Alexandru I. Tomescu

ORCID

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 84

Top Venues

CoRR

RECOMB

ACM Trans. Algorithms

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Manuel Cáceres, Brendan Mumey, Santeri Toivonen, Alexandru I. Tomescu
Practical Minimum Path Cover. SEA (2024)
Sebastian S. Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I. Tomescu
Applying the Safe-And-Complete Framework to Practical Genome Assembly. WABI (2024)
Andreas Grigorjew, Fernando H. C. Dias, Andrea Cracco, Romeo Rizzi, Alexandru I. Tomescu
Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions. SEA (2024)
Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, Elia C. Zirondelli
. ACM Trans. Algorithms 20 (1) (2024)
Nidia Obscura Acosta, Alexandru I. Tomescu
Simplicity in Eulerian circuits: Uniqueness and safety. Inf. Process. Lett. 183 (2024)
Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams
Width Helps and Hinders Splitting Flows. ACM Trans. Algorithms 20 (2) (2024)
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Algorithms and Complexity on Indexing Founder Graphs. Algorithmica 85 (6) (2023)
Fernando H. C. Dias, Manuel Cáceres, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
A safety framework for flow decomposition problems via integer linear programming. Bioinform. 39 (10) (2023)
Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian S. Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Cut Paths and Their Remainder Structure, with Applications. STACS (2023)
Jun Ma, Manuel Cáceres, Leena Salmela, Veli Mäkinen, Alexandru I. Tomescu
Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. Bioinform. 39 (8) (2023)
Lucia Williams, Alexandru I. Tomescu, Brendan Mumey
Flow Decomposition With Subpath Constraints. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (1) (2023)
Manuel Cáceres, Brendan Mumey, Santeri Toivonen, Alexandru I. Tomescu
Minimum Path Cover: The Power of Parameterization. CoRR (2023)
Fernando H. C. Dias, Manuel Cáceres, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
A Safety Framework for Flow Decomposition Problems via Integer Linear Programming. CoRR (2023)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu, Roberto Grossi
On the Complexity of String Matching for Graphs. ACM Trans. Algorithms 19 (3) (2023)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. Theor. Comput. Sci. 975 (2023)
Manuel Cáceres, Brendan Mumey, Edin Husic, Romeo Rizzi, Massimo Cairo, Kristoffer Sahlin, Alexandru I. Tomescu
Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Shahbaz Khan, Alexandru I. Tomescu
Optimizing Safe Flow Decompositions in DAGs. ESA (2022)
Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu
Safety and Completeness in Flow Decompositions for RNA Assembly. CoRR (2022)
Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
Efficient Minimum Flow Decomposition via Integer Linear Programming. J. Comput. Biol. 29 (11) (2022)
Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams
Width Helps and Hinders Splitting Flows. ESA (2022)
Nicola Rizzo, Alexandru I. Tomescu, Alberto Policriti
Solving String Problems on Graphs Using the Labeled Direct Product. Algorithmica 84 (10) (2022)
Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
Minimum Flow Decomposition in Graphs with Cycles using Integer Linear Programming. CoRR (2022)
Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian S. Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Cut paths and their remainder structure, with applications. CoRR (2022)
Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian S. Schmidt, Alexandru I. Tomescu
Safety in s-t Paths, Trails and Walks. Algorithmica 84 (3) (2022)
Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
Sparsifying, Shrinking and Splicing for Minimum Path Cover in Parameterized Linear Time. SODA (2022)
Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, Lucia Williams
Width Helps and Hinders Splitting Flows. CoRR (2022)
Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu
Safety and Completeness in Flow Decompositions for RNA Assembly. RECOMB (2022)
Shahbaz Khan, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu
Improving RNA Assembly via Safety and Completeness in Flow Decompositions. J. Comput. Biol. 29 (12) (2022)
Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
Minimum Path Cover in Parameterized Linear Time. CoRR (2022)
Nidia Obscura Acosta, Alexandru I. Tomescu
Simplicity in Eulerian Circuits: Uniqueness and Safety. CoRR (2022)
Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
Fast, Flexible, and Exact Minimum Flow Decompositions via ILP. RECOMB (2022)
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Algorithms and Complexity on Indexing Founder Graphs. CoRR (2021)
Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
A Linear-Time Parameterized Algorithm for Computing the Width of a DAG. WG (2021)
Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, Elia C. Zirondelli
Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time. ICALP (2021)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails. SOFSEM (2021)
Shahbaz Khan, Alexandru I. Tomescu
Safety of Flow Decompositions in DAGs. CoRR (2021)
Nicola Rizzo, Alexandru I. Tomescu, Alberto Policriti
The Labeled Direct Product Optimally Solves String Problems on Graphs. CoRR (2021)
Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian S. Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
A simplified algorithm computing all s-t bridges and articulation points. Discret. Appl. Math. 305 (2021)
Lucia Williams, Alexandru I. Tomescu, Brendan Mumey
Flow Decomposition with Subpath Constraints. WABI (2021)
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, Veli Mäkinen
Algorithms and Complexity on Indexing Elastic Founder Graphs. ISAAC (2021)
Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
Sparsifying, Shrinking and Splicing for Minimum Path Cover in Parameterized Linear Time. CoRR (2021)
Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu
Linear Time Construction of Indexable Founder Block Graphs. WABI (2020)
Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian S. Schmidt, Alexandru I. Tomescu
Safety in s-t Paths, Trails and Walks. CoRR (2020)
Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, Elia C. Zirondelli
From omnitigs to macrotigs: a linear-time algorithm for safe walks - common to all closed arc-coverings of a directed graph. CoRR (2020)
Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian S. Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Genome assembly, a universal theoretical framework: unifying and generalizing the safe and complete algorithms. CoRR (2020)
Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, Alexandru I. Tomescu
Linear Time Construction of Indexable Founder Block Graphs. CoRR (2020)
Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian S. Schmidt, Alexandru I. Tomescu, Elia C. Zirondelli
Computing all s-t bridges and articulation points simplified. CoRR (2020)
Massimo Equi, Veli Mäkinen, Alexandru I. Tomescu
Conditional Indexing Lower Bounds Through Self-Reducibility. CoRR (2020)
Manuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu
On the parameterized complexity of the Minimum Path Cover problem in DAGs. CoRR (2020)
Romeo Rizzi, Alexandru I. Tomescu
Faster FPTASes for counting and random generation of Knapsack solutions. Inf. Comput. 267 (2019)
Leena Salmela, Alexandru I. Tomescu
Safely Filling Gaps with Partial Solutions Common to All Solutions. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu
) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph. ACM Trans. Algorithms 15 (4) (2019)
Edin Husic, Xinyue Li, Ademir Hujdurovic, Miika Mehine, Romeo Rizzi, Veli Mäkinen, Martin Milanic, Alexandru I. Tomescu
MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP. Bioinform. 35 (5) (2019)
Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi
Sparse Dynamic Programming on DAGs with Small Width. ACM Trans. Algorithms 15 (2) (2019)
Massimo Equi, Roberto Grossi, Veli Mäkinen, Alexandru I. Tomescu
On the Complexity of String Matching for Graphs. ICALP (2019)
Niko Kiirala, Leena Salmela, Alexandru I. Tomescu
Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. CPM (2019)
Romeo Rizzi, Massimo Cairo, Veli Mäkinen, Alexandru I. Tomescu, Daniel Valenzuela
Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Massimo Equi, Roberto Grossi, Alexandru I. Tomescu, Veli Mäkinen
On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching. CoRR (2019)
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. RECOMB (2018)
Nidia Obscura Acosta, Veli Mäkinen, Alexandru I. Tomescu
A safe and complete algorithm for metagenomic assembly. Algorithms Mol. Biol. 13 (1) (2018)
Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries, Alexandru I. Tomescu
Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (1) (2018)
Ademir Hujdurovic, Edin Husic, Martin Milanic, Romeo Rizzi, Alexandru I. Tomescu
Perfect Phylogenies via Branchings in Acyclic Digraphs and a Generalization of Dilworth's Theorem. ACM Trans. Algorithms 14 (2) (2018)
Eugenio G. Omodeo, Alberto Policriti, Alexandru I. Tomescu
Set-syllogistics meet combinatorics. Math. Struct. Comput. Sci. 27 (2) (2017)
Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela, Sebastian Wilzbach
Interval scheduling maximizing minimum coverage. Discret. Appl. Math. 225 (2017)
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. CoRR (2017)
Ademir Hujdurovic, Edin Husic, Martin Milanic, Romeo Rizzi, Alexandru I. Tomescu
The minimum conflict-free row split problem revisited: a branching formulation and (in)approximability issues. CoRR (2017)
Ademir Hujdurovic, Edin Husic, Martin Milanic, Romeo Rizzi, Alexandru I. Tomescu
