Safe and Complete Algorithms for Bioinformatics

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

Practical Minimum Path Cover

Author(s): Manuel Cáceres, Brendan Mumey, Santeri Toivonen, Alexandru I. Tomescu
Published in: 22nd International Symposium on Experimental Algorithms (SEA 2024), Issue 301, 2024, Page(s) 3:1-3:19, ISBN 978-3-95977-325-6
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.sea.2024.3

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

Accelerating ILP solvers for Minimum Flow Decompositions through search space and dimensionality reductions

Author(s): Grigorjew, Andreas; Dias, Fernando H. C.; Cracco, Andrea; Rizzi, Romeo; Tomescu, Alexandru I.
Published in: 22nd International Symposium on Experimental Algorithms (SEA 2024), Issue 301, 2024, Page(s) 14:1-14:19, ISBN 978-3-95977-325-6
Publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.sea.2024.14

Applying the Safe-And-Complete Framework to Practical Genome Assembly

Author(s): Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I. Tomescu
Published in: 24th International Workshop on Algorithms in Bioinformatics (WABI 2024), Issue 312, 2024, Page(s) 8:1-8:16, ISBN 978-3-95977-340-9
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2024.8

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

From Bit-Parallelism to Quantum String Matching for Labelled Graphs

Author(s): Equi, Massimo; Meijer-van de Griend, Arianne; Mäkinen, Veli
Published in: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Issue 1, 2023, Page(s) 9:1–9:20
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik, Dagstuhl Publishing
DOI: 10.4230/lipics.cpm.2023.9

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

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

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

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: Bioinformatics, Issue 39, 2023, Page(s) btad460, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad460

Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time

Author(s): Sebastian Schmidt, Jarno N. Alanko
Published in: Algorithms for Molecular Biology, Issue 18, 2023, Page(s) 5, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-023-00227-1

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

Matchtigs: minimum plain text representation of k-mer sets

Author(s): Sebastian Schmidt, Shahbaz Khan, Jarno N. Alanko, Giulio E. Pibiri, Alexandru I. Tomescu
Published in: Genome Biology, Issue 24, 2023, Page(s) 136, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-023-02968-z

Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD

Author(s): Andreas Grigorjew, Artur Gynter, Fernando H. C. Dias, Benjamin Buchfink, Hajk-Georg Drost, Alexandru I. Tomescu
Published in: Genome Biology, Issue 24, 2023, Page(s) 168, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-023-03008-6

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

Simplicity in Eulerian circuits: Uniqueness and safety

Author(s): Nidia Obscura Acosta, Alexandru I. Tomescu
Published in: Information Processing Letters, Issue 183, 2023, Page(s) 106421, ISSN 0020-0190
Publisher: Elsevier BV
DOI: 10.1016/j.ipl.2023.106421

Flowtigs: safety in flow decompositions for assembly graphs

Author(s): Francisco Sena, Eliel Ingervo, Shahbaz Khan, Andrey Prjibelski, Sebastian Schmidt, Alexandru I. Tomescu
Published in: iScience, Issue 27(12), 2024, Page(s) 111208, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1101/2023.11.17.567499

Flow Decomposition With Subpath Constraints

Author(s): Lucia Williams, Alexandru I. Tomescu, Brendan Mumey
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Issue 20, 2024, Page(s) 360-370, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2022.3147697

Genome Assembly, from Practice to Theory: Safe, Complete and <i>Linear-Time</i>

Author(s): Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, Elia C. Zirondelli
Published in: ACM Transactions on Algorithms, Issue 20, 2023, Page(s) 1-26, ISSN 1549-6325
Publisher: Association for Computing Machinary, Inc.
DOI: 10.1145/3632176

Elastic founder graphs improved and enhanced

Author(s): Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
Published in: Theoretical Computer Science, Issue 982, 2023, Page(s) 114269, ISSN 0304-3975
Publisher: Elsevier BV
DOI: 10.1016/j.tcs.2023.114269

A safety framework for flow decomposition problems via integer linear programming

Author(s): Fernando H C Dias, Manuel Cáceres, Lucia Williams, Brendan Mumey, Alexandru I Tomescu
Published in: Bioinformatics, Issue 39, 2023, Page(s) btad640, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad640

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

Improving RNA Assembly via Safety and Completeness in Flow Decompositions

Author(s): Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu
Published in: Journal of Computational Biology, Issue 29, 2022, Page(s) 1270-1287, ISSN 1557-8666
Publisher: Mary Ann Liebert Inc
DOI: 10.1089/cmb.2022.0261

Algorithms and Complexity on Indexing Founder Graphs

Author(s): Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Published in: Algorithmica, Issue 85, 2024, Page(s) 1586-1623, ISSN 0178-4617
Publisher: Springer Verlag
DOI: 10.1007/s00453-022-01007-w

On the Complexity of String Matching for Graphs

Author(s): Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu, Roberto Grossi
Published in: ACM Transactions on Algorithms, Issue 19, 2023, Page(s) 1-25, ISSN 1549-6325
Publisher: Association for Computing Machinary, Inc.
DOI: 10.1145/3588334

Width Helps and Hinders Splitting Flows

Author(s): Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams
Published in: ACM Transactions on Algorithms, Issue 20, 2024, Page(s) 1-20, ISSN 1549-6325
Publisher: Association for Computing Machinary, Inc.
DOI: 10.1145/3641820

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: Theoretical Computer Science, Issue 975, 2024, Page(s) 114128, ISSN 0304-3975
Publisher: Elsevier BV
DOI: 10.1016/j.tcs.2023.114128

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

Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT

Author(s): Andrea Cracco, Alexandru I. Tomescu
Published in: Genome Research, Issue 33, 2023, Page(s) 1198-1207, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277615.122

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

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