Publications

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

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.

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

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.

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.

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

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.

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.

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.

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.