B. Langmead

发表

Fast gapped-read alignment with Bowtie 2

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

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

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

Cloud-scale RNA-sequencing differential expression analysis with Myrna

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

Searching for SNPs with cloud computing

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

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

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

HISAT: a fast spliced aligner with low memory requirements

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

Increased methylation variation in epigenetic domains across cancer types

A. Feinberg, B. Langmead, K. Hansen, 2011, Nature Genetics.

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

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

Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression

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

Flexible isoform-level differential expression analysis with Ballgown

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

Ballgown bridges the gap between transcriptome assembly and expression analysis

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

Cloud computing for genomic data analysis and collaboration

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

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

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

Aligning Short Sequencing Reads with Bowtie

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

Improved metagenomic analysis with Kraken 2

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

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

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

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.

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

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

Reference flow: reducing reference bias using multiple population genomes

B. Langmead, Brad Solomon, Nae-Chyun Chen, 2021, Genome biology.

FORGe: prioritizing variants for graph genomes

Nae-Chyun Chen, Jacob Pritt, Ben Langmead, 2018, Genome Biology.

Reversible switching between epigenetic states in honeybee behavioral subcastes

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

Samovar: Single-sample mosaic SNV calling with linked reads

Charlotte A. Darby, M. Schatz, R. Wilson, 2019, bioRxiv.

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

Charlotte A. Darby, M. Schatz, R. Wilson, 2019, iScience.

Measurement, Summary, and Methodological Variation in RNA-sequencing

Alyssa C. Frazee, Leonardo Collado Torres, B. Langmead, 2014 .

Recounting the FANTOM CAGEAssociated Transcriptome.

Jay W. Shin, Alexander V. Favorov, B. Langmead, 2020, Genome research.

Recounting the FANTOM CAGE-Associated Transcriptome

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

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

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

Improved metagenomic analysis with Kraken 2

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

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

B. Langmead, Ben Langmead, 2009 .

Unleashing alternative polyadenylation analyses with REPAC

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

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

B. Langmead, C. Boucher, G. Manzini, 2020, Journal of computational biology : a journal of computational molecular cell biology.

ASCOT identifies key regulators of neuronal subtype-specific splicing

Brian S. Clark, B. Langmead, P. Leavey, 2020, Nature Communications.

ASCOT identifies key regulators of neuronal subtype-specific splicing

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

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes

A. Feinberg, B. Langmead, K. Hansen, 2016, bioRxiv.

Choice of reference genome can introduce massive bias in bisulfite sequencing data

A. Feinberg, B. Langmead, K. Hansen, 2016 .

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2016, bioRxiv.

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

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

Flexible expressed region analysis for RNA-seq with derfinder

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

Prefix-free parsing for building big BWTs

B. Langmead, C. Boucher, G. Manzini, 2019, Algorithms for molecular biology : AMB.

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

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

Pangenomic Genotyping with the Marker Array

B. Langmead, Taher Mun, N. Vaddadi, 2022, bioRxiv.

SPUMONI 2: Improved pangenome classification using a compressed index of minimizer digests

B. Langmead, C. Boucher, T. Gagie, 2022, bioRxiv.

Metagenome analysis using the Kraken software suite

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

Dashing 2: genomic sketching with multiplicities and locality-sensitive hashing

Daniel N. Baker, B. Langmead, 2023, bioRxiv.

Dashing 2: genomic sketching with multiplicities and locality-sensitive hashing

Daniel N. Baker, B. Langmead, 2022, bioRxiv.

Computational pan-genomics: status, promises and challenges

Ying Zhang, Eleazar Eskin, Knut Reinert, 2016, bioRxiv.

A scalable and unbiased discordance metric with H+

Daniel N. Baker, B. Langmead, V. Braverman, 2022, bioRxiv.

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

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

Dashing 2: genomic sketching with multiplicities and locality-sensitive hashing

Daniel N. Baker, B. Langmead, 2023, bioRxiv.

Dashing: fast and accurate genomic distances with HyperLogLog

Daniel N. Baker, Benjamin Langmead, Daniel N Baker, 2018, Genome Biology.

Lighter: fast and memory-efficient error correction without counting

Ben Langmead, Li Song, Liliana Florea, 2014, bioRxiv.

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

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

minicore: Fast scRNA-seq clustering with various distances

Daniel N. Baker, B. Langmead, V. Braverman, 2021, bioRxiv.

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

J. V. Moran, Michael E. Coulter, Laurel L. Ball, 2019, bioRxiv.

Reproducible RNA-seq analysis using recount2

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

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

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

Human splicing diversity across the Sequence Read Archive

Siruo Wang, Leonardo Collado-Torres, Andrew E. Jaffe, 2016, bioRxiv.

