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ORCIDTravis Gagie
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- affiliation: Dalhousie University, Halifax, NS, Canada
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2020 – today
- 2024
[j69]Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie:
Pfp-fm: an accelerated FM-index. Algorithms Mol. Biol. 19(1): 15 (2024)- [j68]Nieves R. Brisaboa
, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro:
Two-Dimensional Block Trees. Comput. J. 67(1): 391-406 (2024) - [j67]Brona Brejová, Travis Gagie, Eva Herencsárová, Tomás Vinar:
Maximum-scoring path sets on pangenome graphs of constant treewidth. Frontiers Bioinform. 4 (2024) - [c110]Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola:
Solving the Minimal Positional Substring Cover Problem in Sublinear Space. CPM 2024: 12:1-12:16 - [c109]Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro:
Faster Maximal Exact Matches with Lazy LCP Evaluation. DCC 2024: 123-132 - [c108]Aaron Hong, Christina Boucher, Travis Gagie, Yansong Li, Norbert Zeh:
Another virtue of wavelet forests. DCC 2024: 559 - [c107]Travis Gagie:
How to Find Long Maximal Exact Matches and Ignore Short Ones. DLT 2024: 131-140 - [c106]Travis Gagie, Adrián Goga, Artur Jez, Gonzalo Navarro:
Space-Efficient Conversions from SLPs. LATIN (1) 2024: 146-161 - [c105]Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén:
Wheeler Maps. LATIN (1) 2024: 178-192 - [c104]Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier:
b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index. WABI 2024: 10:1-10:18 - [c103]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. SEA 2024: 10:1-10:13 - [i124]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 abs/2402.06935 (2024) - [i123]Travis Gagie:
How to Find Long Maximal Exact Matches and Ignore Short Ones. CoRR abs/2403.02008 (2024) - [i122]Peter Peresíni, Nathaniel K. Brown, Travis Gagie, Ben Langmead:
MIOV: Reordering MOVI for even better locality. CoRR abs/2407.18956 (2024) - [i121]Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Marinella Sciortino:
Movelet Trees. CoRR abs/2408.04537 (2024) - 2023
- [j66]Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni:
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. Bioinform. 39(9) (2023) - [j65]Travis Gagie, Mozhgan Saeidi, Allan Sapucaia:
Ruler Wrapping. Int. J. Comput. Geom. Appl. 33(1&2): 3-12 (2023) - [j64]Guillermo de Bernardo, Travis Gagie, Susana Ladra, Gonzalo Navarro, Diego Seco:
Faster compressed quadtrees. J. Comput. Syst. Sci. 131: 86-104 (2023) - [c102]Xing Lyu, Travis Gagie, Meng He, Yakov Nekrich, Norbert Zeh:
Sum-of-Local-Effects Data Structures for Separable Graphs. COCOON (1) 2023: 195-206 - [c101]Igor Tatarnikov, Ardavan Shahrabi Farahani, Sana Kashgouli, Travis Gagie:
MONI Can Find k-MEMs. CPM 2023: 26:1-26:14 - [c100]Marco Oliva, Travis Gagie, Christina Boucher:
Recursive Prefix-Free Parsing for Building Big BWTs. DCC 2023: 62-70 - [c99]Alessio Conte, Nicola Cotumaccio, Travis Gagie, Giovanni Manzini, Nicola Prezza, Marinella Sciortino:
Computing matching statistics on Wheeler DFAs. DCC 2023: 150-159 - [c98]César Martínez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik Köppl, Travis Gagie, Susana Ladra:
Augmented Thresholds for MONI. DCC 2023: 268-277 - [c97]Travis Gagie:
Flexible Grammar-based Indexes (invited paper). ITAT 2023: 2 - [c96]Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi:
Data Structures for SMEM-Finding in the PBWT. SPIRE 2023: 89-101 - [c95]Nicola Cotumaccio, Travis Gagie, Dominik Köppl, Nicola Prezza:
Space-Time Trade-Offs for the LCP Array of Wheeler DFAs. SPIRE 2023: 143-156 - [c94]Travis Gagie, Meng He, Michael St Denis:
Dynamic Compact Planar Embeddings. SPIRE 2023: 233-245 - [c93]Travis Gagie, Sana Kashgouli, Gonzalo Navarro:
