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

On the parameterized complexity of the Minimum Path Cover problem in DAGs. - Manuel Cáceres; Massimo Cairo; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu (CoRR, 2020)

A Linear-Time Parameterized Algorithm for Computing the Width of a DAG. - Manuel Cáceres; Massimo Cairo; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu (WG, 2021)

Block trees. - Djamal Belazzougui; Manuel Cáceres; Travis Gagie; Pawel Gawrychowski; Juha Kärkkäinen; Gonzalo Navarro 001; Alberto Ordóñez Pereira; Simon J. Puglisi; Yasuo Tabei (J. Comput. Syst. Sci., 2021)

Safety and Completeness in Flow Decompositions for RNA Assembly. - Shahbaz Khan 004; Milla Kortelainen; Manuel Cáceres; Lucia Williams; Alexandru I. Tomescu (RECOMB, 2022)

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

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

Faster repetition-aware compressed suffix trees based on Block Trees. - Manuel Cáceres; Gonzalo Navarro 001 (Inf. Comput., 2022)

Improving RNA Assembly via Safety and Completeness in Flow Decompositions. - Shahbaz Khan 004; Milla Kortelainen; Manuel Cáceres; Lucia Williams; Alexandru I. Tomescu (J. Comput. Biol., 2022)

Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG. - Manuel Cáceres; Brendan Mumey; Edin Husic; Romeo Rizzi; Massimo Cairo; Kristoffer Sahlin; Alexandru I. Tomescu (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond. - Manuel Cáceres (CPM, 2023)

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

Minimum Chain Cover in Almost Linear Time. - Manuel Cáceres (ICALP, 2023)

Chaining of Maximal Exact Matches in Graphs. - Nicola Rizzo 001; Manuel Cáceres; Veli Mäkinen (SPIRE, 2023)

Minimum Path Cover: The Power of Parameterization. - Manuel Cáceres; Brendan Mumey; Santeri Toivonen; Alexandru I. Tomescu (CoRR, 2023)

Parameterized and Safe & Complete Graph Algorithms for Bioinformatics. - Manuel Cáceres (2023)

Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. - Jun Ma; Manuel Cáceres; Leena Salmela; Veli Mäkinen; Alexandru I. Tomescu (Bioinform., 2023)

A safety framework for flow decomposition problems via integer linear programming. - Fernando H. C. Dias; Manuel Cáceres; Lucia Williams; Brendan Mumey; Alexandru I. Tomescu (Bioinform., 2023)

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

Width Helps and Hinders Splitting Flows. - Manuel Cáceres; Massimo Cairo; Andreas Grigorjew; Shahbaz Khan 004; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu; Lucia Williams (ACM Trans. Algorithms, 2024)

Finding maximal exact matches in graphs. - Nicola Rizzo 001; Manuel Cáceres; Veli Mäkinen (Algorithms Mol. Biol., 2024)

Practical Colinear Chaining on Sequences Revisited. - Nicola Rizzo 001; Manuel Cáceres; Veli Mäkinen (ISBRA (2), 2025)

Maximum Coverage k-Antichains and Chains: A Greedy Approach. - Manuel Cáceres; Andreas Grigorjew; Wanchote Po Jiamjitrak; Alexandru I. Tomescu (CoRR, 2025)