Alexandru I. Tomescu

Affiliations:
  • University of Helsinki


According to our database1, Alexandru I. Tomescu authored at least 74 papers between 2007 and 2021.

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Bibliography

2021
Sparsifying, Shrinking and Splicing for Minimum Path Cover in Parameterized Linear Time.
CoRR, 2021

Algorithms and Complexity on Indexing Founder Graphs.
CoRR, 2021

Safety of Flow Decompositions in DAGs.
CoRR, 2021

Flow Decomposition with Subpath Constraints.
Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails.
Proceedings of the SOFSEM 2021: Theory and Practice of Computer Science, 2021

Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time.
Proceedings of the 48th International Colloquium on Automata, Languages, and Programming, 2021

2020
Genome assembly, a universal theoretical framework: unifying and generalizing the safe and complete algorithms.
CoRR, 2020

On the parameterized complexity of the Minimum Path Cover problem in DAGs.
CoRR, 2020

Safety in s-t Paths, Trails and Walks.
CoRR, 2020

Computing all s-t bridges and articulation points simplified.
CoRR, 2020

From omnitigs to macrotigs: a linear-time algorithm for safe walks - common to all closed arc-coverings of a directed graph.
CoRR, 2020

Conditional Indexing Lower Bounds Through Self-Reducibility.
CoRR, 2020

Linear Time Construction of Indexable Founder Block Graphs.
Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

2019
Safely Filling Gaps with Partial Solutions Common to All Solutions.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Sparse Dynamic Programming on DAGs with Small Width.
ACM Trans. Algorithms, 2019

An Optimal <i>O</i>(<i>nm</i>) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph.
ACM Trans. Algorithms, 2019

Faster FPTASes for counting and random generation of Knapsack solutions.
Inf. Comput., 2019

On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching.
CoRR, 2019

MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP.
Bioinform., 2019

On the Complexity of String Matching for Graphs.
Proceedings of the 46th International Colloquium on Automata, Languages, and Programming, 2019

Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding.
Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, 2019

2018
Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Perfect Phylogenies via Branchings in Acyclic Digraphs and a Generalization of Dilworth's Theorem.
ACM Trans. Algorithms, 2018

A safe and complete algorithm for metagenomic assembly.
Algorithms Mol. Biol., 2018

Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended.
Proceedings of the Research in Computational Molecular Biology, 2018

2017
Set-syllogistics meet combinatorics.
Math. Struct. Comput. Sci., 2017

Safe and Complete Contig Assembly Through Omnitigs.
J. Comput. Biol., 2017

Interval scheduling maximizing minimum coverage.
Discret. Appl. Math., 2017

Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover.
CoRR, 2017

The minimum conflict-free row split problem revisited: a branching formulation and (in)approximability issues.
CoRR, 2017

The Minimum Conflict-Free Row Split Problem Revisited.
Proceedings of the Graph-Theoretic Concepts in Computer Science, 2017

Optimal Omnitig Listing for Safe and Complete Contig Assembly.
Proceedings of the 28th Annual Symposium on Combinatorial Pattern Matching, 2017

On Sets and Graphs: Perspectives on Logic and Combinatorics
Springer, ISBN: 978-3-319-54980-4, 2017

2016
Graph operations on parity games and polynomial-time algorithms.
Theor. Comput. Sci., 2016

Gap Filling as Exact Path Length Problem.
J. Comput. Biol., 2016

Safe and Complete Contig Assembly Via Omnitigs.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy.
Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016), 2016

2015
Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Set Graphs. V. On representing graphs as membership digraphs.
J. Log. Comput., 2015

Enumeration of the adjunctive hierarchy of hereditarily finite sets.
J. Log. Comput., 2015

Mapping Sets and Hypersets into Numbers.
Fundam. Informaticae, 2015

Interval scheduling maximizing minimum coverage.
CoRR, 2015

SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP.
Bioinform., 2015

Finding a Perfect Phylogeny from Mixed Tumor Samples.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing.
Cambridge University Press, ISBN: 9781107078536, 2015

2014
Set graphs. II. Complexity of set graph recognition and similar problems.
Theor. Comput. Sci., 2014

Motif matching using gapped patterns.
Theor. Comput. Sci., 2014

Set Graphs. III. Proof Pearl: Claw-Free Graphs Mirrored into Transitive Hereditarily Finite Sets.
J. Autom. Reason., 2014

Set graphs. IV. Further connections with claw-freeness.
Discret. Appl. Math., 2014

On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly.
BMC Bioinform., 2014

Hyper-Extensionality and One-Node Elimination on Membership Graphs.
Proceedings of the 29th Italian Conference on Computational Logic, 2014

The Representation of Boolean Algebras in the Spotlight of a Proof Checker.
Proceedings of the 29th Italian Conference on Computational Logic, 2014

2013
Ranking, unranking and random generation of extensional acyclic digraphs.
Inf. Process. Lett., 2013

Well-quasi-ordering hereditarily finite sets.
Int. J. Comput. Math., 2013

Set graphs. I. Hereditarily finite sets and extensional acyclic orientations.
Discret. Appl. Math., 2013

Floating-point arithmetic for approximate counting and random generation problems.
CoRR, 2013

Enumeration of the adjunctive hierarchy of hereditarily finite sets.
CoRR, 2013

A novel min-cost flow method for estimating transcript expression with RNA-Seq.
BMC Bioinform., 2013

Markov chain algorithms for generating sets uniformly at random.
Ars Math. Contemp., 2013

A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Indexes for Jumbled Pattern Matching in Strings, Trees and Graphs.
Proceedings of the String Processing and Information Retrieval, 2013

A Proof-checking Experiment on Representing Graphs as Membership Digraphs.
Proceedings of the 28th Italian Conference on Computational Logic, 2013

2012
Infinity, in short.
J. Log. Comput., 2012

A randomized Numerical Aligner (rNA).
J. Comput. Syst. Sci., 2012

A simpler proof for vertex-pancyclicity of squares of connected claw-free graphs.
Discret. Math., 2012

rNA: a fast and accurate short reads numerical aligner.
Bioinform., 2012

2011
Counting extensional acyclic digraphs.
Inf. Process. Lett., 2011

Computing the Maximum Bisimulation with Spiking Neural P Systems.
Proceedings of the Computation, 2011

2010
On cycles through two arcs in strong multipartite tournaments
CoRR, 2010

2008
Implementing Sorting Networks with Spiking Neural P Systems.
Fundam. Informaticae, 2008

Unicyclic and bicyclic graphs having minimum degree distance.
Discret. Appl. Math., 2008

2007
Simulating the Bitonic Sort Using P Systems.
Proceedings of the Membrane Computing, 8th International Workshop, 2007


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