Travis Gagie

ORCID

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 177

Top Venues

Bielefeld University (PHD)

Education History

Bielefeld University

PHD

Publications

Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro
Two-Dimensional Block Trees. Comput. J. 67 (1) (2024)
Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro
Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests. CoRR (2024)
Christina Boucher, Travis Gagie, Aaron Hong, Yansong Li, Norbert Zeh
Another virtue of wavelet forests? CoRR (2023)
Travis Gagie, Mozhgan Saeidi, Allan Sapucaia
Ruler Wrapping. Int. J. Comput. Geom. Appl. 33 (1&2) (2023)
Nicola Cotumaccio, Travis Gagie, Dominik Köppl, Nicola Prezza
Space-time Trade-offs for the LCP Array of Wheeler DFAs. CoRR (2023)
Alessio Conte, Nicola Cotumaccio, Travis Gagie, Giovanni Manzini, Nicola Prezza, Marinella Sciortino
Computing matching statistics on Wheeler DFAs. DCC (2023)
Igor Tatarnikov, Ardavan Shahrabi Farahani, Sana Kashgouli, Travis Gagie
MONI Can Find k-MEMs. CPM (2023)
Xing Lyu, Travis Gagie, Meng He, Yakov Nekrich, Norbert Zeh
Sum-of-Local-Effects Data Structures for Separable Graphs. COCOON (1) (2023)
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi
Data Structures for SMEM-Finding in the PBWT. SPIRE (2023)
Xing Lyu, Travis Gagie, Meng He, Yakov Nekrich, Norbert Zeh
Sum-of-Local-Effects Data Structures for Separable Graphs. CoRR (2023)
César Martínez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik Köppl, Travis Gagie, Susana Ladra
Augmented Thresholds for MONI. DCC (2023)
Marco Oliva, Travis Gagie, Christina Boucher
Recursive Prefix-Free Parsing for Building Big BWTs. DCC (2023)
Travis Gagie, Meng He, Michael St Denis
Dynamic Compact Planar Embeddings. SPIRE (2023)
Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie
Acceleration of FM-index Queries Through Prefix-free Parsing. CoRR (2023)
Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
Wheeler maps. CoRR (2023)
Travis Gagie, Sana Kashgouli, Gonzalo Navarro
A Simple Grammar-Based Index for Finding Approximately Longest Common Substrings. SPIRE (2023)
Nicola Cotumaccio, Travis Gagie, Dominik Köppl, Nicola Prezza
Space-Time Trade-Offs for the LCP Array of Wheeler DFAs. SPIRE (2023)
Guillermo de Bernardo, Travis Gagie, Susana Ladra, Gonzalo Navarro, Diego Seco
Faster compressed quadtrees. J. Comput. Syst. Sci. 131 (2023)
Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie
Acceleration of FM-Index Queries Through Prefix-Free Parsing. WABI (2023)
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
Faster Maximal Exact Matches with Lazy LCP Evaluation. CoRR (2023)
Travis Gagie
Flexible Grammar-based Indexes (invited paper). ITAT (2023)
Omar Ahmed, Andrej Baláz, Nathaniel K. Brown, Lore Depuydt, Adrián Goga, Alessia Petescia, Mohsen Zakeri, Jan Fostier, Travis Gagie, Ben Langmead, Gonzalo Navarro, Nicola Prezza
r-indexing without backward searching. CoRR (2023)
Alessio Conte, Nicola Cotumaccio, Travis Gagie, Giovanni Manzini, Nicola Prezza, Marinella Sciortino
Computing matching statistics on Wheeler DFAs. CoRR (2023)
Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher
MONI: A Pangenomic Index for Finding Maximal Exact Matches. J. Comput. Biol. 29 (2) (2022)
César Martínez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik Köppl, Travis Gagie, Susana Ladra
Augmented Thresholds for MONI. CoRR (2022)
Travis Gagie
On Representing the Degree Sequences of Sublogarithmic-Degree Wheeler Graphs. SPIRE (2022)
Alexandre P. Francisco, Travis Gagie, Dominik Köppl, Susana Ladra, Gonzalo Navarro
Correction to: Graph Compression for Adjacency-Matrix Multiplication. SN Comput. Sci. 3 (3) (2022)
Marco Oliva, Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie, Christina Boucher
CSTs for Terabyte-Sized Data. DCC (2022)
Antonio Fariña, Travis Gagie, Szymon Grabowski, Giovanni Manzini, Gonzalo Navarro, Alberto Ordóñez Pereira
Efficient and compact representations of some non-canonical prefix-free codes. Theor. Comput. Sci. 907 (2022)
Travis Gagie, Giovanni Manzini, Marinella Sciortino