FORGe: prioritizing variants for graph genomes

B. Langmead, Nae-Chyun Chen, Jacob Pritt, 2018, bioRxiv.

Reducing reference bias using multiple population reference genomes

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

HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts

Steven L. Salzberg, Daehwan Kim, Benjamin Langmead, 2014, bioRxiv.

The DNA data deluge

M. C. Schatz, B. Langmead, M. Schatz, 2013, IEEE Spectrum.

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.

Cloud computing for genomic data analysis and collaboration

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

REPAC: analysis of alternative polyadenylation from RNA-sequencing data

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

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

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

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

Jeffrey T Leek, Ben Langmead, Sarven Sabunciyan, 2016, Human molecular genetics.

Alignment of Next-Generation Sequencing Reads.

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

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

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

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

Christina Boucher, Travis Gagie, Giovanni Manzini, 2018, bioRxiv.

Cloud Computing and the DNA Data Race

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

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

Alexander S. Szalay, Steven L. Salzberg, Tamas Budavari, 2015, PeerJ.

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

Ben Langmead, Michael C Schatz, M. Schatz, 2013, IEEE spectrum.

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.

DandD: efficient measurement of sequence growth and similarity

B. Langmead, J. Bonnie, Omar Ahmed, 2023, bioRxiv.

A tandem simulation framework for predicting mapping quality

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

WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs

B. Langmead, S. Seshia, K. Chao, 2023, bioRxiv.

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2015, bioRxiv.

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2015, bioRxiv.

Unleashing alternative polyadenylation analyses with REPAC

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

MONI: A Pangenomics Index for Finding MEMs

B. Langmead, C. Boucher, T. Gagie, 2021, bioRxiv.

Pan-genomic matching statistics for targeted nanopore sequencing

M. Schatz, B. Langmead, C. Boucher, 2021, bioRxiv.

LevioSAM: fast lift-over of variant-aware reference alignments

B. Langmead, Nae-Chyun Chen, Taher Mun, 2021, Bioinform..

Flexible analysis of transcriptome assemblies with Ballgown

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

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

Alyssa C. Frazee, Jeffrey T. Leek, Ben Langmead, 2011, BMC Bioinformatics.

MONI: A Pangenomic Index for Finding Maximal Exact Matches

B. Langmead, C. Boucher, T. Gagie, 2022, J. Comput. Biol..

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

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

PHONI: Streamed Matching Statistics with Multi-Genome References pdf

Christina Boucher, Gonzalo Navarro, Travis Gagie, 2020, 2021 Data Compression Conference (DCC).

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.

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

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

LevioSAM: Fast lift-over of alternate reference alignments

Nae-Chyun Chen, Ben Langmead, Taher Mun, 2021, bioRxiv.

Control-independent mosaic single nucleotide variant detection with DeepMosaic

Ryan E. Mills, J. V. Moran, Michael E. Coulter, 2023, Nature Biotechnology.

Megadepth: efficient coverage quantification for BigWigs and BAMs

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

Snaptron: querying and visualizing splicing across tens of thousands of RNA-seq samples

Christopher Wilks, Abhinav Nellore, Benjamin Langmead, 2017, bioRxiv.

recount: A large-scale resource of analysis-ready RNA-seq expression data

Leonardo Collado-Torres, Andrew E. Jaffe, Kasper Daniel Hansen, 2016, bioRxiv.

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

Jacob Pritt, Ben Langmead, B. Langmead, 2016, bioRxiv.

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

Lana S. Martin, F. Hormozdiari, B. Langmead, 2019, Nature Biotechnology.

Dashing: fast and accurate genomic distances with HyperLogLog

Ben Langmead, Daniel N. Baker, B. Langmead, 2019, Genome Biology.

SPUMONI 2: improved classification using a pangenome index of minimizer digests

B. Langmead, C. Boucher, T. Gagie, 2023, Genome Biology.

Sigmoni: classification of nanopore signal with a compressed pangenome index

B. Langmead, Mohsen Zakeri, S. Kovaka, 2023, bioRxiv.

Prefix-free parsing for building big BWTs pdf

Travis Gagie, Giovanni Manzini, B. Langmead, 2018, Algorithms for Molecular Biology.

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.

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

Abhinav Nellore, Christopher Wilks, Ben Langmead, 2017, Bioinform..

Genotyping in the Cloud with Crossbow

Ben Langmead, Michael C Schatz, James Gurtowski, 2012, Current protocols in bioinformatics.

Cloud-scale RNA-sequencing differential

Jeffrey T. Leek, Kasper Daniel Hansen, Ben Langmead, 2010 .