Travis Gagie

Also affiliated with Universidad Diego Portales

Computer ScienceBiochemistry, Genetics and Molecular Biology

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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 35 papers. Top paper: “Pan-genomic matching statistics for targeted nanopore sequencing”.

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

Syotti: scalable bait design for DNA enrichment

Bioinformatics(2022)10.1093/bioinformatics/btac226

N/A

0.442DataRank · unranked

18 citations

Ilya B. Slizovskiy, Daniel Lokshtanov, Travis Gagie, Noelle Noyes, Christina Boucher +1 more

How to Find Long Maximal Exact Matches and Ignore Short Ones

Lecture notes in computer science(2024)10.1007/978-3-031-66159-4_10

N/A

0.269DataRank · unranked

5 citations

Travis Gagie

PFP Compressed Suffix Trees

Society for Industrial and Applied Mathematics eBooks(2021)10.1137/1.9781611976472.5

N/A

0DataRank · unranked

20 citations

Ondřej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro +2 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

Buffering Updates Enables Efficient Dynamic de Bruijn Graphs

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.16.435535

N/A

0DataRank · unranked

1 citations

Bahar Alipanahi, Jonathen Settle, Christina Boucher, Travis Gagie, Jarno Alanko

Efficiently Merging r-indexes

CINECA IRIS Institutial research information system (University of Pisa)(2021)10.1109/dcc50243.2021.00028

N/A

0DataRank · unranked

1 citations

Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie +2 more

CSTs for Terabyte-Sized Data

PubMed(2022)10.1109/dcc52660.2022.00017

N/A

0DataRank · unranked

4 citations

Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie, Christina Boucher +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

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data

Bioinformatics(2023)10.1093/bioinformatics/btad552

N/A

0DataRank · unranked

4 citations

Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher +2 more

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

Computing matching statistics on Wheeler DFAs

PubMed(2023)10.1109/dcc55655.2023.00023

N/A

0DataRank · unranked

6 citations

Nicola Cotumaccio, Travis Gagie, Giovanni Manzini, Nicola Prezza, Marinella Sciortino +1 more

Recursive Prefix-Free Parsing for Building Big BWTs

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.18.524557

N/A

0DataRank · unranked

2 citations

Travis Gagie, Christina Boucher, Marco Antônio Oliva

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

Augmented Thresholds for MONI

PubMed(2023)10.1109/dcc55655.2023.00035

N/A

0DataRank · unranked

2 citations

Nathaniel K. Brown, Fernando Silva‐Coira, Dominik Köppl, Travis Gagie, Susana Ladra +1 more

A Simple Grammar-Based Index for Finding Approximately Longest Common Substrings

Lecture notes in computer science(2023)10.1007/978-3-031-43980-3_19

N/A

0DataRank · unranked

1 citations

Sana Kashgouli, Gonzalo Navarro, Travis Gagie

Computing matching statistics on Wheeler DFAs

arXiv (Cornell University)(2023)10.48550/arxiv.2301.05338

N/A

0DataRank · unranked

0 citations

Nicola Cotumaccio, Travis Gagie, Giovanni Manzini, Nicola Prezza, Marinella Sciortino +1 more

Acceleration of FM-index Queries Through Prefix-free Parsing

arXiv (Cornell University)(2023)10.48550/arxiv.2305.05893

N/A

0DataRank · unranked

0 citations

Marco Antônio Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie +1 more

Space-time Trade-offs for the LCP Array of Wheeler DFAs

arXiv (Cornell University)(2023)10.48550/arxiv.2306.05684

N/A

0DataRank · unranked

0 citations

Travis Gagie, Dominik Köppl, Nicola Prezza, Nicola Cotumaccio

Data Structures for SMEM-Finding in the PBWT

Lecture notes in computer science(2023)10.1007/978-3-031-43980-3_8

N/A

0DataRank · unranked

0 citations

Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi +1 more

Acceleration of FM-index Queries Through Prefix-free Parsing.

(2023)10.4230/lipics.wabi.2023.13

N/A

0DataRank · unranked

0 citations

Marco Antônio Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie +1 more

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

Building a pangenome alignment index via recursive prefix-free parsing

iScience(2024)10.1016/j.isci.2024.110933

N/A

0DataRank · unranked

5 citations

Marco Antônio Oliva, Travis Gagie, Christina Boucher, Eddie Ferro

Pfp-fm: an accelerated FM-index

Algorithms for Molecular Biology(2024)10.1186/s13015-024-00260-8

N/A

0DataRank · unranked

6 citations

Marco Antônio Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie +1 more

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

b-move: faster bidirectional character extensions in a run-length compressed index

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.30.596587

N/A

0DataRank · unranked

0 citations

Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier +1 more

Maximum-scoring path sets on pangenome graphs of constant treewidth

Frontiers in Bioinformatics(2024)10.3389/fbinf.2024.1391086

N/A

0DataRank · unranked

0 citations

Travis Gagie, Eva Herencsárová, Tomáš Vinař, Broňa Brejová

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

Faster run-length compressed suffix arrays

arXiv (Cornell University)(2024)10.48550/arxiv.2408.04537

N/A

0DataRank · unranked

0 citations

Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Marinella Sciortino, Brown, Nathaniel K.

Faster run-length compressed suffix arrays.

PubMed(2025)10.4230/oasics.grossi.10

N/A

0DataRank · unranked

1 citations

Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Marinella Sciortino, Nathaniel K Brown

b-move: faster lossless approximate pattern matching in a run-length compressed index

Algorithms for Molecular Biology(2025)10.1186/s13015-025-00281-x

N/A

0DataRank · unranked

1 citations

Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier +1 more

Efficient Grammar Compression via RLZ-based RePair

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.22.666196

N/A

0DataRank · unranked

0 citations

Travis Gagie, Christina Boucher, Rahul Varki

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

Buffering updates enables efficient dynamic de Bruijn graphs

Computational and Structural Biotechnology Journal(2021)10.1016/j.csbj.2021.06.047

N/A

0DataRank · unranked

12 citations

Bahar Alipanahi, Jonathen Settle, Christina Boucher, Travis Gagie, Jarno Alanko

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