Ben Langmead

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 29

Top Topics

Visual Languages

Sequence Classification

Tens Of Thousands

Top Venues

J. Comput. Biol.

Publications

Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro
Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. SEA (2024)
Peter Peresíni, Nathaniel K. Brown, Travis Gagie, Ben Langmead
MIOV: Reordering MOVI for even better locality. CoRR (2024)
Li Song, Ben Langmead
Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification. RECOMB (2024)
Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro
Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests. CoRR (2024)
Stephen Hwang, Nathaniel K. Brown, Omar Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead
MEM-Based Pangenome Indexing for k-mer Queries. WABI (2024)
Taher Mun, Vaddadi Naga Sai Kavya, Ben Langmead
Pangenomic genotyping with the marker array. Algorithms Mol. Biol. 18 (1) (2023)
Omar Ahmed, Andrej Baláz, Nathaniel K. Brown, Lore Depuydt, Adrián Goga, Alessia Petescia, Mohsen Zakeri, Jan Fostier, Travis Gagie, Ben Langmead, Gonzalo Navarro, Nicola Prezza
r-indexing without backward searching. CoRR (2023)
Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher
MONI: A Pangenomic Index for Finding Maximal Exact Matches. J. Comput. Biol. 29 (2) (2022)
Travis Gagie, Sana Kashgouli, Ben Langmead
KATKA: A KRAKEN-Like Tool with k Given at Query Time. SPIRE (2022)
Taher Mun, Vaddadi Naga Sai Kavya, Ben Langmead
Pangenomic Genotyping with the Marker Array. WABI (2022)
Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
Finding Maximal Exact Matches Using the r-Index. J. Comput. Biol. 29 (2) (2022)
Christopher Wilks, Omar Ahmed, Daniel N. Baker, David Zhang, Leonardo Collado-Torres, Ben Langmead
Megadepth: efficient coverage quantification for BigWigs and BAMs. Bioinform. 37 (18) (2021)
Dominik Kempa, Ben Langmead
Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing. CoRR (2021)
Dominik Kempa, Ben Langmead
Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing. ESA (2021)
Taher Mun, Nae-Chyun Chen, Ben Langmead
LevioSAM: fast lift-over of variant-aware reference alignments. Bioinform. 37 (22) (2021)
Daniel N. Baker, Nathan Dyjack, Vladimir Braverman, Stephanie C. Hicks, Ben Langmead
-means clustering with various distances. BCB (2021)
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
PHONI: Streamed Matching Statistics with Multi-Genome References. DCC (2021)
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. J. Comput. Biol. 27 (4) (2020)
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
PHONI: Streamed Matching Statistics with Multi-Genome References. CoRR (2020)
Charlotte A. Darby, Ravi Gaddipati, Michael C. Schatz, Ben Langmead
Vargas: heuristic-free alignment for assessing linear and graph read aligners. Bioinform. 36 (12) (2020)
Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Matching Reads to Many Genomes with the r-Index. J. Comput. Biol. 27 (4) (2020)
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. RECOMB (2019)
Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Matching reads to many genomes with the r-index. CoRR (2019)
Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun
Prefix-free parsing for building big BWTs. Algorithms Mol. Biol. 14 (1) (2019)
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
Scaling read aligners to hundreds of threads on general-purpose processors. Bioinform. 35 (3) (2019)
Christopher Wilks, Phani Gaddipati, Abhinav Nellore, Ben Langmead
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. Bioinform. 34 (1) (2018)
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. CoRR (2018)
Abhinav Nellore, Leonardo Collado-Torres, Andrew E. Jaffe, José Alquicira-Hernández, Christopher Wilks, Jacob Pritt, James Morton, Jeffrey T. Leek, Ben Langmead
Rail-RNA: scalable analysis of RNA-seq splicing and coverage. Bioinform. 33 (24) (2017)
Abhinav Nellore, Christopher Wilks, Kasper D. Hansen, Jeffrey T. Leek, Ben Langmead
Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. Bioinform. 32 (16) (2016)
Alyssa C. Frazee, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek
: simulating RNA-seq datasets with differential transcript expression. Bioinform. 31 (17) (2015)
Ben Langmead
Practical software for big genomics data. ICCABS (2013)
Alyssa C. Frazee, Ben Langmead, Jeffrey T. Leek
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinform. 12 (2011)