Publications

Manuel Cáceres, Brendan Mumey, Santeri Toivonen, Alexandru I. Tomescu (2024). Practical Minimum Path Cover. In SEA 2024.

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Nicola Rizzo, Manuel Cáceres, Veli Makinen (2024). Finding Maximal Exact Matches in Graphs. In AMB.

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Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams (2024). Width Helps and Hinders Splitting Flows. In TALG.

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Ruben Becker, Manuel Cáceres, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Francisco Olivares, Nicola Prezza (2023). Sorting Finite Automata via Partition Refinement. In ESA 2023.

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Manuel Cáceres (2023). Minimum Chain Cover in Almost Linear Time. Best student paper (track A) in ICALP 2023.

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Manuel Cáceres (2023). Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond. Best paper in CPM 2023.

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Nicola Rizzo, Manuel Cáceres, Veli Makinen (2023). Finding Maximal Exact Matches in Graphs. In WABI 2023.

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Nicola Rizzo, Manuel Cáceres, Veli Makinen (2023). Chaining of Maximal Exact Matches in Graphs. In SPIRE 2023.

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Fernando H. C. Dias, Manuel Cáceres, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu (2023). A Safety Framework for Flow Decomposition Problems via Integer Linear Programming. In Bioinformatics.

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Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu (2022). Minimum Path Cover in Parameterized Linear Time. In arXiv.

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Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu (2022). Improving RNA Assembly via Safety and Completeness in Flow Decompositions. In Journal of Computational Biology.

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Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams (2022). Width Helps and Hinders Splitting Flows. In ESA 2022.

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Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu (2022). Safety and Completeness in Flow Decompositions for RNA Assembly. In RECOMB 2022.

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Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu (2022). Sparsifying, Shrinking and Splicing for Minimum Path Cover in Parameterized Linear Time. In SODA 2022.

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Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu (2022). Chaining for Accurate Alignment of Erroneous Long Reads to Acyclic Variation Graphs. In Bioinformatics.

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Manuel Cáceres, Brendan Mumey, Edin Husic, Romeo Rizzi, Massimo Cairo, Kristoffer Sahlin, Alexandru I. Tomescu (2022). Safety in multi-assembly via paths appearing in all path covers of a DAG. In IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu (2021). A linear-time parameterized algorithm for computing the width of a DAG. In WG 2021.

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Manuel Cáceres, Gonzalo Navarro (2021). Faster repetition-aware compressed suffix trees based on block trees. In Information and Compuation.

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Djamal Belazzougui, Manuel Cáceres, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Gonzalo Navarro, Alberto Ordóñez, Simon J. Puglisi, Yasuo Tabei (2020). Block Trees. In Journal of Computer and System Sciences.

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Manuel Cáceres, Simon J. Puglisi, Bella Zhukova (2020). Fast Indexes for Gapped Pattern Matching. In SOFSEM 2020.

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Manuel Cáceres, Gonzalo Navarro (2019). Faster Repetition-Aware Compressed Suffix Trees Based on Block Trees. In SPIRE 2019.

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