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Metagenome analysis using the Kraken software suite.
Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. Lu J, et al. Among authors: langmead b. Nat Protoc. 2022 Dec;17(12):2815-2839. doi: 10.1038/s41596-022-00738-y. Epub 2022 Sep 28. Nat Protoc. 2022. PMID: 36171387 Free PMC article. Review.
MEM-based pangenome indexing for k-mer queries.
Hwang S, Brown NK, Ahmed OY, Jenike KM, Kovaka S, Schatz MC, Langmead B. Hwang S, et al. Among authors: langmead b. bioRxiv [Preprint]. 2024 May 22:2024.05.20.595044. doi: 10.1101/2024.05.20.595044. bioRxiv. 2024. PMID: 38826299 Free PMC article. Preprint.
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.
Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R. Guccione C, et al. Among authors: langmead b. Res Sq [Preprint]. 2024 Oct 23:rs.3.rs-4721159. doi: 10.21203/rs.3.rs-4721159/v1. Res Sq. 2024. PMID: 39502785 Free PMC article. Preprint.
Searching for SNPs with cloud computing.
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Langmead B, et al. Genome Biol. 2009;10(11):R134. doi: 10.1186/gb-2009-10-11-r134. Epub 2009 Nov 20. Genome Biol. 2009. PMID: 19930550 Free PMC article.
Cloud computing and the DNA data race.
Schatz MC, Langmead B, Salzberg SL. Schatz MC, et al. Among authors: langmead b. Nat Biotechnol. 2010 Jul;28(7):691-3. doi: 10.1038/nbt0710-691. Nat Biotechnol. 2010. PMID: 20622843 Free PMC article. No abstract available.
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL. Langmead B, et al. Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923. Nat Methods. 2012. PMID: 22388286 Free PMC article.
98 results