Teaching the Burrows-Wheeler Transform via the Positional Burrows-Wheeler Transform. CoRR (2022)
Xing Lyu, Travis Gagie
Rectangular Ruler Wrapping. CoRR (2022)
Travis Gagie, Sana Kashgouli, Ben Langmead
KATKA: A KRAKEN-Like Tool with k Given at Query Time. SPIRE (2022)
Travis Gagie
Space-efficient RLZ-to-LZ77 conversion. CoRR (2022)
Alexandre P. Francisco, Travis Gagie, Dominik Köppl, Susana Ladra, Gonzalo Navarro
Graph Compression for Adjacency-Matrix Multiplication. SN Comput. Sci. 3 (3) (2022)
Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi
RLBWT Tricks. SEA (2022)
Travis Gagie, Sana Kashgouli
KATKA: A KRAKEN-like tool with k given at query time. CoRR (2022)
Travis Gagie
Preface to Special Issue for DCC 2020. Inf. Comput. 285 (Part) (2022)
Nick Fagan, Jorge Hermo González, Travis Gagie
A fast and simple O(z log n)-space index for finding approximately longest common substrings. CoRR (2022)
Travis Gagie, Artur Jez, Gonzalo Navarro
Space-efficient conversions from SLPs. CoRR (2022)
Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi
RLBWT Tricks. DCC (2022)
Adrián Goga, Andrej Baláz, Alessia Petescia, Travis Gagie
MARIA: Multiple-alignment r-index with aggregation. CoRR (2022)
Travis Gagie
Simple Worst-Case Optimal Adaptive Prefix-Free Coding. DCC (2022)
Paolo Ferragina, Travis Gagie, Dominik Köppl, Giovanni Manzini, Gonzalo Navarro, Manuel Striani, Francesco Tosoni
Improving Matrix-vector Multiplication via Lossless Grammar-Compressed Matrices. CoRR (2022)
Travis Gagie
-compressed searchable partial-sums data structure for static sequences of sublogarithmic positive integers. CoRR (2022)
Travis Gagie
Simple Worst-Case Optimal Adaptive Prefix-Free Coding. ESA (2022)
Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
Finding Maximal Exact Matches Using the r-Index. J. Comput. Biol. 29 (2) (2022)
Paolo Ferragina, Giovanni Manzini, Travis Gagie, Dominik Köppl, Gonzalo Navarro, Manuel Striani, Francesco Tosoni
Improving Matrix-vector Multiplication via Lossless Grammar-Compressed Matrices. Proc. VLDB Endow. 15 (10) (2022)
Travis Gagie
MONI can find k-MEMs. CoRR (2022)
Travis Gagie, Garance Gourdel, Giovanni Manzini
Compressing and Indexing Aligned Readsets. WABI (2021)
Djamal Belazzougui, Manuel Cáceres, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Gonzalo Navarro, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei
Block trees. J. Comput. Syst. Sci. 117 (2021)
Travis Gagie
$r$-indexing Wheeler graphs. CoRR (2021)
Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi
RLBWT Tricks. CoRR (2021)
Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá
An index for moving objects with constant-time access to their compressed trajectories. Int. J. Geogr. Inf. Sci. 35 (7) (2021)
Patrick Hagge Cording, Travis Gagie, Mathias Bæk Tejs Knudsen, Tomasz Kociumaka
Maximal unbordered factors of random strings. Theor. Comput. Sci. 852 (2021)
Travis Gagie, Mozhgan Saeidi, Allan Sapucaia
Ruler Wrapping. CoRR (2021)
Travis Gagie
Compact Euler Tours of Trees with Small Maximum Degree. CoRR (2021)
Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher
Efficiently Merging r-indexes. DCC (2021)
Travis Gagie
Simple Worst-Case Optimal Adaptive Prefix-Free Coding. CoRR (2021)
Dustin Cobas, Travis Gagie, Gonzalo Navarro
A Fast and Small Subsampled R-Index. CPM (2021)
Dustin Cobas, Travis Gagie, Gonzalo Navarro
A Fast and Small Subsampled R-index. CoRR (2021)
Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi
PFP Compressed Suffix Trees. ALENEX (2021)
Djamal Belazzougui, Travis Gagie, J. Ian Munro, Gonzalo Navarro, Yakov Nekrich
Range Majorities and Minorities in Arrays. Algorithmica 83 (6) (2021)
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
PHONI: Streamed Matching Statistics with Multi-Genome References. DCC (2021)
Travis Gagie, Sebastian Wild
Succinct Euler-Tour Trees. CCCG (2021)
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. J. Comput. Biol. 27 (4) (2020)
Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Louisa Seelbach Benkner, Yoshimasa Takabatake
Practical Random Access to SLP-Compressed Texts. SPIRE (2020)
Travis Gagie, Gonzalo Navarro, Nicola Prezza
Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space. J. ACM 67 (1) (2020)
Travis Gagie, Gonzalo Navarro
Computation over compressed data. Inf. Comput. 273 (2020)
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
PHONI: Streamed Matching Statistics with Multi-Genome References. CoRR (2020)
Hideo Bannai, Travis Gagie, Tomohiro I
-index. Theor. Comput. Sci. 812 (2020)
Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi
PFP Data Structures. CoRR (2020)
Hideo Bannai, Travis Gagie, Gary Hoppenworth, Simon J. Puglisi, Luís M. S. Russo
More Time-Space Tradeoffs for Finding a Shortest Unique Substring. Algorithms 13 (9) (2020)
Travis Gagie, Meng He, Gonzalo Navarro
Compressed Dynamic Range Majority and Minority Data Structures. Algorithmica 82 (7) (2020)
Travis Gagie, Meng He, Gonzalo Navarro, Carlos Ochoa
Tree path majority data structures. Theor. Comput. Sci. 833 (2020)
Leo Ferres, José Fuentes-Sepúlveda, Travis Gagie, Meng He, Gonzalo Navarro
Fast and compact planar embeddings. Comput. Geom. 89 (2020)
Philip Bille, Mikko Berggren Ettienne, Travis Gagie, Inge Li Gørtz, Nicola Prezza
Decompressing Lempel-Ziv Compressed Text. DCC (2020)
Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Matching Reads to Many Genomes with the r-Index. J. Comput. Biol. 27 (4) (2020)
Diego Díaz-Domínguez, Travis Gagie, Gonzalo Navarro
Simulating the DNA String Graph in Succinct Space. CoRR (2019)
Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. RECOMB (2019)
Diego Arroyuelo, Guillermo de Bernardo, Travis Gagie, Gonzalo Navarro
Faster Dynamic Compressed d-ary Relations. SPIRE (2019)
Travis Gagie, Meng He, Gonzalo Navarro
Path queries on functions. Theor. Comput. Sci. 770 (2019)
Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Louisa Seelbach Benkner, Yoshimasa Takabatake
Tree-Shape Grammars for Random Access. CoRR (2019)
Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Jens Stoye
25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241). Dagstuhl Reports 9 (6) (2019)
Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini
Matching reads to many genomes with the r-index. CoRR (2019)
Gianni Decaroli, Travis Gagie, Giovanni Manzini
A compact index for order-preserving pattern matching. Softw. Pract. Exp. 49 (6) (2019)
Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Yoshimasa Takabatake
Rpair: Rescaling RePair with Rsync. SPIRE (2019)
Diego Arroyuelo, Guillermo de Bernardo, Travis Gagie, Gonzalo Navarro
Faster Dynamic Compressed d-ary Relations. CoRR (2019)
Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun
Prefix-free parsing for building big BWTs. Algorithms Mol. Biol. 14 (1) (2019)
Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi
Sparse Dynamic Programming on DAGs with Small Width. ACM Trans. Algorithms 15 (2) (2019)
Jarno N. Alanko, Travis Gagie, Gonzalo Navarro, Louisa Seelbach Benkner
Tunneling on Wheeler Graphs. DCC (2019)
Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Yoshimasa Takabatake
Rpair: Rescaling RePair with Rsync. CoRR (2019)
Diego Díaz-Domínguez, Travis Gagie, Gonzalo Navarro
Simulating the DNA Overlap Graph in Succinct Space. CPM (2019)
Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
Bidirectional Variable-Order de Bruijn Graphs. Int. J. Found. Comput. Sci. 29 (8) (2018)
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. RECOMB (2018)
Jarno Alanko, Travis Gagie, Gonzalo Navarro, Louisa Seelbach Benkner
Tunneling on Wheeler Graphs. CoRR (2018)
Hideo Bannai, Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Shiho Sugimoto
Diverse Palindromic Factorization is NP-Complete. Int. J. Found. Comput. Sci. 29 (2) (2018)
Travis Gagie, Gonzalo Navarro, Nicola Prezza
Optimal-Time Text Indexing in BWT-runs Bounded Space. SODA (2018)
Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro
Two-Dimensional Block Trees. CoRR (2018)
Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá
Relative compression of trajectories. CoRR (2018)
Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie
Practical dynamic de Bruijn graphs. Bioinform. 34 (24) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Travis Gagie