A Simple Grammar-Based Index for Finding Approximately Longest Common Substrings. SPIRE 2023: 246-252 - [c92]Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie:
Acceleration of FM-Index Queries Through Prefix-Free Parsing. WABI 2023: 13:1-13:16 - [i120]Alessio Conte, Nicola Cotumaccio, Travis Gagie, Giovanni Manzini, Nicola Prezza, Marinella Sciortino:
Computing matching statistics on Wheeler DFAs. CoRR abs/2301.05338 (2023) - [i119]Xing Lyu, Travis Gagie, Meng He, Yakov Nekrich, Norbert Zeh:
Sum-of-Local-Effects Data Structures for Separable Graphs. CoRR abs/2305.03240 (2023) - [i118]Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, Travis Gagie:
Acceleration of FM-index Queries Through Prefix-free Parsing. CoRR abs/2305.05893 (2023) - [i117]Nicola Cotumaccio, Travis Gagie, Dominik Köppl, Nicola Prezza:
Space-time Trade-offs for the LCP Array of Wheeler DFAs. CoRR abs/2306.05684 (2023) - [i116]Christina Boucher, Travis Gagie, Aaron Hong, Yansong Li, Norbert Zeh:
Another virtue of wavelet forests? CoRR abs/2308.07809 (2023) - [i115]Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén:
Wheeler maps. CoRR abs/2308.09836 (2023) - [i114]Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro:
Faster Maximal Exact Matches with Lazy LCP Evaluation. CoRR abs/2311.04538 (2023) - [i113]Lore Depuydt, Travis Gagie, Ben Langmead, Giovanni Manzini, Nicola Prezza:
Suffixient Sets. CoRR abs/2312.01359 (2023) - 2022
- [j63]Travis Gagie:
Preface to Special Issue for DCC 2020. Inf. Comput. 285(Part): 104880 (2022) - [j62]Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher:
MONI: A Pangenomic Index for Finding Maximal Exact Matches. J. Comput. Biol. 29(2): 169-187 (2022) - [j61]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): 188-194 (2022) - [j60]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): 2175-2187 (2022) - [j59]Alexandre P. Francisco, Travis Gagie, Dominik Köppl, Susana Ladra, Gonzalo Navarro:
Graph Compression for Adjacency-Matrix Multiplication. SN Comput. Sci. 3(3): 193 (2022) - [j58]Alexandre P. Francisco, Travis Gagie, Dominik Köppl, Susana Ladra, Gonzalo Navarro:
Correction to: Graph Compression for Adjacency-Matrix Multiplication. SN Comput. Sci. 3(3): 228 (2022) - [j57]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: 11-25 (2022) - [c91]Marco Oliva, Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie, Christina Boucher:
CSTs for Terabyte-Sized Data. DCC 2022: 93-102 - [c90]Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi:
RLBWT Tricks. DCC 2022: 444 - [c89]Travis Gagie:
Simple Worst-Case Optimal Adaptive Prefix-Free Coding. DCC 2022: 453 - [c88]Travis Gagie:
Simple Worst-Case Optimal Adaptive Prefix-Free Coding. ESA 2022: 57:1-57:5 - [c87]Travis Gagie, Sana Kashgouli, Ben Langmead:
KATKA: A KRAKEN-Like Tool with k Given at Query Time. SPIRE 2022: 191-197 - [c86]Travis Gagie:
On Representing the Degree Sequences of Sublogarithmic-Degree Wheeler Graphs. SPIRE 2022: 250-256 - [c85]Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi:
RLBWT Tricks. SEA 2022: 16:1-16:16 - [i112]Travis Gagie:
MONI can find k-MEMs. CoRR abs/2202.05085 (2022) - [i111]Paolo Ferragina, Travis Gagie, Dominik Köppl, Giovanni Manzini, Gonzalo Navarro, Manuel Striani, Francesco Tosoni:
Improving Matrix-vector Multiplication via Lossless Grammar-Compressed Matrices. CoRR abs/2203.14540 (2022) - [i110]Travis Gagie:
An n Hk-compressed searchable partial-sums data structure for static sequences of sublogarithmic positive integers. CoRR abs/2204.07916 (2022) - [i109]Travis Gagie, Sana Kashgouli:
KATKA: A KRAKEN-like tool with k given at query time. CoRR abs/2206.06053 (2022) - [i108]Travis Gagie, Giovanni Manzini, Marinella Sciortino:
