Ben Langmead

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Fast gapped-read alignment with Bowtie 2

Steven L Salzberg, Ben Langmead, S. Salzberg, 2012, Nature Methods.

Improved metagenomic analysis with Kraken 2

Jennifer Lu, Ben Langmead, Derrick E. Wood, 2019, Genome Biology.

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

Cole Trapnell, S. Salzberg, B. Langmead, 2009, Genome Biology.

HISAT: a fast spliced aligner with low memory requirements

Steven L Salzberg, Ben Langmead, Daehwan Kim, 2015, Nature Methods.

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

Christopher Wilks, Ben Langmead, Valentin Antonescu, 2017, bioRxiv.

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

B. Langmead, K. Hansen, R. Irizarry, 2012, Genome Biology.

Alignment of Next-Generation Sequencing Reads.

Knut Reinert, David Weese, Ben Langmead, 2015, Annual review of genomics and human genetics.

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

David M. Simcha, D. Geman, B. Langmead, 2010, Nature Reviews Genetics.

Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development

Sara B. Linker, Ryan E. Mills, Kiely N. James, 2023, Nature Genetics.

REPAC: analysis of alternative polyadenylation from RNA-sequencing data

B. Langmead, L. Marchionni, C. Wilks, 2023, Genome Biology.

Unleashing alternative polyadenylation analyses with REPAC

B. Langmead, L. Marchionni, C. Wilks, 2022, bioRxiv.

Ballgown bridges the gap between transcriptome assembly and expression analysis

Alyssa C. Frazee, S. Salzberg, B. Langmead, 2015, Nature Biotechnology.

Reversible switching between epigenetic states in honeybee behavioral subcastes

Andrew P. Feinberg, Martin J. Aryee, Ben Langmead, 2012, Nature Neuroscience.

Aligning Short Sequencing Reads with Bowtie

B. Langmead, Ben Langmead, 2010, Current protocols in bioinformatics.

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

Shannon E. Ellis, B. Langmead, A. Pandey, 2019, Proteomics.

Recounting the FANTOM CAGE-Associated Transcriptome

Jay W. Shin, B. Langmead, J. Leek, 2019, bioRxiv.

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

Sara B. Linker, Ryan E. Mills, J. V. Moran, 2021, Nature Neuroscience.

ASCOT identifies key regulators of neuronal subtype-specific splicing

Brian S. Clark, B. Langmead, C. Wilks, 2018, Nature Communications.

recount3: summaries and queries for large-scale RNA-seq expression and splicing

Shijie C. Zheng, B. Langmead, K. Hansen, 2021, Genome Biology.

Megadepth: efficient coverage quantification for BigWigs and BAMs

Leonardo Collado-Torres, Christopher Wilks, Ben Langmead, 2020, bioRxiv.

A tandem simulation framework for predicting mapping quality

Ben Langmead, B. Langmead, Ben Langmead, 2017, Genome Biology.

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

A. Feinberg, B. Langmead, K. Hansen, 2014, Genome research.

Cloud-scale RNA-sequencing differential expression analysis with Myrna

B. Langmead, K. Hansen, J. Leek, 2010, Genome Biology.

Flexible analysis of transcriptome assemblies with Ballgown

Alyssa C. Frazee, Andrew E. Jaffe, Jeffrey T. Leek, 2014, bioRxiv.

Searching for SNPs with cloud computing

M. Schatz, S. Salzberg, B. Langmead, 2009, Genome Biology.

Flexible isoform-level differential expression analysis with Ballgown

Alyssa C. Frazee, S. Salzberg, B. Langmead, 2014 .

Two-stage Linked Component Analysis for Joint Decomposition of Multiple Biologically Related Data Sets

B. Langmead, B. Caffo, Luo Xiao, 2022, bioRxiv.

Reproducible RNA-seq analysis using recount2

Jeffrey T Leek, Leonardo Collado-Torres, Abhinav Nellore, 2017, Nature Biotechnology.

Cloud Computing and the DNA Data Race

Michael C. Schatz, Steven L. Salzberg, Ben Langmead, 2010, Nature Biotechnology.

Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions

Sara B. Linker, Evan Z. Macosko, Thomas G. Gilgenast, 2023, Cell genomics.

Vargas: heuristic-free alignment for assessing linear and graph read aligners

Michael C. Schatz, Ben Langmead, Ravi Gaddipati, 2019, bioRxiv.

Title of Document : Highly Scalable Short Read Alignment with the Burrows-Wheeler Transform and Cloud Computing

B. Langmead, Ben Langmead, 2009 .

Cloud computing for genomic data analysis and collaboration

B. Langmead, Abhinav Nellore, Ben Langmead, 2018, Nature Reviews Genetics.

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

B. Langmead, K. Hansen, J. Leek, 2016, Genome Biology.

Metagenome analysis using the Kraken software suite

Derrick E. Wood, S. Salzberg, B. Langmead, 2022, Nature Protocols.

Cell-specific regulation of gene expression using splicing-dependent frameshifting

Kristina J. Nielsen, Leighton H. Duncan, B. Langmead, 2022, bioRxiv.

Quality score compression improves genotyping accuracy

Bonnie Berger, Jian Peng, Alyssa C. Frazee, 2015, Nature Biotechnology.

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

K. Hansen, R. Irizarry, Benjamin Langmead, 2012, Genome Biology.

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

Eleazar Eskin, Pavel Pevzner, Serghei Mangul, 2019, Nature Biotechnology.

Fast and memory-efficient scRNA-seq k-means clustering with various distances

Vladimir Braverman, Stephanie C. Hicks, Ben Langmead, 2021, BCB.

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2015, bioRxiv.

Cloud computing for genomic data analysis and collaboration

Abhinav Nellore, Ben Langmead, B. Langmead, 2018, Nature Reviews Genetics.

Sigmoni: classification of nanopore signal with a compressed pangenome index

Mohsen Zakeri, S. Kovaka, Omar Y. Ahmed, 2023, bioRxiv.

Improved sequence mapping using a complete reference genome and lift-over

S. Koren, A. Phillippy, B. Langmead, 2022, bioRxiv.

Reducing reference bias using multiple population reference genomes

Nae-Chyun Chen, Ben Langmead, Brad Solomon, 2020, bioRxiv.

Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability

Sara B. Linker, Ryan E. Mills, J. V. Moran, 2022, Science.

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

B. Langmead, L. Florea, Li Song, 2014, Genome Biology.