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Ben Langmead - Publications

Affiliations: 
Computer Science Johns Hopkins University, Baltimore, MD 
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Chen NC, Paulin LF, Sedlazeck FJ, Koren S, Phillippy AM, Langmead B. Improved sequence mapping using a complete reference genome and lift-over. Nature Methods. PMID 38036856 DOI: 10.1038/s41592-023-02069-6  0.34
2023 Song L, Langmead B. Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. Biorxiv : the Preprint Server For Biology. PMID 38014029 DOI: 10.1101/2023.11.15.567129  0.389
2023 Lin MJ, Iyer S, Chen NC, Langmead B. Measuring, visualizing and diagnosing reference bias with biastools. Biorxiv : the Preprint Server For Biology. PMID 37745608 DOI: 10.1101/2023.09.13.557552  0.303
2023 Baker DN, Langmead B. Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2. Genome Research. PMID 37414575 DOI: 10.1101/gr.277655.123  0.438
2023 Ahmed O, Rossi M, Boucher C, Langmead B. Efficient taxa identification using a pangenome index. Genome Research. PMID 37258301 DOI: 10.1101/gr.277642.123  0.33
2023 Ahmed OY, Rossi M, Gagie T, Boucher C, Langmead B. SPUMONI 2: improved classification using a pangenome index of minimizer digests. Genome Biology. 24: 122. PMID 37202771 DOI: 10.1186/s13059-023-02958-1  0.353
2023 Bonnie JK, Ahmed O, Langmead B. DandD: efficient measurement of sequence growth and similarity. Biorxiv : the Preprint Server For Biology. PMID 36778393 DOI: 10.1101/2023.02.02.526837  0.36
2023 Imada EL, Wilks C, Langmead B, Marchionni L. REPAC: analysis of alternative polyadenylation from RNA-sequencing data. Genome Biology. 24: 22. PMID 36759904 DOI: 10.1186/s13059-023-02865-5  0.364
2022 Ling JP, Bygrave AM, Santiago CP, Carmen-Orozco RP, Trinh VT, Yu M, Li Y, Liu Y, Bowden KD, Duncan LH, Han J, Taneja K, Dongmo R, Babola TA, Parker P, ... ... Langmead B, et al. Cell-specific regulation of gene expression using splicing-dependent frameshifting. Nature Communications. 13: 5773. PMID 36182931 DOI: 10.1038/s41467-022-33523-2  0.648
2022 Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. Metagenome analysis using the Kraken software suite. Nature Protocols. PMID 36171387 DOI: 10.1038/s41596-022-00738-y  0.654
2022 Rossi M, Oliva M, Bonizzoni P, Langmead B, Gagie T, Boucher C. Finding Maximal Exact Matches Using the r-Index. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 29: 188-194. PMID 35041518 DOI: 10.1089/cmb.2021.0445  0.351
2021 Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B. recount3: summaries and queries for large-scale RNA-seq expression and splicing. Genome Biology. 22: 323. PMID 34844637 DOI: 10.1186/s13059-021-02533-6  0.604
2021 Ahmed O, Rossi M, Kovaka S, Schatz MC, Gagie T, Boucher C, Langmead B. Pan-genomic matching statistics for targeted nanopore sequencing. Iscience. 24: 102696. PMID 34195571 DOI: 10.1016/j.isci.2021.102696  0.588
2021 Wilks C, Ahmed O, Baker DN, Zhang D, Collado-Torres L, Langmead B. Megadepth: efficient coverage quantification for BigWigs and BAMs. Bioinformatics (Oxford, England). PMID 33693500 DOI: 10.1093/bioinformatics/btab152  0.397
2021 Chen NC, Solomon B, Mun T, Iyer S, Langmead B. Reference flow: reducing reference bias using multiple population genomes. Genome Biology. 22: 8. PMID 33397413 DOI: 10.1186/s13059-020-02229-3  0.334
2020 Darby CA, Gaddipati R, Schatz MC, Langmead B. Vargas: heuristic-free alignment for assessing linear and graph read aligners. Bioinformatics (Oxford, England). PMID 32321164 DOI: 10.1093/Bioinformatics/Btaa265  0.527
