ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets. - Alyssa C. Frazee; Ben Langmead; Jeffrey T. Leek (BMC Bioinform., 2011)

Algorithms and High Performance Computing Approaches for sequencing-based Comparative genomics. - Benjamin Thomas Langmead (2012)

Practical software for big genomics data. - Ben Langmead (ICCABS, 2013)

Polyester: simulating RNA-seq datasets with differential transcript expression. - Alyssa C. Frazee; Andrew E. Jaffe; Ben Langmead; Jeffrey T. Leek (Bioinform., 2015)

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. - Abhinav Nellore; Christopher Wilks; Kasper D. Hansen; Jeffrey T. Leek; Ben Langmead (Bioinform., 2016)

Rail-RNA: scalable analysis of RNA-seq splicing and coverage. - Abhinav Nellore; Leonardo Collado-Torres; Andrew E. Jaffe; José Alquicira-Hernández; Christopher Wilks; Jacob Pritt; James Morton; Jeffrey T. Leek; Ben Langmead (Bioinform., 2017)

Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. - Christopher Wilks; Phani Gaddipati; Abhinav Nellore; Ben Langmead (Bioinform., 2018)

Prefix-free parsing for building big BWTs. - Christina Boucher 001; Travis Gagie; Alan Kuhnle; Ben Langmead; Giovanni Manzini; Taher Mun (Algorithms Mol. Biol., 2019)

Scaling read aligners to hundreds of threads on general-purpose processors. - Ben Langmead; Christopher Wilks; Valentin Antonescu; Rone Charles (Bioinform., 2019)

Vargas: heuristic-free alignment for assessing linear and graph read aligners. - Charlotte A. Darby; Ravi Gaddipati; Michael C. Schatz; Ben Langmead (Bioinform., 2020)

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. - Alan Kuhnle; Taher Mun; Christina Boucher 001; Travis Gagie; Ben Langmead; Giovanni Manzini (J. Comput. Biol., 2020)

Matching Reads to Many Genomes with the r-Index. - Taher Mun; Alan Kuhnle; Christina Boucher 001; Travis Gagie; Ben Langmead; Giovanni Manzini (J. Comput. Biol., 2020)

Fast and memory-efficient scRNA-seq k-means clustering with various distances. - Daniel N. Baker; Nathan Dyjack; Vladimir Braverman; Stephanie C. Hicks; Ben Langmead (BCB, 2021)

PHONI: Streamed Matching Statistics with Multi-Genome References. - Christina Boucher 001; Travis Gagie; Tomohiro I; Dominik Köppl; Ben Langmead; Giovanni Manzini; Gonzalo Navarro 001; Alejandro Pacheco; Massimiliano Rossi 001 (DCC, 2021)

Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing. - Dominik Kempa; Ben Langmead (ESA, 2021)

Megadepth: efficient coverage quantification for BigWigs and BAMs. - Christopher Wilks; Omar Y. Ahmed; Daniel N. Baker; David Zhang; Leonardo Collado-Torres; Ben Langmead (Bioinform., 2021)

LevioSAM: fast lift-over of variant-aware reference alignments. - Taher Mun; Nae-Chyun Chen; Ben Langmead (Bioinform., 2021)

KATKA: A KRAKEN-Like Tool with k Given at Query Time. - Travis Gagie; Sana Kashgouli; Ben Langmead (SPIRE, 2022)

Finding Maximal Exact Matches Using the r-Index. - Massimiliano Rossi 001; Marco Oliva; Paola Bonizzoni; Ben Langmead; Travis Gagie; Christina Boucher 001 (J. Comput. Biol., 2022)

MONI: A Pangenomic Index for Finding Maximal Exact Matches. - Massimiliano Rossi 001; Marco Oliva; Ben Langmead; Travis Gagie; Christina Boucher 001 (J. Comput. Biol., 2022)

Minimizing Reference Bias: The Impute-First Approach for Personalized Genome Analysis. - Naga Sai Kavya Vaddadi; Taher Mun; Benjamin Thomas Langmead (BCB, 2023)

Suffixient Sets. - Lore Depuydt; Travis Gagie; Ben Langmead; Giovanni Manzini; Nicola Prezza (CoRR, 2023)

Pangenomic genotyping with the marker array. - Taher Mun; Naga Sai Kavya Vaddadi; Ben Langmead (Algorithms Mol. Biol., 2023)

Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification. - Li Song; Ben Langmead (RECOMB, 2024)

Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. - Dominika Draesslerová; Omar Y. Ahmed; Travis Gagie; Jan Holub 001; Ben Langmead; Giovanni Manzini; Gonzalo Navarro 001 (SEA, 2024)

Sigmoni: classification of nanopore signal with a compressed pangenome index. - Vikram Shivakumar; Omar Y. Ahmed; Sam Kovaka; Mohsen Zakeri; Ben Langmead (Bioinform., 2024)

MIOV: Reordering MOVI for even better locality. - Peter Peresíni; Nathaniel K. Brown; Travis Gagie; Ben Langmead (CoRR, 2024)

StephenHwang/MEMO. - Stephen Hwang; Nathaniel K. Brown; Omar Y. Ahmed; Katharine M. Jenike; Sam Kovaka; Michael C. Schatz; Ben Langmead (DROPS Artifacts, 2024)

StephenHwang/MEMO_experiments. - Stephen Hwang; Nathaniel K. Brown; Omar Y. Ahmed; Katharine M. Jenike; Sam Kovaka; Michael C. Schatz; Ben Langmead (DROPS Artifacts, 2024)

Phasing Data from Genotype Queries via the μ-PBWT. - Davide Cozzi; Paola Bonizzoni; Christina Boucher 001; Ben Langmead; Yuri Pirola (The Expanding World of Compressed Data, 2025)

Improved Pangenomic Classification Accuracy with Chain Statistics. - Nathaniel K. Brown; Vikram Shivakumar; Ben Langmead (RECOMB, 2025)

We Are What We Index; a Primer for the Wheeler Graph Era (Invited Talk). - Ben Langmead (WABI, 2025)

Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract). - Vikram Shivakumar; Ben Langmead (WABI, 2025)

EvANI benchmarking workflow for evolutionary distance estimation. - Sina Majidian; Stephen Hwang; Mohsen Zakeri; Ben Langmead (Briefings Bioinform., 2025)

Prefix-free parsing for merging big BWTs. - Diego Díaz-Domínguez; Travis Gagie; Veronica Guerrini; Ben Langmead; Zsuzsanna Lipták; Giovanni Manzini; Francesco Masillo; Vikram Shivakumar (CoRR, 2025)

Mem-based pangenome indexing for k-mer queries. - Stephen Hwang; Nathaniel K. Brown; Omar Y. Ahmed; Katharine M. Jenike; Sam Kovaka; Michael C. Schatz; Ben Langmead (Algorithms Mol. Biol., 2025)