Photo of Alexandru Tomescu

Alexandru Tomescu

  • PL 68 (Pietari Kalmin katu 5)

    00014

    Finland

20072019
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Publications 2007 2019

Article

An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph

Cairo, M., Medvedev, P., Acosta, N. O., Rizzi, R. & Tomescu, A. I., Oct 2019, In : ACM Transactions on Algorithms. 15, 4, 17 p., 48.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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A novel min-cost flow method for estimating transcript expression with RNA-Seq

Tomescu, A. I., Kuosmanen, A., Rizzi, R. & Mäkinen, V., 10 Apr 2013, In : BMC Bioinformatics. 14, (Suppl 5):S15, 10 p.

Research output: Contribution to journalArticleScientificpeer-review

A randomized Numerical Aligner (rNA)

Policriti, A., Tomescu, A. I. & Vezzi, F., Nov 2012, In : Journal of Computer and System Sciences. 78, 6, p. 1868-1882 15 p.

Research output: Contribution to journalArticleScientificpeer-review

A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis

Dinu, L. P., Ionescu, R. T. & Tomescu, A. I., 18 Aug 2014, In : PLoS One. 9, 8, 18 p., 104006.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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A safe and complete algorithm for metagenomic assembly

Acosta, N. O., Mäkinen, V. & Tomescu, A. I., 7 Feb 2018, In : Algorithms for Molecular Biology. 13, 12 p., 3.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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A simpler proof for vertex-pancyclicity of squares of connected claw-free graphs

Tomescu, A. I., 6 Aug 2012, In : Discrete Mathematics. 312, 15, p. 2388-2391 4 p.

Research output: Contribution to journalArticleScientificpeer-review

Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples

Hujdurovic, A., Kacar, U., Milanic, M., Ries, B. & Tomescu, A. I., Jan 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 1, p. 96-108 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Counting extensional acyclic digraphs

Policriti, A. & Tomescu, A. I., 30 Aug 2011, In : Information Processing Letters. 111, 16, p. 787-791 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Enumeration of the adjunctive hierarchy of hereditarily finite sets

Audrito, G., Tomescu, A. I. & Wagner, S., Jun 2015, In : Journal of Logic and Computation. 25, 3, p. 943-963 21 p.

Research output: Contribution to journalArticleScientificpeer-review

Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly

Tomescu, A. I., Gagie, T., Popa, A., Rizzi, R., Kuosmanen, A. E. & Mäkinen, V. A. T., Dec 2015, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12, 6, p. 1345-1354 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Faster FPTASes for counting and random generation of Knapsack solutions

Rizzi, R. & Tomescu, A. I., Aug 2019, In : Information and Computation. 267, p. 135-144 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Gap Filling as Exact Path Length Problem

Salmela, L., Sahlin, K., Mäkinen, V. & Tomescu, A. I., 9 May 2016, In : Journal of Computational Biology. 23, 5, p. 347-361 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Graph operations on parity games and polynomial-time algorithms

Dittmann, C., Kreutzer, S. & Tomescu, A. I., 8 Feb 2016, In : Theoretical Computer Science. 614, p. 97-108 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics

Rizzi, R., Cairo, M., Mäkinen, V., Tomescu, A. I. & Valenzuela, D., Feb 2019, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 1, p. 23-30 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Implementing Sorting Networks with Spiking Neural P Systems

Ceterchi, R. & Tomescu, A. I., 2008, In : Fundamenta Informaticae. 87, 1, p. 35-48 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Infinity, in short

Omodeo, E. G., Policriti, A. & Tomescu, A. I., Dec 2012, In : Journal of Logic and Computation. 22, 6, p. 1391-1403 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Interval scheduling maximizing minimum coverage

Mäkinen, V., Staneva, V., Tomescu, A. I., Valenzuela, D. & Wilzbach, S., 10 Jul 2017, In : Discrete Applied Mathematics. 225, p. 130-135 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Mapping Sets and Hypersets into Numbers

D’Agostino, G., Omodeo, E. G., Policriti, A. & Tomescu, A. I., 14 Sep 2015, In : Fundamenta Informaticae. 140, 3-4, p. 307-328 22 p.

Research output: Contribution to journalArticleScientificpeer-review

Markov chain algorithms for generating sets uniformly at random

Policriti, A. & Tomescu, A. I., 2013, In : Ars mathematica contemporanea. 6, 1, p. 57-68 12 p.