2020 Mun T, Kuhnle A, Boucher C, Gagie T, Langmead B, Manzini G. Matching Reads to Many Genomes with the -Index. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 32181686 DOI: 10.1089/Cmb.2019.0316  0.431
2020 Kuhnle A, Mun T, Boucher C, Gagie T, Langmead B, Manzini G. Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 32181684 DOI: 10.1089/Cmb.2019.0309  0.426
2020 Ling JP, Wilks C, Charles R, Leavey PJ, Ghosh D, Jiang L, Santiago CP, Pang B, Venkataraman A, Clark BS, Nellore A, Langmead B, Blackshaw S. ASCOT identifies key regulators of neuronal subtype-specific splicing. Nature Communications. 11: 137. PMID 31919425 DOI: 10.1038/S41467-019-14020-5  0.701
2019 Baker DN, Langmead B. Dashing: fast and accurate genomic distances with HyperLogLog. Genome Biology. 20: 265. PMID 31801633 DOI: 10.1186/S13059-019-1875-0  0.433
2019 Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biology. 20: 257. PMID 31779668 DOI: 10.1186/S13059-019-1891-0  0.742
2019 Wulfridge P, Langmead B, Feinberg AP, Hansen KD. Analyzing whole genome bisulfite sequencing data from highly divergent genotypes. Nucleic Acids Research. PMID 31392989 DOI: 10.1093/Nar/Gkz674  0.401
2019 Darby CA, Fitch JR, Brennan PJ, Kelly BJ, Bir N, Magrini V, Leonard J, Cottrell CE, Gastier-Foster JM, Wilson RK, Mardis ER, White P, Langmead B, Schatz MC. Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads. Iscience. 18: 1-10. PMID 31271967 DOI: 10.1016/J.Isci.2019.05.037  0.595
2019 Boucher C, Gagie T, Kuhnle A, Langmead B, Manzini G, Mun T. Prefix-free parsing for building big BWTs. Algorithms For Molecular Biology : Amb. 14: 13. PMID 31149025 DOI: 10.1186/S13015-019-0148-5  0.456
2019 Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim MS, Pandey A. Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial cells. Proteomics. e1800315. PMID 30983154 DOI: 10.1002/Pmic.201800315  0.367
2019 Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E. How bioinformatics and open data can boost basic science in countries and universities with limited resources. Nature Biotechnology. 37: 324-326. PMID 30833765 DOI: 10.1038/S41587-019-0053-Y  0.322
2019 Imada EL, Sanchez DF, Matam T, Collado-Torres L, Wilks C, Dinalankara W, Stupnikov A, Langmead B, Lupold SE, Marchionni L. Abstract 908: Comprehensive analysis of alternative polyadenylation across cancer phenotypes Cancer Research. 79: 908-908. DOI: 10.1158/1538-7445.Am2019-908  0.336
2018 Pritt J, Chen NC, Langmead B. FORGe: prioritizing variants for graph genomes. Genome Biology. 19: 220. PMID 30558649 DOI: 10.1186/S13059-018-1595-X  0.443
2018 Langmead B, Wilks C, Antonescu V, Charles R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics (Oxford, England). PMID 30020410 DOI: 10.1093/Bioinformatics/Bty648  0.417
2018 Langmead B, Nellore A. Cloud computing for genomic data analysis and collaboration. Nature Reviews. Genetics. PMID 29430012 DOI: 10.1038/Nrg.2018.8  0.427
2018 Langmead B, Nellore A. Cloud computing for genomic data analysis and collaboration. Nature Reviews. Genetics. PMID 29379135 DOI: 10.1038/Nrg.2017.113  0.468
2018 Luidy-Imada E, Matam T, Collado-Torres L, Dinalankara W, Stupnikov A, Wilks C, Jaffe AE, Langmead B, Leek JT, Favorov A, Marchionni L. Abstract 2297: Differential analysis of gene expression across the human genome using recount2 and FANTOM-CAT Cancer Research. 78: 2297-2297. DOI: 10.1158/1538-7445.Am2018-2297  0.361
2017 Wilks C, Gaddipati P, Nellore A, Langmead B. Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples. Bioinformatics (Oxford, England). PMID 28968689 DOI: 10.1093/Bioinformatics/Btx547  0.404
2017 Langmead B. A tandem simulation framework for predicting mapping quality. Genome Biology. 18: 152. PMID 28806977 DOI: 10.1186/S13059-017-1290-3  0.339
