Ben Langmead

45 papers A 1B 5C 7Journal 29Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
Bounding the Average Move Structure Query for Faster and Smaller RLBWT Permutations.
CoRR
Nathaniel K. Brown, Ben Langmead
2026 J jnl
Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification.
J. Comput. Biol.
Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead
2026 J jnl
Optimal-Time Move Structure Balancing and LCP Array Computation from the RLBWT.
CoRR
Nathaniel K. Brown, Ahsan Sanaullah, Shaojie Zhang, Ben Langmead
2025 J jnl
EvANI benchmarking workflow for evolutionary distance estimation.
Briefings Bioinform.
Sina Majidian, Stephen Hwang, Mohsen Zakeri, Ben Langmead
2025 J jnl
Fast and flexible minimizer digestion with <tt>digest</tt>.
Bioinform.
Alan Zheng, Ishmeal Lee, Vikram Shivakumar, Omar Y. Ahmed, Ben Langmead
2025 B conf
Improved Pangenomic Classification Accuracy with Chain Statistics.
RECOMB
Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead
2025 C conf
KeBaB: k-mer Based Breaking for Finding Long MEMs.
SPIRE
Nathaniel K. Brown, Lore Depuydt, Mohsen Zakeri, Anas Alhadi, Nour Allam, Dove Begleiter, Nithin Bharathi Kabilan Karpagavalli, Suchith Sridhar Khajjayam, Hamza Wahed, Travis Gagie, Ben Langmead
2025 J jnl
Mem-based pangenome indexing for k-mer queries.
Algorithms Mol. Biol.
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead
2025 C conf
Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract).
WABI
Vikram Shivakumar, Ben Langmead
2025 — conf
Phasing Data from Genotype Queries via the μ-PBWT.
The Expanding World of Compressed Data
Davide Cozzi, Paola Bonizzoni, Christina Boucher, Ben Langmead, Yuri Pirola
2025 C conf
Prefix-Free Parsing for Merging Big BWTs.
SPIRE
Diego Díaz-Domínguez, Travis Gagie, Veronica Guerrini, Ben Langmead, Zsuzsanna Lipták, Giovanni Manzini, Francesco Masillo, Vikram Shivakumar
2025 J jnl
Prefix-free parsing for merging big BWTs.
CoRR
Diego Díaz-Domínguez, Travis Gagie, Veronica Guerrini, Ben Langmead, Zsuzsanna Lipták, Giovanni Manzini, Francesco Masillo, Vikram Shivakumar
2025 C conf
We Are What We Index; a Primer for the Wheeler Graph Era (Invited Talk).
WABI
Ben Langmead
2024 B conf
Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification.
RECOMB
Li Song, Ben Langmead
2024 C conf
MEM-Based Pangenome Indexing for k-mer Queries.
WABI
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead
2024 J jnl
MIOV: Reordering MOVI for even better locality.
CoRR
Peter Peresíni, Nathaniel K. Brown, Travis Gagie, Ben Langmead
2024 J jnl
Sigmoni: classification of nanopore signal with a compressed pangenome index.
Bioinform.
Vikram Shivakumar, Omar Y. Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead
2024 B conf
Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests.
SEA
Dominika Draesslerová, Omar Y. Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro
2024 J jnl
Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests.
CoRR
Dominika Draesslerová, Omar Y. Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro
2023 J jnl
Pangenomic genotyping with the marker array.
Algorithms Mol. Biol.
Taher Mun, Naga Sai Kavya Vaddadi, Ben Langmead
2023 J jnl
Suffixient Sets.
CoRR
Lore Depuydt, Travis Gagie, Ben Langmead, Giovanni Manzini, Nicola Prezza
2022 J jnl
Finding Maximal Exact Matches Using the r-Index.
J. Comput. Biol.
Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
2022 C conf
KATKA: A KRAKEN-Like Tool with k Given at Query Time.
SPIRE
Travis Gagie, Sana Kashgouli, Ben Langmead
2022 J jnl
MONI: A Pangenomic Index for Finding Maximal Exact Matches.
J. Comput. Biol.
Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher
2022 C conf
Pangenomic Genotyping with the Marker Array.
WABI
Taher Mun, Naga Sai Kavya Vaddadi, Ben Langmead
2021 A conf
Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing.
ESA
Dominik Kempa, Ben Langmead
2021 J jnl
Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing.
CoRR
Dominik Kempa, Ben Langmead
2021 — conf
Fast and memory-efficient scRNA-seq
BCB
Daniel N. Baker, Nathan Dyjack, Vladimir Braverman, Stephanie C. Hicks, Ben Langmead
2021 J jnl
LevioSAM: fast lift-over of variant-aware reference alignments.
Bioinform.
Taher Mun, Nae-Chyun Chen, Ben Langmead
2021 J jnl
Megadepth: efficient coverage quantification for BigWigs and BAMs.
Bioinform.
Christopher Wilks, Omar Y. Ahmed, Daniel N. Baker, David Zhang, Leonardo Collado-Torres, Ben Langmead
2021 B conf
PHONI: Streamed Matching Statistics with Multi-Genome References.
DCC
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
2020 J jnl
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.
J. Comput. Biol.
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2020 J jnl
Matching Reads to Many Genomes with the r-Index.
J. Comput. Biol.
Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2020 J jnl
PHONI: Streamed Matching Statistics with Multi-Genome References.
CoRR
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
2020 J jnl
Vargas: heuristic-free alignment for assessing linear and graph read aligners.
Bioinform.
Charlotte A. Darby, Ravi Gaddipati, Michael C. Schatz, Ben Langmead
2019 B conf
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.
RECOMB
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2019 J jnl
Matching reads to many genomes with the r-index.
CoRR
Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2019 J jnl
Prefix-free parsing for building big BWTs.
Algorithms Mol. Biol.
Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun
2019 J jnl
Scaling read aligners to hundreds of threads on general-purpose processors.
Bioinform.
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
2018 J jnl
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.
CoRR
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
2018 J jnl
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.
Bioinform.
Christopher Wilks, Phani Gaddipati, Abhinav Nellore, Ben Langmead
2017 J jnl
Rail-RNA: scalable analysis of RNA-seq splicing and coverage.
Bioinform.
Abhinav Nellore, Leonardo Collado-Torres, Andrew E. Jaffe, José Alquicira-Hernández, Christopher Wilks, Jacob Pritt, James Morton, Jeffrey T. Leek, Ben Langmead
2016 J jnl
Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.
Bioinform.
Abhinav Nellore, Christopher Wilks, Kasper D. Hansen, Jeffrey T. Leek, Ben Langmead
2013 — conf
Practical software for big genomics data.
ICCABS
Ben Langmead
2011 J jnl
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets.
BMC Bioinform.
Alyssa C. Frazee, Ben Langmead, Jeffrey T. Leek