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  1. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ..., Gainesville, Florida 32611, USA Corresponding author: langmea@cs.jhu.eduAbstractTaxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with the r-index enable full-text pattern matching against large sequence collections...
  2. Reviewer Index: Reviewer Index, Volume 34, 2024 Genome Res. December 2024 34: 2335-2340
    ...(Chuck) Zook, Justin M. Zuchner, Stephan Zuffardi, Orsetta Zuo, Yongchun Zwart, Wilbert Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 ;34/12/2335 2335 34/12/2335 Reviewer Index 12...
  3. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    ...Accurate short-read alignment through r-index-based pan indexing Rahul Varki1,4, Massimiliano Rossi1,4, Eddie Ferro1, Marco Oliva1, Erik Garrison2, Ben Langmead3 and Christina Boucher1 1Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611...
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  4. Reviewer Index: Reviewer Index, Volume 33, 2023 Genome Res. December 2023 33: 2174-2178
    ..., Justin M. Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 ;33/12/2174 2174 33/12/2174 Reviewer Index 12 2023 22 12 2023 22 12 2023 33 33 33 12 ;33/12 12 33/12 2174 2178 Published...
  5. Method: Efficient taxa identification using a pangenome index
    • Omar Ahmed,
    • Massimiliano Rossi,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. July 2023 33: 1069-1077; Published in Advance May 31, 2023, doi:10.1101/gr.277642.123
    ...Efficient taxa identification using a pan index Omar Ahmed1, Massimiliano Rossi2, Christina Boucher2 and Ben Langmead1 1Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA; 2Department of Computer and Information Science and Engineering, Herbert Wertheim College...
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  6. Reviewer Index: Reviewer Index, Volume 32, 2022 Genome Res. November/December 2022 32: 2146-2149
    ...Kazazian, who passed away January 20, 2022. Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 ;32/11-12/2146 2146 32/11-12/2146 Reviewer Index 11-12 2022 20 12 2022 20 12 2022 32 32 32 11...
  7. Reviewer Index: Reviewer Index, Volume 31, 2021 Genome Res. December 2021 31: 2362-2365
    .../12/2362 Reviewer Index 12 2021 1 12 2021 1 12 2021 31 31 31 12 ;31/12 12 31/12 2362 2365 Published by Cold Spring Harbor Laboratory Press 2021 Absher, Devin Adams, Mark Adebali, Ogün Adelman, Karen Adey, Andrew Aerts, Stein Agüero, Fernán Ahituv, Nadav Ahmad, Kami Alani, Eric Alba, Mar Alexandrov, Ludmil Alkan...
  8. Reviewer Index: Reviewer Index, Volume 30, 2020 Genome Res. December 2020 30: 1857-1861
    .... Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 ;30/12/1857 1857 30/12/1857 Reviewer Index 12 2020 24 11 2020 24 11 2020 30 30 30 12 ;30/12 12 30/12 1857 1861 Published by Cold Spring Harbor Laboratory Press 2020 Absher, Devin Abyzov, Alexej Adameyko, Igor Adams, Mark Adebali...
  9. Reviewer Index: Reviewer Index, Volume 29, 2019 Genome Res. December 2019 29: 2117-2121
    ...-5469 Cold Spring Harbor Laboratory Press 9509184 ;29/12/2117 2117 29/12/2117 Reviewer Index 12 2019 28 11 2019 28 11 2019 29 29 29 12 ;29/12 12 29/12 2117 2121 Published by Cold Spring Harbor Laboratory Press 2019 Abyzov, Alexej Adelson, David L. Adey, Andrew Aerts, Stein Ahrens, Christian Akey, Joshua M...
  10. Reviewer Index: Reviewer Index, Volume 28, 2018 Genome Res. December 2018 28: 1957-1961
    .... Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9518021 ;28/12/1957 1957 28/12/1957 Reviewer Index 12 2018 29 11 2018 29 11 2018 28 28 28 12 ;28/12 12 28/12 1957 1961 Published by Cold Spring Harbor Laboratory Press 2018 Adams, Mark Adams, Peter D. Adelson, David L. Adey, Andrew Adli...
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