Foto på Alexandru Tomescu
  • PL 68 (Pietari Kalmin katu 5)

    00014

    Finland

20072019
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Publikationer 2007 2019

2019

Faster FPTASes for counting and random generation of Knapsack solutions

Rizzi, R. & Tomescu, A. I., aug 2019, I : Information and Computation. 267, s. 135-144 10 s.

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

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

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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, I : Bioinformatics. 35, 5, s. 769-777 9 s.

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Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding

Kiirala, N., Salmela, L. & Tomescu, A., 2019, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Pisanti, N. & Pissis, S. P. (red.). Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, s. 8:1-8:16 16 s. (Edit Leibniz International Proceedings in Informatics (LIPIcs); vol. 128).

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Safely Filling Gaps with Partial Solutions Common to All Solutions

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

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Sparse Dynamic Programming on DAGs with Small Width

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

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2018

A safe and complete algorithm for metagenomic assembly

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

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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, I : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 1, s. 96-108 13 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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, I : ACM Transactions on Algorithms. 14, 2, 26 s., 20.

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Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended

Kuosmanen, A., Paavilainen, T., Gagie, T., Chikhi, R., Tomescu, A. & Mäkinen, V., apr 2018, Research in Computational Molecular Biology : 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings. Raphael, B. J. (red.). Cham: Springer International Publishing AG, s. 105-121 17 s. (Lecture Notes in Bioinformatics; vol. 10812).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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2017

Interval scheduling maximizing minimum coverage

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

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On Sets and Graphs: Perspectives on Logic and Combinatorics

Omodeo, E. G., Policriti, A. & Tomescu, A. I., maj 2017, Springer International Publishing . 275 s.

Forskningsoutput: Bok/rapportBokVetenskapligPeer review

Optimal Omnitig Listing for Safe and Complete Contig Assembly

Cairo, M., Medvedev, P., Acosta, N. O., Rizzi, R. & Tomescu, A. I., 2017, 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Radoszewski, J., Kärkkäinen, J. & Rytter, W. (red.). Schloss Dagstuhl - Leibniz-Zentrum für Informatik, s. 29:1-29:12 29. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 78).

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Safe and Complete Contig Assembly Through Omnitigs

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

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Set-syllogistics meet combinatorics

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

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The Minimum Conflict-Free Row Split Problem Revisited

Hujdurović, A., Husić, E., Milanič, M., Rizzi, R. & Tomescu, A. I., 2 nov 2017, Graph-Theoretic Concepts in Computer Science: 43rd International Workshop, WG 2017, Eindhoven, The Netherlands, June 21-23, 2017, Revised Selected Papers. Bodlaender, H. L. & Woeginger, G. J. (red.). Cham: Springer, s. 303-315 13 s. (Lecture Notes in Computer Science; vol. 10520).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

2016

Gap Filling as Exact Path Length Problem

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

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Graph operations on parity games and polynomial-time algorithms

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer 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. (red.). Cham: Springer International Publishing AG, s. 111-121 11 s. (Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); vol. 9649).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy

Kuosmanen, A. E., Sobih, A. A. M., Rizzi, R., Mäkinen, V. A. T. & Tomescu, A. I., 2016, Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies. Gilbert, J., Azhari, H., Ali, H., Quintão, C., Sliwa, J., Ruiz, C., Fred, A. & Gamboa, H. (red.). SCITEPRESS Science And Technology Publications , s. 272-277 6 s.

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Safe and Complete Contig Assembly Via Omnitigs

Tomescu, A. I. & Medvedev, P., 8 apr 2016, Research in Computational Molecular Biology : 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings. Singh, M. (red.). Cham: Springer International Publishing AG, s. 152-163 12 s. (Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); vol. 9649).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

2015

Enumeration of the adjunctive hierarchy of hereditarily finite sets

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer 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, I : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12, 6, s. 1345-1354 10 s.

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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. (red.). Berlin: Springer-Verlag, s. 80-92 13 s. (Lecture Notes in Computer Science; vol. 9289).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Gap2Seq

Salmela, L. M., Sahlin, K., Mäkinen, V. A. T. & Tomescu, A. I., 2015

Forskningsoutput: Icke-textbaserad outputProgramvaraVetenskaplig

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. (red.). Cham: Springer International Publishing AG, s. 281-292 12 s. (Lecture Notes in Bioinformatics; vol. 9029).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing

Mäkinen, V. A. T., Belazzougui, D., Cunial, F. & Tomescu, A. I., maj 2015, Cambrigde University Press. 391 s.

Forskningsoutput: Bok/rapportBokVetenskapligPeer review

Mapping Sets and Hypersets into Numbers

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

On representing graphs as membership digraphs - A proof scenario checked by Referee

Omodeo, E. & Tomescu, A. I., 2015

Forskningsoutput: Icke-textbaserad outputProgramvaraVetenskaplig

Set Graphs. V. On representing graphs as membership digraphs

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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, I : Bioinformatics. 31, 7, s. 1133-1135 3 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

SNV-PPILP

van Rens, K., Mäkinen, V. A. T. & Tomescu, A. I., 2015

Forskningsoutput: Icke-textbaserad outputProgramvaraVetenskaplig

2014

A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis

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

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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. (red.). Springer-Verlag, s. 762-773 12 s. (Lecture Notes in Computer Science; vol. 8737).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer 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. (red.). CEUR Workshop Proceedings, Vol. 1195 . s. 341-346 6 s. (CEUR Workshop Proceedings; vol. 1195).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Motif matching using gapped patterns

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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

Rizzi, R., Tomescu, A. I. & Mäkinen, V., 10 sep 2014, I : BMC Bioinformatics. 15, S9, s. S5

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

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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

Omodeo, E. G. & Tomescu, A. I., jan 2014, I : Journal of Automated Reasoning. 52, 1, s. 1-29 29 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Set graphs. IV. Further connections with claw-freeness

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

The representation of Boolean algebras in the spotlight of a proof checker

Ceterchi, R., Omodeo, E. G. & 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. (red.). CEUR Workshop Proceedings, s. 287-301 15 s. (CEUR Workshop Proceedings; vol. 1195).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

2013

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. (red.). Springer-Verlag, s. 85-98 (Lecture Notes in Computer Science; nr. 8126).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

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, I : BMC Bioinformatics. 14, (Suppl 5):S15, 10 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer 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. s. 227-233

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer 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. (red.). Springer-Verlag, s. 56-63 (Lecture Notes in Computer Science; vol. 8214).

Forskningsoutput: Kapitel i bok/rapport/konferenshandlingKonferensbidragVetenskapligPeer review

Markov chain algorithms for generating sets uniformly at random

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Ranking, unranking and random generation of extensional acyclic digraphs

Rizzi, R. & Tomescu, A. I., mar 2013, I : Information Processing Letters. 113, 5-6, s. 183-187 5 s.

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

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

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

Well-quasi-ordering hereditarily finite sets

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review

2012

A randomized Numerical Aligner (rNA)

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

Forskningsoutput: TidskriftsbidragArtikelVetenskapligPeer review