Ben Langmead

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 44

Top Venues

bioRxiv : the preprint server for biology

Genome biology

Bioinformatics (Oxford, England)

Genome research

Johns Hopkins University

University of Maryland (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Johns Hopkins University Jul 01 2019

United States

Associate Professor :: Computer Science

Johns Hopkins University - Jun 30 2019

United States

Assistant Professor :: Computer Science

Johns Hopkins University

United States

Research Associate :: Biostatistics

Reservoir Labs, Inc

United States

Engineer

Education History

University of Maryland

United States

PHD :: Computer Science

University of Maryland

United States

MSC :: Computer Science

Publications

Vikram S Shivakumar, Omar Y Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead
Sigmoni: classification of nanopore signal with a compressed pangenome index. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Stephen Hwang, Nathaniel K Brown, Omar Y Ahmed, Katharine M Jenike, Sam Kovaka, Michael C Schatz, Ben Langmead
MEM-based pangenome indexing for k -mer queries. bioRxiv : the preprint server for biology (2024)
Mao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, Ben Langmead
Measuring, visualizing, and diagnosing reference bias with biastools. Genome biology 25 (1) (2024)
Vikram S Shivakumar, Omar Y Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead
Sigmoni: classification of nanopore signal with a compressed pangenome index. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Vikram S Shivakumar, Omar Y Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead
Sigmoni: classification of nanopore signal with a compressed pangenome index. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Omar Y Ahmed, Christina Boucher, Ben Langmead
Cliffy: robust 16S rRNA classification based on a compressed LCA index. bioRxiv : the preprint server for biology (2024)
Mao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, Ben Langmead
Measuring, visualizing, and diagnosing reference bias with biastools. Genome biology 25 (1) (2024)
Mao-Jan Lin, Ben Langmead, Yana Safonova
IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads. bioRxiv : the preprint server for biology (2024)
Mao-Jan Lin, Ben Langmead, Yana Safonova
IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads. bioRxiv : the preprint server for biology (2024)
Stephen Hwang, Nathaniel K Brown, Omar Y Ahmed, Katharine M Jenike, Sam Kovaka, Michael C Schatz, Ben Langmead
MEM-based pangenome indexing for k -mer queries. bioRxiv : the preprint server for biology (2024)
Stephen Hwang, Nathaniel K Brown, Omar Y Ahmed, Katharine M Jenike, Sam Kovaka, Michael C Schatz, Ben Langmead
MEM-based pangenome indexing for k -mer queries. bioRxiv : the preprint server for biology (2024)
Mao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, Ben Langmead
Measuring, visualizing, and diagnosing reference bias with biastools. Genome biology 25 (1) (2024)
Vikram S Shivakumar, Omar Y Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead
Sigmoni: classification of nanopore signal with a compressed pangenome index. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Mao-Jan Lin, Ben Langmead, Yana Safonova
IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads. bioRxiv : the preprint server for biology (2024)
Mao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, Ben Langmead
Measuring, visualizing, and diagnosing reference bias with biastools. Genome biology 25 (1) (2024)
Mao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, Ben Langmead
Measuring, visualizing, and diagnosing reference bias with biastools. Genome biology 25 (1) (2024)
Stephen Hwang, Nathaniel K Brown, Omar Y Ahmed, Katharine M Jenike, Sam Kovaka, Michael C Schatz, Ben Langmead
MEM-based pangenome indexing for k -mer queries. bioRxiv : the preprint server for biology (2024)
Omar Y Ahmed, Massimiliano Rossi, Travis Gagie, Christina Boucher, Ben Langmead
SPUMONI 2: improved classification using a pangenome index of minimizer digests. Genome biology 24 (1) (2023)
Daniel N Baker, Ben Langmead
Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2. Genome research (2023)
Mao-Jan Lin, Sheila Iyer, Nae-Chyun Chen, Ben Langmead
Measuring, visualizing and diagnosing reference bias with biastools. bioRxiv : the preprint server for biology (2023)
Naga Sai Kavya Vaddadi, Taher Mun, Ben Langmead
Minimizing Reference Bias with an Impute-First Approach. bioRxiv : the preprint server for biology (2023)
Vikram S Shivakumar, Omar Y Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead
Sigmoni: classification of nanopore signal with a compressed pangenome index. bioRxiv : the preprint server for biology (2023)
Nae-Chyun Chen, Luis F Paulin, Fritz J Sedlazeck, Sergey Koren, Adam M Phillippy, Ben Langmead