Teaching the Burrows-Wheeler Transform via the Positional Burrows-Wheeler Transform. CoRR abs/2208.09840 (2022) - [i107]Adrián Goga, Andrej Baláz, Alessia Petescia, Travis Gagie:
MARIA: Multiple-alignment r-index with aggregation. CoRR abs/2209.09218 (2022) - [i106]Xing Lyu, Travis Gagie:
Rectangular Ruler Wrapping. CoRR abs/2210.01954 (2022) - [i105]César Martínez-Guardiola, Nathaniel K. Brown, Fernando Silva-Coira, Dominik Köppl, Travis Gagie, Susana Ladra:
Augmented Thresholds for MONI. CoRR abs/2211.07794 (2022) - [i104]Travis Gagie:
Space-efficient RLZ-to-LZ77 conversion. CoRR abs/2211.13254 (2022) - [i103]Nick Fagan, Jorge Hermo González, Travis Gagie:
A fast and simple O(z log n)-space index for finding approximately longest common substrings. CoRR abs/2211.13434 (2022) - [i102]Travis Gagie, Artur Jez, Gonzalo Navarro:
Space-efficient conversions from SLPs. CoRR abs/2212.02327 (2022) - 2021
- [j56]Djamal Belazzougui, Travis Gagie, J. Ian Munro, Gonzalo Navarro, Yakov Nekrich:
Range Majorities and Minorities in Arrays. Algorithmica 83(6): 1707-1733 (2021) - [j55]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): 1392-1424 (2021) - [j54]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: 1-22 (2021) - [j53]Patrick Hagge Cording, Travis Gagie, Mathias Bæk Tejs Knudsen, Tomasz Kociumaka:
Maximal unbordered factors of random strings. Theor. Comput. Sci. 852: 78-83 (2021) - [c84]Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi:
PFP Compressed Suffix Trees. ALENEX 2021: 60-72 - [c83]Travis Gagie, Sebastian Wild:
Succinct Euler-Tour Trees. CCCG 2021: 368-376 - [c82]Dustin Cobas, Travis Gagie, Gonzalo Navarro:
A Fast and Small Subsampled R-Index. CPM 2021: 13:1-13:16 - [c81]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: 193-202 - [c80]Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher:
Efficiently Merging r-indexes. DCC 2021: 203-212 - [c79]Travis Gagie, Garance Gourdel, Giovanni Manzini:
Compressing and Indexing Aligned Readsets. WABI 2021: 13:1-13:21 - [i101]Travis Gagie:
$r$-indexing Wheeler graphs. CoRR abs/2101.12341 (2021) - [i100]Dustin Cobas, Travis Gagie, Gonzalo Navarro:
A Fast and Small Subsampled R-index. CoRR abs/2103.15329 (2021) - [i99]Travis Gagie:
Compact Euler Tours of Trees with Small Maximum Degree. CoRR abs/2105.04965 (2021) - [i98]Travis Gagie:
Simple Worst-Case Optimal Adaptive Prefix-Free Coding. CoRR abs/2109.02997 (2021) - [i97]Travis Gagie, Mozhgan Saeidi, Allan Sapucaia:
Ruler Wrapping. CoRR abs/2109.14497 (2021) - [i96]Nathaniel K. Brown, Travis Gagie, Massimiliano Rossi:
RLBWT Tricks. CoRR abs/2112.04271 (2021) - 2020
- [j52]Travis Gagie, Meng He, Gonzalo Navarro:
Compressed Dynamic Range Majority and Minority Data Structures. Algorithmica 82(7): 2063-2086 (2020) - [j51]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): 234 (2020) - [j50]Leo Ferres, José Fuentes-Sepúlveda, Travis Gagie, Meng He, Gonzalo Navarro:
Fast and compact planar embeddings. Comput. Geom. 89: 101630 (2020) - [j49]Travis Gagie, Gonzalo Navarro:
Computation over compressed data. Inf. Comput. 273: 104515 (2020) - [j48]Travis Gagie, Gonzalo Navarro, Nicola Prezza:
Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space. J. ACM 67(1): 2:1-2:54 (2020) - [j47]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): 500-513 (2020) - [j46]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): 514-518 (2020) - [j45]Hideo Bannai, Travis Gagie, Tomohiro I:
Refining the r-index. Theor. Comput. Sci. 812: 96-108 (2020) - [j44]Travis Gagie, Meng He, Gonzalo Navarro, Carlos Ochoa:
Tree path majority data structures. Theor. Comput. Sci. 833: 107-119 (2020) - [c78]Philip Bille, Mikko Berggren Ettienne, Travis Gagie, Inge Li Gørtz, Nicola Prezza:
