sequencing Reads. Annual Reviews: Genomics and Human Genetics. 2015;16:133-51.

Frazee AC, Jaffe AE, Langmead B, Leek JT. Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics. 2015 Sep 1;31(17):2778-84.

Describes the Polyester software tool.

Kim D, Langmead B, Salzberg S. HISAT: a fast spliced aligner with low memory requirementsNature Methods 2015 Apr;12(4):357-60.

Describes the HISAT software tool, based on Bowtie 2.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT.  Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology 2015 Mar;33(3):243-6.

Describes the Ballgown software tool.

Wilton R, Budavari T, Langmead B, Wheelan S, Salzberg S, Szalay, A. Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space. PeerJ 2015 3:e808.

Describes the Arioc software tool.

2014

Frazee AC, Collado Torres L, Jaffe AE, Langmead B, Leek JT. Measurement, Summary, and Methodological Variation in RNA-sequencing. Statistical Analysis of Next Generation Sequencing Data. Springer International Publishing, 2014. 115-128.

Song L, Florea L, Langmead B.  Lighter: fast and memory-efficient error correction without countingGenome Biology, 2014 Nov 15;15(11):509.

Describes the Lighter software tool.

Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalizationGenome Research. 2014 Feb;24(2):177-84.

2013

Schatz MC, Langmead B. The DNA Data DelugeIEEE Spectrum. July, 2013.

Slashdotted. JHU news release and magazine article.

2012

Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP. Reversible switching between epigenetic states in honeybee behavioral subcastesNature Neuroscience. 2012 Oct;15(10):1371-3.

Johns Hopkins Medicine news piece

Gurtowski J, Schatz MC, Langmead B. Genotyping in the cloud with crossbowCurr Protoc Bioinformatics. 2012 Sep;Chapter 15:Unit15.3.

KD Hansen*, Langmead B*, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biology, 2012;13:R83. * Equal contribution

Describes the BSmooth software tool.

Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2Nature Methods. 2012, 9:357-359.

Describes the Bowtie 2 software tool. Selected for author profile.

2011

Frazee A, Langmead B, Leek JT. ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasetsBMC Bioinformatics. 2011, 12:449.

Describes the ReCount database.

Hansen KD*, Timp W*, Corrada Bravo H*, Sabunciyan S*, Langmead B*, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. Increased methylation variation in epigenetic domains across cancer types .Nature Genetics. 2011 Jun 26;43(8):768-75. * Equal contribution

Langmead B. Aligning Short Sequencing Reads with BowtieCurr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7.

2010

Leek JT, Scharpf RB, Corrada Bravo H, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput dataNature Reviews Genetics. 2010 Sep 14.

Langmead B, Hansen KD, Leek JT. Cloud-scale RNA-sequencing differential expression analysis with MyrnaGenome Biology. 2010;11(8):R83

Describes the Myrna software tool.

Langmead B. Cloud Computing for Data Analysis: Toward the Plateau of ProductivityBio IT-World. 2010 August; Vol. 9, No. 4: 36.

Schatz MC, Langmead B, Salzberg SL. Cloud computing and the DNA data race.Nature Biotechnology. 2010 Jul;28(7):691-3.

2009

Langmead B Highly Scalable Short Read Alignment with the Burrows-Wheeler Transform and Cloud Computing 2009; Master’s thesis, University of Maryland.

Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computingGenome Biology. 2009;10(11):R134

Describes the Crossbow software tool.

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology. 2009;10(3):R25

Describes the Bowtie software tool. Winner: Genome Biology Award for outstanding article in the journal Genome Biology in 2009. Selected for minireview: The Need for Speed