Ben Langmead

ORCID: 0000-0003-2437-1976

Also affiliated with Johns Hopkins Medicine

Biochemistry, Genetics and Molecular BiologyComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 3%percentile

1.4Author DataRank

Indexed papers

5in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 5 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Recounting the FANTOM CAGE-Associated Transcriptome

Genome Research(2020)10.1101/gr.254656.119

Top 22%

0.928DataRank

Top 22%33 citations

Diego F. Sánchez, Leonardo Collado‐Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara +19 more

Papers

Driven by 64 papers — median percentile 44. Top paper: “Fast gapped-read alignment with Bowtie 2”.

Fast gapped-read alignment with Bowtie 2

Nature Methods(2012)10.1038/nmeth.1923

N/A

1.6DataRank · unranked

59681 citations

Steven L. Salzberg, Ben Langmead

HISAT: a fast spliced aligner with low memory requirements

Nature Methods(2015)10.1038/nmeth.3317

N/A

1.5DataRank · unranked

25688 citations

Ben Langmead, Steven L. Salzberg, Daehwan Kim

Somatic mosaicism reveals clonal distributions of neocortical development

Nature(2022)10.1038/s41586-022-04602-7

N/A

1.4DataRank · unranked

65 citations

Xiaoxu Yang, Johannes C. M. Schlachetzki, Danny Antaki, Addison J. Lana, Xin Xu +91 more

Improved metagenomic analysis with Kraken 2

Genome Biology(2019)10.1186/s13059-019-1891-0

N/A

1.3DataRank · unranked

6841 citations

Jennifer Lu, Ben Langmead, Derrick E. Wood

Control-independent mosaic single nucleotide variant detection with DeepMosaic

Nature Biotechnology(2023)10.1038/s41587-022-01559-w

N/A

1.1DataRank · unranked

40 citations

Xin Xu, Martin W. Breuss, Danny Antaki, Laurel Ball, Changuk Chung +95 more

Recounting the FANTOM CAGE-Associated Transcriptome

Genome Research(2020)10.1101/gr.254656.119

Top 22%

0.928DataRank

Top 22%33 citations

Diego F. Sánchez, Leonardo Collado‐Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara +19 more

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data

Nature Communications(2025)10.1038/s41467-025-56077-5

N/A

0.744DataRank · unranked

24 citations

Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio González, Gregory D. Sepich‐Poore +14 more

Reference flow: reducing reference bias using multiple population genomes

Genome biology(2021)10.1186/s13059-020-02229-3

N/A

0.717DataRank · unranked

118 citations

Brad Solomon, Taher Mun, Sheila Iyer, Ben Langmead, Nae-Chyun Chen

Megadepth: efficient coverage quantification for BigWigs and BAMs

Bioinformatics(2021)10.1093/bioinformatics/btab152

N/A

0.598DataRank · unranked

53 citations

Omar Ahmed, Daniel N. Baker, David Zhang, Leonardo Collado‐Torres, Ben Langmead +1 more

Pan-genomic matching statistics for targeted nanopore sequencing

iScience(2021)10.1016/j.isci.2021.102696

N/A

0.598DataRank · unranked

53 citations

Massimiliano Rossi, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher +2 more

Vargas: heuristic-free alignment for assessing linear and graph read aligners

Bioinformatics(2020)10.1093/bioinformatics/btaa265

N/A

0.529DataRank · unranked

33 citations

Ravi Gaddipati, Michael C. Schatz, Ben Langmead, Charlotte A. Darby

Two-stage linked component analysis for joint decomposition of multiple biologically related data sets

Biostatistics(2022)10.1093/biostatistics/kxac005

N/A

0.450DataRank · unranked

11 citations

Brian Caffo, Genevieve L. Stein-O’Brien, Jinrui Liu, Ben Langmead, Carlo Colantuoni +2 more

Efficient taxa identification using a pangenome index

Genome Research(2023)10.1101/gr.277642.123

N/A

0.406DataRank · unranked

14 citations

Massimiliano Rossi, Christina Boucher, Ben Langmead, Omar Ahmed

Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn

Nature Communications(2024)10.1038/s41467-024-45601-8

N/A

0.345DataRank · unranked

9 citations

Thiagarajan Venkataraman, William R. Morgenlander, Miso Na, Tomasz Kula, Kathleen Waugh +9 more