2016 Darby MM, Leek JT, Langmead B, Yolken RH, Sabunciyan S. Widespread splicing of repetitive element loci into coding regions of gene transcripts. Human Molecular Genetics. 25: 4962-4982. PMID 28171598 DOI: 10.1093/Hmg/Ddw321  0.41
2016 Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips Iii RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. Genome Biology. 17: 266. PMID 28038678 DOI: 10.1186/S13059-016-1118-6  0.461
2016 Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Research. PMID 27694310 DOI: 10.1093/Nar/Gkw852  0.427
2016 Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B. Rail-RNA: Scalable analysis of RNA-seq splicing and coverage. Bioinformatics (Oxford, England). PMID 27592709 DOI: 10.1093/Bioinformatics/Btw575  0.374
2016 Pritt J, Langmead B. Boiler: lossy compression of RNA-seq alignments using coverage vectors. Nucleic Acids Research. 44: e133. PMID 27298258 DOI: 10.1093/Nar/Gkw540  0.45
2016 Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B. Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. Bioinformatics (Oxford, England). PMID 27153614 DOI: 10.1093/Bioinformatics/Btw177  0.445
2015 Reinert K, Langmead B, Weese D, Evers DJ. Alignment of Next-Generation Sequencing Reads. Annual Review of Genomics and Human Genetics. 16: 133-51. PMID 25939052 DOI: 10.1146/Annurev-Genom-090413-025358  0.471
2015 Frazee AC, Jaffe AE, Langmead B, Leek JT. Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics (Oxford, England). PMID 25926345 DOI: 10.1093/Bioinformatics/Btv272  0.355
2015 Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. Peerj. 3: e808. PMID 25780763 DOI: 10.7717/Peerj.808  0.65
2015 Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 12: 357-60. PMID 25751142 DOI: 10.1038/Nmeth.3317  0.718
2015 Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology. 33: 243-6. PMID 25748911 DOI: 10.1038/Nbt.3172  0.502
2014 Song L, Florea L, Langmead B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biology. 15: 509. PMID 25398208 DOI: 10.1186/S13059-014-0509-9  0.4
2014 Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Research. 24: 177-84. PMID 24068705 DOI: 10.1101/Gr.157743.113  0.318
2013 Schatz MC, Langmead B. The DNA Data Deluge: Fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze. Ieee Spectrum. 50: 26-33. PMID 24920863 DOI: 10.1109/Mspec.2013.6545119  0.595
2012 Gurtowski J, Schatz MC, Langmead B. Genotyping in the cloud with Crossbow. Current Protocols in Bioinformatics. Unit15.3. PMID 22948728 DOI: 10.1002/0471250953.Bi1503S39  0.528
2012 Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2 Nature Methods. 9: 357-359. PMID 22388286 DOI: 10.1038/Nmeth.1923  0.597
2011 Frazee AC, Langmead B, Leek JT. ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. Bmc Bioinformatics. 12: 449. PMID 22087737 DOI: 10.1186/1471-2105-12-449  0.43
2010 Langmead B. Aligning short sequencing reads with Bowtie. Current Protocols in Bioinformatics. Unit 11.7. PMID 21154709 DOI: 10.1002/0471250953.Bi1107S32  0.48
2010 Langmead B, Hansen KD, Leek JT. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology. 11: R83. PMID 20701754 DOI: 10.1186/Gb-2010-11-8-R83  0.482
2010 Schatz MC, Langmead B, Salzberg SL. Cloud computing and the DNA data race Nature Biotechnology. 28: 691-693. PMID 20622843 DOI: 10.1038/Nbt0710-691  0.646
2009 Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology. 10: R134. PMID 19930550 DOI: 10.1186/Gb-2009-10-11-R134  0.669
2009 Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 10: R25. PMID 19261174 DOI: 10.1186/Gb-2009-10-3-R25  0.735
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