The Minimum Conflict-Free Row Split Problem Revisited. WG (2017)
Alexandru I. Tomescu, Paul Medvedev
Safe and Complete Contig Assembly Through Omnitigs. J. Comput. Biol. 24 (6) (2017)
Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu
Optimal Omnitig Listing for Safe and Complete Contig Assembly. CPM (2017)
Alexandru I. Tomescu, Paul Medvedev
Safe and complete contig assembly via omnitigs. CoRR (2016)
Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
Gap Filling as Exact Path Length Problem. J. Comput. Biol. 23 (5) (2016)
Christoph Dittmann, Stephan Kreutzer, Alexandru I. Tomescu
Graph operations on parity games and polynomial-time algorithms. Theor. Comput. Sci. 614 (2016)
Anna Kuosmanen, Ahmed Sobih, Romeo Rizzi, Veli Mäkinen, Alexandru I. Tomescu
On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy. BIOINFORMATICS (2016)
Alexandru I. Tomescu, Paul Medvedev
Safe and Complete Contig Assembly Via Omnitigs. RECOMB (2016)
Ahmed Sobih, Alexandru I. Tomescu, Veli Mäkinen
MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. RECOMB (2016)
Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu
Gap Filling as Exact Path Length Problem. RECOMB (2015)
Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries, Alexandru I. Tomescu
Finding a Perfect Phylogeny from Mixed Tumor Samples. WABI (2015)
Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries, Alexandru I. Tomescu
Finding a perfect phylogeny from mixed tumor samples. CoRR (2015)
Giorgio Audrito, Alexandru I. Tomescu, Stephan G. Wagner
Enumeration of the adjunctive hierarchy of hereditarily finite sets. J. Log. Comput. 25 (3) (2015)
Veli Mäkinen, Valeria Staneva, Alexandru I. Tomescu, Daniel Valenzuela
Interval scheduling maximizing minimum coverage. CoRR (2015)
Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu
SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. Bioinform. 31 (7) (2015)
Eugenio G. Omodeo, Alexandru I. Tomescu
Set Graphs. V. On representing graphs as membership digraphs. J. Log. Comput. 25 (3) (2015)
Alexandru I. Tomescu, Travis Gagie, Alexandru Popa, Romeo Rizzi, Anna Kuosmanen, Veli Mäkinen
Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Giovanna D'Agostino, Eugenio G. Omodeo, Alberto Policriti, Alexandru I. Tomescu
Mapping Sets and Hypersets into Numbers. Fundam. Informaticae 140 (3-4) (2015)
Martin Milanic, Alexandru I. Tomescu
Set graphs. IV. Further connections with claw-freeness. Discret. Appl. Math. 174 (2014)
Rodica Ceterchi, Eugenio G. Omodeo, Alexandru I. Tomescu
The Representation of Boolean Algebras in the Spotlight of a Proof Checker. CILC (2014)
Eugenio G. Omodeo, Alexandru I. Tomescu
Set Graphs. III. Proof Pearl: Claw-Free Graphs Mirrored into Transitive Hereditarily Finite Sets. J. Autom. Reason. 52 (1) (2014)
Emanuele Giaquinta, Kimmo Fredriksson, Szymon Grabowski, Alexandru I. Tomescu, Esko Ukkonen
Motif matching using gapped patterns. Theor. Comput. Sci. 548 (2014)
Eugenio G. Omodeo, Carla Piazza, Alberto Policriti, Alexandru I. Tomescu
Hyper-Extensionality and One-Node Elimination on Membership Graphs. CILC (2014)
Martin Milanic, Romeo Rizzi, Alexandru I. Tomescu
Set graphs. II. Complexity of set graph recognition and similar problems. Theor. Comput. Sci. 547 (2014)
Romeo Rizzi, Alexandru I. Tomescu, Veli Mäkinen
On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. BMC Bioinform. 15 (S-9) (2014)
Romeo Rizzi, Alexandru I. Tomescu
Faster FPTASes for Counting and Random Generation of Knapsack Solutions. ESA (2014)
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
A novel min-cost flow method for estimating transcript expression with RNA-Seq. BMC Bioinform. 14 (S-5) (2013)
Romeo Rizzi, Alexandru I. Tomescu
Floating-point arithmetic for approximate counting and random generation problems. CoRR (2013)
Ferdinando Cicalese, Travis Gagie, Emanuele Giaquinta, Eduardo Sany Laber, Zsuzsanna Lipták, Romeo Rizzi, Alexandru I. Tomescu
Indexes for Jumbled Pattern Matching in Strings, Trees and Graphs CoRR (2013)
Martin Milanic, Alexandru I. Tomescu
Set graphs. I. Hereditarily finite sets and extensional acyclic orientations. Discret. Appl. Math. 161 (4-5) (2013)
Pierpaolo Calligaris, Eugenio G. Omodeo, Alexandru I. Tomescu
A Proof-checking Experiment on Representing Graphs as Membership Digraphs. CILC (2013)
Emanuele Giaquinta, Kimmo Fredriksson, Szymon Grabowski, Alexandru I. Tomescu, Esko Ukkonen
Motif matching using gapped patterns. CoRR (2013)
Giorgio Audrito, Alexandru I. Tomescu
Enumeration of the adjunctive hierarchy of hereditarily finite sets. CoRR (2013)
Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen
A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. WABI (2013)

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Publication Activity (10 Years)

Top Topics

Top Venues

Alexandru I. Tomescu