Pangenomic genotyping with the marker array

Algorithms for Molecular Biology(2023)10.1186/s13015-023-00225-3

N/A

0.330DataRank · unranked

8 citations

Kavya Vaddadi, Ben Langmead, Taher Mun

Fast and memory-efficient scRNA-seq k -means clustering with various distances

PubMed(2021)10.1145/3459930.3469523

N/A

0.312DataRank · unranked

7 citations

Nathan Dyjack, Vladimir Braverman, Stephanie C. Hicks, Ben Langmead, Daniel N. Baker

Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases

Scientific Data(2023)10.1038/s41597-023-02645-7

Top 56%

0.293DataRank

Top 56%5 citations

Yeongjun Jang, Taejeong Bae, Adriana Cherskov, Sarah B. Emery, Liana Fasching +90 more

IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101033

N/A

0.269DataRank · unranked

5 citations

Ben Langmead, Yana Safonova, Mao-Jan Lin

Using the linear references from the pangenome to discover missing autism variants

Nature Communications(2026)10.1038/s41467-026-68378-4

Top 65%

0.208DataRank

Top 65%3 citations

Jiadong Lin, Michelle D. Noyes, Young-Jun Kwon, Isaac Wong, Nidhi Koundinya +252 more

LevioSAM: Fast lift-over of alternate reference alignments

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.05.429867

N/A

0.130DataRank · unranked

1 citations

Nae-Chyun Chen, Ben Langmead, Taher Mun

Mem-based pangenome indexing for k-mer queries

Algorithms for Molecular Biology(2025)10.1186/s13015-025-00272-y

N/A

0.104DataRank · unranked

1 citations

Nathaniel K. Brown, Omar Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz +2 more

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data

Research Square(2024)10.21203/rs.3.rs-4721159/v1

N/A

0.104DataRank · unranked

1 citations

Caitlin Guccione, Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio González +13 more

Improved pangenomic classification accuracy with chain statistics

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.29.620953

N/A

0.104DataRank · unranked

1 citations

Vikram S. Shivakumar, Ben Langmead, Nathaniel K. Brown

Minimizing Reference Bias: The Impute-First Approach for Personalized Genome Analysis

(2023)10.1145/3584371.3613034

N/A

0DataRank · unranked

1 citations

Taher Mun, Ben Langmead, Kavya Vaddadi

Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification

Genome biology(2024)10.1186/s13059-024-03244-4

N/A

0DataRank · unranked

34 citations

Ben Langmead, Li Song

Movi: A fast and cache-efficient full-text pangenome index

iScience(2024)10.1016/j.isci.2024.111464

N/A

0DataRank · unranked

32 citations

Nathaniel K. Brown, Omar Ahmed, Travis Gagie, Ben Langmead, Mohsen Zakeri

Sigmoni: classification of nanopore signal with a compressed pangenome index

Bioinformatics(2024)10.1093/bioinformatics/btae213

N/A

0DataRank · unranked

27 citations

Omar Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead, Vikram S Shivakumar

Measuring, visualizing, and diagnosing reference bias with biastools

Genome biology(2024)10.1186/s13059-024-03240-8

N/A

0DataRank · unranked

20 citations

Sheila Iyer, Nae-Chyun Chen, Ben Langmead, Mao-Jan Lin

DandD: Efficient measurement of sequence growth and similarity

iScience(2024)10.1016/j.isci.2024.109054

N/A

0DataRank · unranked

12 citations

Omar Ahmed, Ben Langmead, Jessica Bonnie

Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests

arXiv (Cornell University)(2024)10.48550/arxiv.2402.06935

N/A

0DataRank · unranked

0 citations

Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini +2 more

MEM-based pangenome indexing for k -mer queries

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.20.595044

N/A

0DataRank · unranked

0 citations

Nathaniel K. Brown, Omar Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz +2 more

Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests

PubMed(2024)10.4230/lipics.sea.2024.10

N/A

0DataRank · unranked

0 citations

Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini +2 more

Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons

Nature Communications(2025)10.1038/s41467-025-62004-5

N/A

0DataRank · unranked

6 citations

Parker S. Sandal, Holly Spence, G Burns, Aswathy Peethambaran Mallika, Fatemeh Abbasinejad +10 more

Fast and flexible minimizer digestion with digest

Bioinformatics(2025)10.1093/bioinformatics/btaf368

N/A

0DataRank · unranked

1 citations

Ishmeal Lee, Vikram S Shivakumar, Omar Ahmed, Ben Langmead, Alan Zheng

Accurate short-read alignment throughr-index-based pangenome indexing

Genome Research(2025)10.1101/gr.279858.124

N/A

0DataRank · unranked

4 citations

Massimiliano Rossi, Eddie Ferro, Marco Antônio Oliva, Erik Garrison, Ben Langmead +2 more

Robust 16S rRNA classification based on a compressed LCA index

Genome Research(2025)10.1101/gr.279846.124

N/A

0DataRank · unranked

2 citations

Christina Boucher, Ben Langmead, Omar Ahmed

Partitioned multi-MUM finding for scalable pangenomics with MumemtoM

Genome Research(2025)10.1101/gr.280940.125

N/A

0DataRank · unranked

1 citations

Ben Langmead, Vikram S. Shivakumar

Movi Color: fast and accurate long-read classification with the move structure

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.22.655637

N/A

0DataRank · unranked

0 citations

Sina Majidian, Ben Langmead, Mohsen Zakeri, Steven Tan

Run-length compressed metagenomic read classification with SMEM-finding and tagging

iScience(2025)10.1016/j.isci.2025.114029

N/A

0DataRank · unranked

0 citations

Omar Ahmed, Jan Fostier, Ben Langmead, Travis Gagie, Lore Depuydt

Movi Color: fast and accurate taxonomic classification with the move structure

PubMed(2025)10.1145/3765612.3767233

N/A

0DataRank · unranked

0 citations

Sina Majidian, Ben Langmead, Mohsen Zakeri, Steven Tan

694. RNA-Seq Samples Beyond the Known Transcriptome with Derfinder Available via Recount

Biological Psychiatry(2017)10.1016/j.biopsych.2017.02.761

N/A

0DataRank · unranked

0 citations

Abhinav Nellore, Kai Kammers, Shannon Ellis, Margaret Taub, Kasper Hansen +4 more

Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.30.551179

N/A

0DataRank · unranked

0 citations

Thiagarajan Venkataraman, William R. Morgenlander, Miso Na, Tomasz Kula, Kathleen Waugh +9 more

ASCOT identifies key regulators of neuronal subtype-specific splicing

Nature Communications(2020)10.1038/s41467-019-14020-5

N/A

0DataRank · unranked

152 citations

Christopher Wilks, Rone Charles, Patrick J. Leavey, D. Ghosh, Lizhi Jiang +8 more

Reducing reference bias using multiple population reference genomes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.03.975219

N/A

0DataRank · unranked

19 citations

Brad Solomon, Taher Mun, Sheila Iyer, Ben Langmead, Nae-Chyun Chen

Megadepth: efficient coverage quantification for BigWigs and BAMs

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.17.423317

N/A

0DataRank · unranked

5 citations

Omar Ahmed, Daniel N. Baker, David Zhang, Leonardo Collado‐Torres, Ben Langmead +1 more

LevioSAM: fast lift-over of variant-aware reference alignments

Bioinformatics(2021)10.1093/bioinformatics/btab396

N/A

0DataRank · unranked

13 citations

Nae-Chyun Chen, Ben Langmead, Taher Mun

Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing

PubMed(2021)10.4230/lipics.esa.2021.56

N/A

0DataRank · unranked

1 citations

Ben Langmead, Dominik Kempa

PHONI: Streamed Matching Statistics with Multi-Genome References

CINECA IRIS Institutial research information system (University of Pisa)(2021)10.1109/dcc50243.2021.00027

N/A

0DataRank · unranked

22 citations

Travis Gagie, I Tomohiro, Dominik Köppl, Ben Langmead, Giovanni Manzini +4 more

MONI: A Pangenomics Index for Finding MEMs

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.06.451246

N/A

0DataRank · unranked

6 citations

Marco Antônio Oliva, Ben Langmead, Travis Gagie, Christina Boucher, Massimiliano Rossi