Research output: Contribution to journalArticleScientificpeer-review

MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP

Husic, E., Li, X., Hujdurovic, A., Mehine, M., Rizzi, R., Mäkinen, V., Milanic, M. & Tomescu, A. I., 1 Mar 2019, In : Bioinformatics. 35, 5, p. 769-777 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Motif matching using gapped patterns

Giaquinta, E., Fredriksson, K., Grabowski, S., Tomescu, A. I. & Ukkonen, E., 4 Sep 2014, In : Theoretical Computer Science. 548, p. 1-13 13 p.

Research output: Contribution to journalArticleScientificpeer-review

On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly

Rizzi, R., Tomescu, A. I. & Mäkinen, V., 10 Sep 2014, In : BMC Bioinformatics. 15, S9, p. S5

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Perfect Phylogenies via Branchings in Acyclic Digraphs and a Generalization of Dilworth's Theorem

Hujdurovic, A., Husic, E., Milanic, M., Rizzi, R. & Tomescu, A. I., Jun 2018, In : ACM Transactions on Algorithms. 14, 2, 26 p., 20.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Ranking, unranking and random generation of extensional acyclic digraphs

Rizzi, R. & Tomescu, A. I., Mar 2013, In : Information Processing Letters. 113, 5-6, p. 183-187 5 p.

Research output: Contribution to journalArticleScientificpeer-review

rNA: a fast and accurate short reads numerical aligner

Vezzi, F., Del Fabbro, C., Tomescu, A. I. & Policriti, A., 1 Jan 2012, In : Bioinformatics. 28, 1, p. 123-124 2 p.

Research output: Contribution to journalArticleScientificpeer-review

Safe and Complete Contig Assembly Through Omnitigs

Tomescu, A. I. & Medvedev, P., 1 Jun 2017, In : Journal of Computational Biology. 24, 6, p. 590-602 13 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Safely Filling Gaps with Partial Solutions Common to All Solutions

Salmela, L. & Tomescu, A. I., 2019, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 2, p. 617-626 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Set graphs. I. Hereditarily finite sets and extensional acyclic orientations

Milanic, M. & Tomescu, A. I., Mar 2013, In : Discrete Applied Mathematics. 161, 4-5, p. 677-690 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Set graphs. II. Complexity of set graph recognition and similar problems

Milanic, M., Rizzi, R. & Tomescu, A. I., 28 Aug 2014, In : Theoretical Computer Science. 547, p. 70-81 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Set Graphs. III. Proof Pearl: Claw-Free Graphs Mirrored into Transitive Hereditarily Finite Sets

Omodeo, E. G. & Tomescu, A. I., Jan 2014, In : Journal of Automated Reasoning. 52, 1, p. 1-29 29 p.

Research output: Contribution to journalArticleScientificpeer-review

Set graphs. IV. Further connections with claw-freeness

Milanic, M. & Tomescu, A. I., 2014, In : Discrete Applied Mathematics. 174, p. 113-121 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Set Graphs. V. On representing graphs as membership digraphs

Omodeo, E. G. & Tomescu, A. I., Jun 2015, In : Journal of Logic and Computation. 25, 3, p. 899-919 21 p.

Research output: Contribution to journalArticleScientificpeer-review

Set-syllogistics meet combinatorics

Omodeo, E., Policriti, A. & Tomescu, A. I., Feb 2017, In : MSCS : mathematical structures in computer science.. 27, 2 (Special Issue: XIV ICTCS), p. 296-310 15 p.

Research output: Contribution to journalArticleScientificpeer-review

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SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP

van Rens, K. E., Mäkinen, V. & Tomescu, A. I., 1 Apr 2015, In : Bioinformatics. 31, 7, p. 1133-1135 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Sorting with P Systems: A Biological Perspective

Ardelean, I. I., Ceterchi, R. & Tomescu, A. I., 2008, In : Romanian journal of information science and technology. 11, 3, p. 243-252 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Sparse Dynamic Programming on DAGs with Small Width

Mäkinen, V., Tomescu, A. I., Kuosmanen, A., Paavilainen, T., Gagie, T. & Chikhi, R., May 2019, In : ACM Transactions on Algorithms. 15, 2, 21 p., 29.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Unicyclic and bicyclic graphs having minimum degree distance

Tomescu, A. I., 1 Jan 2008, In : Discrete Applied Mathematics. 156, 1, p. 125-130 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Well-quasi-ordering hereditarily finite sets

Policriti, A. & Tomescu, A. I., 1 Jun 2013, In : International Journal of Computer Mathematics. 90, 6, p. 1278-1291 14 p.

