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Manuel Cáceres
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Sparsifying, shrinking and splicing for minimum path cover in parameterized linear time
M Cáceres, M Cairo, B Mumey, R Rizzi, AI Tomescu
Proceedings of the 2022 Annual ACM-SIAM Symposium on Discrete Algorithms …, 2022
302022
Block trees
D Belazzougui, M Cáceres, T Gagie, P Gawrychowski, J Kärkkäinen, ...
Journal of Computer and System Sciences 117, 1-22, 2021
252021
Faster repetition-aware compressed suffix trees based on block trees
M Cáceres, G Navarro
Information and Computation 285, 104749, 2022
182022
Chaining for accurate alignment of erroneous long reads to acyclic variation graphs
J Ma, M Cáceres, L Salmela, V Mäkinen, AI Tomescu
Bioinformatics 39 (8), btad460, 2023
16*2023
Safety in multi-assembly via paths appearing in all path covers of a DAG
M Cáceres, B Mumey, E Husić, R Rizzi, M Cairo, K Sahlin, AI Tomescu
IEEE/ACM Transactions on Computational Biology and Bioinformatics 19 (6 …, 2021
142021
A linear-time parameterized algorithm for computing the width of a DAG
M Cáceres, M Cairo, B Mumey, R Rizzi, AI Tomescu
Graph-Theoretic Concepts in Computer Science: 47th International Workshop …, 2021
142021
Safety and completeness in flow decompositions for RNA assembly
S Khan, M Kortelainen, M Cáceres, L Williams, AI Tomescu
International Conference on Research in Computational Molecular Biology, 177-192, 2022
132022
Fast indexes for gapped pattern matching
M Cáceres, SJ Puglisi, B Zhukova
SOFSEM 2020: Theory and Practice of Computer Science: 46th International …, 2020
112020
Width helps and hinders splitting flows
M Cáceres, M Cairo, A Grigorjew, S Khan, B Mumey, R Rizzi, AI Tomescu, ...
ACM Transactions on Algorithms 20 (2), 1-20, 2024
82024
Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond
MA Caceres Reyes
Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2023
8*2023
Improving RNA assembly via safety and completeness in flow decompositions
S Khan, M Kortelainen, M Cáceres, L Williams, AI Tomescu
Journal of Computational Biology 29 (12), 1270-1287, 2022
72022
Chaining of maximal exact matches in graphs
N Rizzo, M Cáceres, V Mäkinen
International Symposium on String Processing and Information Retrieval, 353-366, 2023
62023
Sorting finite automata via partition refinement
R Becker, M Cáceres, D Cenzato, SH Kim, B Kodric, F Olivares, N Prezza
arXiv preprint arXiv:2305.05129, 2023
62023
Minimum path cover in parameterized linear time
M Caceres, M Cairo, B Mumey, R Rizzi, AI Tomescu
arXiv preprint arXiv:2211.09659, 2022
52022
Finding maximal exact matches in graphs
N Rizzo, M Cáceres, V Mäkinen
Algorithms for Molecular Biology 19 (1), 10, 2024
42024
Minimum Chain Cover in Almost Linear Time
MA Caceres Reyes
Schloss Dagstuhl-Leibniz-Zentrum für Informatik, 2023
4*2023
A safety framework for flow decomposition problems via integer linear programming
FHC Dias, M Caceres, L Williams, B Mumey, AI Tomescu
Bioinformatics 39 (11), btad640, 2023
22023
Minimum Path Cover: The Power of Parameterization
M Cáceres, B Mumey, S Toivonen, AI Tomescu
arXiv preprint arXiv:2308.08960, 2023
22023
Parameterized and Safe & Complete Graph Algorithms for Bioinformatics
M Cáceres
Helsingin yliopisto, 2023
2023
Compressed suffix trees for repetitive collections based on block trees
MA Cáceres Reyes
Universidad de Chile, 2019
2019
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Articles 1–20