Decompressing Lempel-Ziv Compressed Text. DCC 2020: 143-152 - [c77]Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Louisa Seelbach Benkner, Yoshimasa Takabatake:
Practical Random Access to SLP-Compressed Texts. SPIRE 2020: 221-231 - [i95]Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi:
PFP Data Structures. CoRR abs/2006.11687 (2020) - [i94]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 abs/2011.05610 (2020)
2010 – 2019
- 2019
- [j43]Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, Taher Mun:
Prefix-free parsing for building big BWTs. Algorithms Mol. Biol. 14(1): 13:1-13:15 (2019) - [j42]Gianni Decaroli, Travis Gagie, Giovanni Manzini:
A compact index for order-preserving pattern matching. Softw. Pract. Exp. 49(6): 1041-1051 (2019) - [j41]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): 29:1-29:21 (2019) - [j40]Travis Gagie, Meng He, Gonzalo Navarro:
Path queries on functions. Theor. Comput. Sci. 770: 34-50 (2019) - [c76]Diego Díaz-Domínguez, Travis Gagie, Gonzalo Navarro:
Simulating the DNA Overlap Graph in Succinct Space. CPM 2019: 26:1-26:20 - [c75]Jarno N. Alanko, Travis Gagie, Gonzalo Navarro, Louisa Seelbach Benkner:
Tunneling on Wheeler Graphs. DCC 2019: 122-131 - [c74]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: 158-173 - [c73]Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Yoshimasa Takabatake:
Rpair: Rescaling RePair with Rsync. SPIRE 2019: 35-44 - [c72]Diego Arroyuelo, Guillermo de Bernardo, Travis Gagie, Gonzalo Navarro:
Faster Dynamic Compressed d-ary Relations. SPIRE 2019: 419-433 - [r4]Travis Gagie, Gonzalo Navarro:
Compressed Indexes for Repetitive Textual Datasets. Encyclopedia of Big Data Technologies 2019 - [i93]Diego Díaz-Domínguez, Travis Gagie, Gonzalo Navarro:
Simulating the DNA String Graph in Succinct Space. CoRR abs/1901.10453 (2019) - [i92]Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Yoshimasa Takabatake:
Rpair: Rescaling RePair with Rsync. CoRR abs/1906.00809 (2019) - [i91]Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Matching reads to many genomes with the r-index. CoRR abs/1908.01263 (2019) - [i90]Travis Gagie, Tomohiro I, Giovanni Manzini, Gonzalo Navarro, Hiroshi Sakamoto, Louisa Seelbach Benkner, Yoshimasa Takabatake:
Tree-Shape Grammars for Random Access. CoRR abs/1910.07145 (2019) - [i89]Diego Arroyuelo, Guillermo de Bernardo, Travis Gagie, Gonzalo Navarro:
Faster Dynamic Compressed d-ary Relations. CoRR abs/1911.08971 (2019) - [i88]Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Jens Stoye:
25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241). Dagstuhl Reports 9(6): 55-68 (2019) - 2018
- [j39]Travis Gagie, Gonzalo Navarro:
Guest Editorial: Special Issue on Compact Data Structures. Algorithmica 80(7): 1983-1985 (2018) - [j38]Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie:
Practical dynamic de Bruijn graphs. Bioinform. 34(24): 4189-4195 (2018) - [j37]Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Relative Suffix Trees. Comput. J. 61(5): 773-788 (2018) - [j36]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): 143-164 (2018) - [j35]Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi:
Bidirectional Variable-Order de Bruijn Graphs. Int. J. Found. Comput. Sci. 29(8): 1279-1295 (2018) - [j34]Philip Bille, Travis Gagie, Inge Li Gørtz, Nicola Prezza:
A separation between RLSLPs and LZ77. J. Discrete Algorithms 50: 36-39 (2018) - [c71]Hideo Bannai, Travis Gagie, Tomohiro I:
Online LZ77 Parsing and Matching Statistics with RLBWTs. CPM 2018: 7:1-7:12 - [c70]Nieves R. Brisaboa, Travis Gagie, Adrián Gómez-Brandón, Gonzalo Navarro:
Two-Dimensional Block Trees. DCC 2018: 227-236 - [c69]Alexandre P. Francisco, Travis Gagie, Susana Ladra, Gonzalo Navarro:
Exploiting Computation-Friendly Graph Compression Methods for Adjacency-Matrix Multiplication. DCC 2018: 307-314 - [c68]