Research output: Contribution to journalArticleScientificpeer-review

On Sets and Graphs: Perspectives on Logic and Combinatorics

Omodeo, E. G., Policriti, A. & Tomescu, A. I., May 2017, Springer International Publishing . 275 p.

Research output: Book/ReportBook

Conference contribution

A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths

Tomescu, A. I., Kuosmanen, A., Rizzi, R. & Mäkinen, V., 2013, Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings. Darling, A. & Stoye, J. (eds.). Springer-Verlag, p. 85-98 (Lecture Notes in Computer Science; no. 8126).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

A Proof-checking Experiment on Representing Graphs as Membership Digraphs

Calligaris, P., Omodeo, E. G. & Tomescu, A. I., 2013, CILC 2013 Italian Conference on Computational Logic. CEUR Workshop Proceedings, Vol. 1068. p. 227-233

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

A Randomized Numerical Aligner (rNA)

Policriti, A., Tomescu, A. I. & Vezzi, F., 2010, Language and Automata Theory and Applications (LATA). Dediu, AH., Fernau, H. & MartinVide, C. (eds.). p. 512-523 12 p. (Lecture Notes in Computer Science; vol. 6031).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Faster FPTASes for Counting and Random Generation of Knapsack Solutions

Rizzi, R. & Tomescu, A. I., 2014, Algorithms - ESA 2014: 22th Annual European Symposium, Wroclaw, Poland, September 8-10, 2014. Proceedings. Schulz, A. S. & Wagner, D. (eds.). Springer-Verlag, p. 762-773 12 p. (Lecture Notes in Computer Science; vol. 8737).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Finding a perfect phylogeny from mixed tumor samples

Hujdurović, A., Kačar, U., Milanič, M., Ries, B. & Tomescu, A. I., 2015, Algorithms in Bioinformatics: 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings. Pop, M. & Touzet, H. (eds.). Berlin: Springer-Verlag, p. 80-92 13 p. (Lecture Notes in Computer Science; vol. 9289).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Gap filling as exact path length problem

Salmela, L., Sahlin, K., Mäkinen, V. & Tomescu, A. I., 2015, Research in Computational Molecular Biology : 19th Annual International Conference, RECOMB 2015, Warsaw, Poland, April 12-15, 2015, Proceedings . Przytycka, T. M. (ed.). Cham: Springer International Publishing AG, p. 281-292 12 p. (Lecture Notes in Bioinformatics; vol. 9029).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Hyper-Extensionality and One-Node Elimination on Membership Graphs

Omodeo, E., Piazza, C., Policriti, A. & Tomescu, A. I., 2014, Proceedings of the 29th Italian Conference on Computational Logic: Torino, Italy, June 16-18, 2014. Giordano, L., Gliozzi, V. & Pozzato, G. L. (eds.). CEUR Workshop Proceedings, Vol. 1195 . p. 341-346 6 p. (CEUR Workshop Proceedings; vol. 1195).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Indexes for Jumbled Pattern Matching in Strings, Trees and Graphs

Cicalese, F., Gagie, T., Giaquinta, E., Laber, E. S., Lipták, Z., Rizzi, R. & Tomescu, A., 2013, String Processing and Information Retrieval: 20th International Symposium, SPIRE 2013, Jerusalem, Israel, October 7-9, 2013, Proceedings. Kurland, O., Lewenstein, M. & Porat, E. (eds.). Springer-Verlag, p. 56-63 (Lecture Notes in Computer Science; vol. 8214).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows

Sobih, A. A. M., Tomescu, A. I. & Mäkinen, V. A. T., 8 Apr 2016, Research in Computational Molecular Biology: 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings. Singh, M. (ed.). Cham: Springer International Publishing AG, p. 111-121 11 p. (Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); vol. 9649).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

On the Complexity of String Matching for Graphs

Equi, M., Grossi, R., Mäkinen, V. & Tomescu, A., 2019, 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Baier, C., Chatzigiannakis, I., Flocchini, P. & Leonardi, S. (eds.). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, p. 55:1--55:15 15 p. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 132).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
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