Two-stage Linked Component Analysis for Joint Decomposition of Multiple Biologically Related Data Sets

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.22.435728

N/A

0DataRank · unranked

1 citations

Brian Caffo, Genevieve L. Stein-O’Brien, Jinrui Liu, Ben Langmead, Carlo Colantuoni +2 more

Cell-specific regulation of gene expression using splicing-dependent frameshifting

Nature Communications(2022)10.1038/s41467-022-33523-2

N/A

0DataRank · unranked

39 citations

Alexei M. Bygrave, Clayton P. Santiago, Rogger P. Carmen‐Orozco, Vickie Trinh, Minzhong Yu +31 more

A scalable and unbiased discordance metric with H +

Biostatistics(2022)10.1093/biostatistics/kxac035

N/A

0DataRank · unranked

5 citations

Daniel N. Baker, Vladimir Braverman, Ben Langmead, Stephanie C. Hicks, Nathan Dyjack

Improved sequence mapping using a complete reference genome and lift-over

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.27.489683

N/A

0DataRank · unranked

6 citations

Luis F. Paulin, Fritz J. Sedlazeck, Sergey Koren, Adam M. Phillippy, Ben Langmead +1 more

SPUMONI 2: Improved pangenome classification using a compressed index of minimizer digests

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.08.506805

N/A

0DataRank · unranked

3 citations

Massimiliano Rossi, Travis Gagie, Christina Boucher, Ben Langmead, Omar Ahmed

Cell-specific regulation of gene expression using splicing-dependent frameshifting

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.02.481623

N/A

0DataRank · unranked

2 citations

Alexei M. Bygrave, Clayton P. Santiago, Rogger P. Carmen‐Orozco, Vickie Trinh, Minzhong Yu +29 more

Unleashing alternative polyadenylation analyses with REPAC

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.14.484280

N/A

0DataRank · unranked

0 citations

Christopher Wilks, Ben Langmead, Luigi Marchionni, Eddie L. Imada

Cell-specific regulation of gene expression using splicing-dependent frameshifting.

Research Square(2022)10.21203/rs.3.rs-1416757/v1

N/A

0DataRank · unranked

0 citations

Jonathan P. Ling, Alexei M. Bygrave, Clayton P. Santiago, Rogger P. Carmen‐Orozco, Vickie Trinh +28 more

Improved sequence mapping using a complete reference genome and lift-over

Nature Methods(2023)10.1038/s41592-023-02069-6

N/A

0DataRank · unranked

30 citations

Luis F. Paulin, Fritz J. Sedlazeck, Sergey Koren, Adam M. Phillippy, Ben Langmead +1 more

REPAC: analysis of alternative polyadenylation from RNA-sequencing data

Genome biology(2023)10.1186/s13059-023-02865-5

N/A

0DataRank · unranked

16 citations

Christopher Wilks, Ben Langmead, Luigi Marchionni, Eddie L. Imada

WGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs

iScience(2023)10.1016/j.isci.2023.107402

N/A

0DataRank · unranked

2 citations

Pei-Wei Chen, Sanjit A. Seshia, Ben Langmead, Kuan-Hao Chao

Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2

Genome Research(2023)10.1101/gr.277655.123

N/A

0DataRank · unranked

25 citations

Ben Langmead, Daniel N. Baker

Movi: a fast and cache-efficient full-text pangenome index

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.04.565615

N/A

0DataRank · unranked

13 citations

Nathaniel K. Brown, Omar Ahmed, Travis Gagie, Ben Langmead, Mohsen Zakeri

Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.15.567129

N/A

0DataRank · unranked

3 citations

Ben Langmead, Li Song

Suffixient Sets

arXiv (Cornell University)(2023)10.48550/arxiv.2312.01359

N/A

0DataRank · unranked

2 citations

Travis Gagie, Ben Langmead, Manzini, Giovanni, Nicola Prezza, Lore Depuydt

Ben Langmead

Indexed papers

Top data-sharing exemplar

Papers