Improved sequence mapping using a complete reference genome and lift-over. Nature methods (2023)
Jessica K Bonnie, Omar Y Ahmed, Ben Langmead
DandD: efficient measurement of sequence growth and similarity. bioRxiv : the preprint server for biology (2023)
Omar Y Ahmed, Massimiliano Rossi, Travis Gagie, Christina Boucher, Ben Langmead
SPUMONI 2: improved classification using a pangenome index of minimizer digests. Genome biology 24 (1) (2023)
Mohsen Zakeri, Nathaniel K Brown, Omar Y Ahmed, Travis Gagie, Ben Langmead
Movi: a fast and cache-efficient full-text pangenome index. bioRxiv : the preprint server for biology (2023)
Anna-Maria Liebhoff, Thiagarajan Venkataraman, William R Morgenlander, Miso Na, Tomasz Kula, Kathleen Waugh, Charles S Morrison, Marian J Rewers, Randy S Longman, June L Round, Stephen J Elledge, Ingo Ruczinski, Ben Langmead, H Benjamin Larman
Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn. bioRxiv : the preprint server for biology (2023)
Omar Y Ahmed, Massimiliano Rossi, Travis Gagie, Christina Boucher, Ben Langmead
SPUMONI 2: improved classification using a pangenome index of minimizer digests. Genome biology 24 (1) (2023)
Li Song, Ben Langmead
Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. bioRxiv : the preprint server for biology (2023)
Omar Ahmed, Massimiliano Rossi, Christina Boucher, Ben Langmead
Efficient taxa identification using a pangenome index. Genome research (2023)
Jessica K Bonnie, Omar Y Ahmed, Ben Langmead
DandD: efficient measurement of sequence growth and similarity. bioRxiv : the preprint server for biology (2023)
Omar Y Ahmed, Massimiliano Rossi, Travis Gagie, Christina Boucher, Ben Langmead
SPUMONI 2: improved classification using a pangenome index of minimizer digests. Genome biology 24 (1) (2023)
Huan Chen, Brian Caffo, Genevieve L Stein-O'Brien, Jinrui Liu, Ben Langmead, Carlo Colantuoni, Luo Xiao
Two-stage linked component analysis for joint decomposition of multiple biologically related data sets. Biostatistics (Oxford, England) 23 (4) (2022)
Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
Finding Maximal Exact Matches Using the r-Index. Journal of computational biology : a journal of computational molecular cell biology 29 (2) (2022)
Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher
MONI: A Pangenomic Index for Finding Maximal Exact Matches. Journal of computational biology : a journal of computational molecular cell biology 29 (2) (2022)
Jonathan P Ling, Alexei M Bygrave, Clayton P Santiago, Rogger P Carmen-Orozco, Vickie T Trinh, Minzhong Yu, Yini Li, Ying Liu, Kyra D Bowden, Leighton H Duncan, Jeong Han, Kamil Taneja, Rochinelle Dongmo, Travis A Babola, Patrick Parker, Lizhi Jiang, Patrick J Leavey, Jennifer J Smith, Rachel Vistein, Megan Y Gimmen, Benjamin Dubner, Eric Helmenstine, Patric Teodorescu, Theodoros Karantanos, Gabriel Ghiaur, Patrick O Kanold, Dwight E Bergles, Ben Langmead, Shuying Sun, Kristina J Nielsen, Neal S Peachey, Mandeep S Singh, W Brian Dalton, Fatemeh Rajaii, Richard L Huganir, Seth Blackshaw
Cell-specific regulation of gene expression using splicing-dependent frameshifting. Nature communications 13 (1) (2022)
Christopher Wilks, Shijie C Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T Leek, Andrew E Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D Hansen, Ben Langmead
recount3: summaries and queries for large-scale RNA-seq expression and splicing. Genome biology 22 (1) (2021)
Nae-Chyun Chen, Brad Solomon, Taher Mun, Sheila Iyer, Ben Langmead
Reference flow: reducing reference bias using multiple population genomes. Genome biology 22 (1) (2021)
Jonathan P Ling, Christopher Wilks, Rone Charles, Patrick J Leavey, Devlina Ghosh, Lizhi Jiang, Clayton P Santiago, Bo Pang, Anand Venkataraman, Brian S Clark, Abhinav Nellore, Ben Langmead, Seth Blackshaw
ASCOT identifies key regulators of neuronal subtype-specific splicing. Nature communications 11 (1) (2020)
Eddie Luidy Imada, Diego Fernando Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Pereira Lobo, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, Michiel J L de Hoon, Jay W Shin, Piero Carnici, Andrew E Jaffe, Jeffery T Leek, Alexander V Favorov, Gloria R Franco, Ben Langmead, Luigi Marchionni
Recounting the FANTOM CAGE-Associated Transcriptome. Genome research 30 (7) (2020)
Derrick E Wood, Jennifer Lu, Ben Langmead
Improved metagenomic analysis with Kraken 2. Genome biology 20 (1) (2019)
Daniel N Baker, Ben Langmead
Dashing: fast and accurate genomic distances with HyperLogLog. Genome biology 20 (1) (2019)
Jacob Pritt, Nae-Chyun Chen, Ben Langmead
FORGe: prioritizing variants for graph genomes. Genome biology 19 (1) (2018)
Ben Langmead
A tandem simulation framework for predicting mapping quality. Genome biology 18 (1) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Ben Langmead