Safe and Complete Algorithms for Bioinformatics

Linear Time Construction of Indexable Founder Block Graphs

Auteurs: Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu
Publié dans: 20th International Workshop on Algorithms in Bioinformatics (WABI 2020), Numéro Leibniz International Proceedings in Informatics (LIPIcs) vol. 172, 2020, Page(s) 7:1--7:18, ISBN 978-3-95977-161-0
Éditeur: Schloss Dagstuhl--Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2020.7

Algorithms and Complexity on Indexing Elastic Founder Graphs

Auteurs: Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Publié dans: 32nd International Symposium on Algorithms and Computation (ISAAC 2021), Numéro 212, 2021, Page(s) 20:1--20:18
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2021.20

Sparsifying, Shrinking and Splicing for Minimum Path Cover in Parameterized Linear Time

Auteurs: Manuel Càceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
Publié dans: Proceedings of the 2022 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 2022, Page(s) 359-376
Éditeur: Society for Industrial and Applied Mathematics
DOI: 10.1137/1.9781611977073.18

Optimal Construction of Hierarchical Overlap Graphs

Auteurs: Shahbaz Khan
Publié dans: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Numéro Leibniz International Proceedings in Informatics (LIPIcs) vol. 191, 2021, Page(s) 17:1--17:11, ISBN 978-3-95977-186-3
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.17

Width Helps and Hinders Splitting Flows

Auteurs: Manuel Càceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams
Publié dans: 30th Annual European Symposium on Algorithms (ESA 2022), Numéro 244, 2022, Page(s) 31:1--31:14
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2022.31

Fast, Flexible, and Exact Minimum Flow Decompositions via ILP

Auteurs: Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
Publié dans: RECOMB 2022 - 26th Annual International Conference on Research in Computational Molecular Biology, Numéro 13278, 2022, Page(s) 230--245
Éditeur: Springer
DOI: 10.1007/978-3-031-04749-7_14

Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time

Auteurs: Sebastian Schmidt, Jarno Alanko
Publié dans: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Numéro 242, 2022, Page(s) 2:1--2:21, ISBN 978-3-95977-243-3
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2022.2

Safety and Completeness in Flow Decompositions for RNA Assembly

Auteurs: Shahbaz Khan, Milla Kortelainen, Manuel Càceres, Lucia Williams, Alexandru I. Tomescu
Publié dans: RECOMB 2022 - 26th Annual International Conference on Research in Computational Molecular Biology, Numéro 13278, 2022, Page(s) 177--192
Éditeur: Springer
DOI: 10.1007/978-3-031-04749-7_11

Optimizing Safe Flow Decompositions in DAGs

Auteurs: Shahbaz Khan, Alexandru I. Tomescu
Publié dans: 30th Annual European Symposium on Algorithms (ESA 2022), Numéro 244, 2022, ISBN 978-3-95977-247-1
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2022.72

Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time

Auteurs: Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, Elia C. Zirondelli:
Publié dans: 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021), Numéro Leibniz International Proceedings in Informatics (LIPIcs), vol. 198, 2021, Page(s) 43:1--43:18, ISBN 978-3-95977-195-5
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.icalp.2021.43

Flow Decomposition with Subpath Constraints

Auteurs: Lucia Williams, Alexandru I. Tomescu, Brendan Mumey
Publié dans: 21st International Workshop on Algorithms in Bioinformatics (WABI 2021), Numéro Leibniz International Proceedings in Informatics (LIPIcs), vol.201, 2021, Page(s) 16:1--16:15, ISBN 978-3-95977-200-6
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2021.16

Cut Paths and Their Remainder Structure, with Applications

Auteurs: Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Publié dans: 40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023), Numéro 254, 2023, Page(s) 17:1--17:17, ISBN 978-3-95977-266-2
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.stacs.2023.17

Simple dynamic algorithms for Maximal Independent Set, Maximum Flow and Maximum Matching

Auteurs: Manoj Gupta, Shahbaz Khan
Publié dans: Symposium on Simplicity in Algorithms (SOSA), 2021, Page(s) 86-91, ISBN 978-1-61197-649-6
Éditeur: Society for Industrial and Applied Mathematics
DOI: 10.1137/1.9781611976496.10

A Linear-Time Parameterized Algorithm for Computing the Width of a DAG

Auteurs: Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
Publié dans: Graph-Theoretic Concepts in Computer Science - 47th International Workshop, WG 2021, Warsaw, Poland, June 23–25, 2021, Revised Selected Papers, Numéro 12911, 2021, Page(s) 257-269, ISBN 978-3-030-86837-6
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-86838-3_20

Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails

Auteurs: Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Publié dans: SOFSEM 2021: Theory and Practice of Computer Science - 47th International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2021, Bolzano-Bozen, Italy, January 25–29, 2021, Proceedings, Numéro 12607, 2021, Page(s) 608-622, ISBN 978-3-030-67730-5
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-67731-2_44

Efficient Minimum Flow Decomposition via Integer Linear Programming

Auteurs: Fernando H.C. Dias, Lucia Williams, Brendan Mumey and Alexandru I. Tomescu
Publié dans: Journal of Computational Biology, Numéro 29(11), 2022, Page(s) 1252-1267, ISSN 1066-5277
Éditeur: Mary Ann Liebert Inc.
DOI: 10.1089/cmb.2022.0257

Solving String Problems on Graphs Using the Labeled Direct Product

Auteurs: Nicola Rizzo, Alexandru I. Tomescu, Alberto Policriti
Publié dans: Algorithmica, 2022, ISSN 1432-0541
Éditeur: Springer
DOI: 10.1007/s00453-022-00989-x

Safety in multi-assembly via paths appearing in all path covers of a DAG.

Auteurs: Manuel Cáceres; Brendan Mumey; Edin Husić; Romeo Rizzi; Massimo Cairo; Kristoffer Sahlin; Alexandru I. Tomescu
Publié dans: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Numéro 19(6), 2023, Page(s) 3673-3684, ISSN 1545-5963
Éditeur: IEEE Computer Society
DOI: 10.1109/tcbb.2021.3131203

A simplified algorithm computing all s - t bridges and articulation points

Auteurs: Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Publié dans: Discrete Applied Mathematics, Numéro 305, 2021, Page(s) 103-108, ISSN 0166-218X
Éditeur: Elsevier BV
DOI: 10.1016/j.dam.2021.08.026

Safety in s-t Paths, Trails and Walks

Auteurs: Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu
Publié dans: Algorithmica, Numéro 84, 2020, Page(s) 719--741, ISSN 1432-0541
Éditeur: Springer
DOI: 10.1007/s00453-021-00877-w

Chaining for Accurate Alignment of Erroneous Long Reads to Acyclic Variation Graphs

Auteurs: Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu
Publié dans: 2022
Éditeur: bioRxiv
DOI: 10.1101/2022.01.07.475257

The Hydrostructure: a Universal Framework for Safe and Complete Algorithms for Genome Assembly

Auteurs: Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Publié dans: 2021
Éditeur: Preprint

Simplicity in Eulerian Circuits: Uniqueness and Safety

Auteurs: Nidia Obscura Acosta, Alexandru I. Tomescu
Publié dans: 2022
Éditeur: ArXiv
DOI: 10.48550/arxiv.2208.08522

Publications

Partager cette page

Télécharger