Ben Langmead - Publications

Affiliations: 
Computer Science Johns Hopkins University, Baltimore, MD 

16/45 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
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  0.4
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  0.4
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.64
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  0.4
2012 Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nature Neuroscience. 15: 1371-3. PMID 22983211 DOI: 10.1038/Nn.3218  0.64
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  0.4
2012 Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2 Nature Methods. 9: 357-359. PMID 22388286 DOI: 10.1038/nmeth.1923  0.64
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  0.64
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  0.64
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  0.64
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  0.64
Low-probability matches
2020 Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Pereira Lobo FP, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, ... ... Langmead B, et al. Recounting the FANTOM CAGEAssociated Transcriptome. Genome Research. PMID 32079618 DOI: 10.1101/Gr.254656.119  0.28
2017 Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis using recount2. Nature Biotechnology. 35: 319-321. PMID 28398307 DOI: 10.1038/Nbt.3838  0.28
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  0.28
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  0.28
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  0.28
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. PMID 27655402 DOI: 10.1093/hmg/ddw321  0.28
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  0.28
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  0.28
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  0.2
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  0.2
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  0.12
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  0.08
2018 Langmead B, Nellore A. Cloud computing for genomic data analysis and collaboration. Nature Reviews. Genetics. PMID 29430012 DOI: 10.1038/nrg.2018.8  0.04
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  0.04
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
2018 Langmead B, Nellore A. Cloud computing for genomic data analysis and collaboration. Nature Reviews. Genetics. PMID 29379135 DOI: 10.1038/nrg.2017.113  0.01
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  0.01
2017 Langmead B. A tandem simulation framework for predicting mapping quality. Genome Biology. 18: 152. PMID 28806977 DOI: 10.1186/s13059-017-1290-3  0.01
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  0.01
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  0.01
2010 Langmead B. Aligning short sequencing reads with Bowtie. Current Protocols in Bioinformatics. Unit 11.7. PMID 21154709 DOI: 10.1002/0471250953.bi1107s32  0.01
Hide low-probability matches.