Safe and Complete Algorithms for Bioinformatics

Project Information

SAFEBIO

Grant agreement ID: 851093

DOI 10.3030/851093

EC signature date 6 September 2019

Start date 1 March 2020

End date 28 February 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 498 367,00

EU contribution € 1 498 367,00

Coordinated by

HELSINGIN YLIOPISTO
Finland

Publications

Conference proceedings (12)

Linear Time Construction of Indexable Founder Block Graphs

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

Algorithms and Complexity on Indexing Elastic Founder Graphs

Author(s): Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Published in: 32nd International Symposium on Algorithms and Computation (ISAAC 2021), Issue 212, 2021, Page(s) 20:1--20:18
Publisher: 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

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

Optimal Construction of Hierarchical Overlap Graphs

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

Width Helps and Hinders Splitting Flows

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

Fast, Flexible, and Exact Minimum Flow Decompositions via ILP

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

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

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

Safety and Completeness in Flow Decompositions for RNA Assembly

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

Optimizing Safe Flow Decompositions in DAGs

Author(s): Shahbaz Khan, Alexandru I. Tomescu
Published in: 30th Annual European Symposium on Algorithms (ESA 2022), Issue 244, 2022, ISBN 978-3-95977-247-1
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2022.72

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

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

Flow Decomposition with Subpath Constraints

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

Cut Paths and Their Remainder Structure, with Applications

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

Book chapters (3)

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

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

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

Author(s): Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
Published in: Graph-Theoretic Concepts in Computer Science - 47th International Workshop, WG 2021, Warsaw, Poland, June 23–25, 2021, Revised Selected Papers, Issue 12911, 2021, Page(s) 257-269, ISBN 978-3-030-86837-6
Publisher: 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

Author(s): Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Published in: 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, Issue 12607, 2021, Page(s) 608-622, ISBN 978-3-030-67730-5
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-67731-2_44

Peer reviewed articles (5)

Efficient Minimum Flow Decomposition via Integer Linear Programming

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

Solving String Problems on Graphs Using the Labeled Direct Product

Author(s): Nicola Rizzo, Alexandru I. Tomescu, Alberto Policriti
Published in: Algorithmica, 2022, ISSN 1432-0541
Publisher: Springer
DOI: 10.1007/s00453-022-00989-x

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

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

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

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

Safety in s-t Paths, Trails and Walks

Author(s): Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu
Published in: Algorithmica, Issue 84, 2020, Page(s) 719--741, ISSN 1432-0541
Publisher: Springer
DOI: 10.1007/s00453-021-00877-w

Other (3)

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

Author(s): Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu
Published in: 2022
Publisher: bioRxiv
DOI: 10.1101/2022.01.07.475257

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

Author(s): Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Published in: 2021
Publisher: Preprint

Simplicity in Eulerian Circuits: Uniqueness and Safety

Author(s): Nidia Obscura Acosta, Alexandru I. Tomescu
Published in: 2022
Publisher: ArXiv
DOI: 10.48550/arxiv.2208.08522