| Year |
Citation |
Score |
| 2024 |
Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. Author Correction: Metagenome analysis using the Kraken software suite. Nature Protocols. PMID 39210095 DOI: 10.1038/s41596-024-01064-1 |
0.46 |
|
| 2024 |
Draesslerová D, Ahmed O, Gagie T, Holub J, Langmead B, Manzini G, Navarro G. Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests. Lipics : Leibniz International Proceedings in Informatics. 301. PMID 39108341 DOI: 10.4230/LIPIcs.SEA.2024.10 |
0.345 |
|
| 2024 |
Lin MJ, Langmead B, Safonova Y. IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads. Biorxiv : the Preprint Server For Biology. PMID 39091872 DOI: 10.1101/2024.07.20.604421 |
0.361 |
|
| 2024 |
Shivakumar VS, Ahmed OY, Kovaka S, Zakeri M, Langmead B. Sigmoni: classification of nanopore signal with a compressed pangenome index. Bioinformatics (Oxford, England). 40: i287-i296. PMID 38940135 DOI: 10.1093/bioinformatics/btae213 |
0.303 |
|
| 2024 |
Ahmed O, Boucher C, Langmead B. Cliffy: robust 16S rRNA classification based on a compressed LCA index. Biorxiv : the Preprint Server For Biology. PMID 38854039 DOI: 10.1101/2024.05.25.595899 |
0.362 |
|
| 2024 |
Hwang S, Brown NK, Ahmed OY, Jenike KM, Kovaka S, Schatz MC, Langmead B. MEM-based pangenome indexing for -mer queries. Biorxiv : the Preprint Server For Biology. PMID 38826299 DOI: 10.1101/2024.05.20.595044 |
0.525 |
|
| 2024 |
Song L, Langmead B. Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. Genome Biology. 25: 106. PMID 38664753 DOI: 10.1186/s13059-024-03244-4 |
0.391 |
|
| 2024 |
Bonnie JK, Ahmed OY, Langmead B. DandD: Efficient measurement of sequence growth and similarity. Iscience. 27: 109054. PMID 38361606 DOI: 10.1016/j.isci.2024.109054 |
0.392 |
|
| 2023 |
Vaddadi NSK, Mun T, Langmead B. Minimizing Reference Bias with an Impute-First Approach. Biorxiv : the Preprint Server For Biology. PMID 38076784 DOI: 10.1101/2023.11.30.568362 |
0.323 |
|
| 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 |
0.62 |
|
| 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 |
0.391 |
|
| 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 |
0.308 |
|
| 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 |
0.44 |
|
| 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 |
0.332 |
|
| 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 |
Mun T, Vaddadi NSK, Langmead B. Pangenomic genotyping with the marker array. Algorithms For Molecular Biology : Amb. 18: 2. PMID 37147657 DOI: 10.1186/s13015-023-00225-3 |
0.303 |
|
| 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 |
0.361 |
|
| 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 |
0.356 |
|
| 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 |
0.645 |
|
| 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 |
0.664 |
|
| 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 |
0.354 |
|
| 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 |
0.596 |
|
| 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 |
0.584 |
|
| 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 |
0.398 |
|
| 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 |
0.337 |
|
| 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 |
0.438 |
|
| 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 |
0.433 |
|
| 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 |
0.698 |
|
| 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 |
0.44 |
|
| 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 |
0.745 |
|
| 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 |
0.457 |
|
| 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 |
0.364 |
|
| 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 |
0.319 |
|
| 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 |
0.334 |
|
| 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 |
0.449 |
|
| 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 |
0.421 |
|
| 2018 |
Langmead B, Nellore A. Cloud computing for genomic data analysis and collaboration. Nature Reviews. Genetics. PMID 29430012 DOI: 10.1038/Nrg.2018.8 |
0.429 |
|
| 2018 |
Langmead B, Nellore A. Cloud computing for genomic data analysis and collaboration. Nature Reviews. Genetics. PMID 29379135 DOI: 10.1038/Nrg.2017.113 |
0.465 |
|
| 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 |
0.359 |
|
| 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 |
0.403 |
|
| 2017 |
Langmead B. A tandem simulation framework for predicting mapping quality. Genome Biology. 18: 152. PMID 28806977 DOI: 10.1186/S13059-017-1290-3 |
0.346 |
|
| 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 |
0.408 |
|
| 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 |
0.457 |
|
| 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 |
0.425 |
|
| 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 |
0.368 |
|
| 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 |
0.441 |
|
| 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 |
0.467 |
|
| 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 |
0.351 |
|
| 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 |
0.719 |
|
| 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 |
0.499 |
|
| 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 |
0.398 |
|
| 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 |
0.316 |
|
| 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 |
0.592 |
|
| 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 |
0.524 |
|
| 2012 |
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2 Nature Methods. 9: 357-359. PMID 22388286 DOI: 10.1038/Nmeth.1923 |
0.593 |
|
| 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 |
0.425 |
|
| 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 |
0.477 |
|
| 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 |
0.641 |
|
| 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 |
0.666 |
|
| 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 |
0.733 |
|
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