Simulating the Bitonic Sort Using P Systems. - Rodica Ceterchi; Mario J. Pérez-Jiménez; Alexandru Ioan Tomescu (Workshop on Membrane Computing, 2007)

Unicyclic and bicyclic graphs having minimum degree distance. - Alexandru Ioan Tomescu (Discret. Appl. Math., 2008)

Implementing Sorting Networks with Spiking Neural P Systems. - Rodica Ceterchi; Alexandru Ioan Tomescu (Fundam. Informaticae, 2008)

On cycles through two arcs in strong multipartite tournaments - Alexandru I. Tomescu (CoRR, 2010)

Computing the Maximum Bisimulation with Spiking Neural P Systems. - Rodica Ceterchi; Alexandru Ioan Tomescu (Computation, Cooperation, and Life, 2011)

Counting extensional acyclic digraphs. - Alberto Policriti; Alexandru I. Tomescu (Inf. Process. Lett., 2011)

rNA: a fast and accurate short reads numerical aligner. - Francesco Vezzi; Cristian Del Fabbro; Alexandru I. Tomescu; Alberto Policriti (Bioinform., 2012)

A simpler proof for vertex-pancyclicity of squares of connected claw-free graphs. - Alexandru I. Tomescu (Discret. Math., 2012)

A randomized Numerical Aligner (rNA). - Alberto Policriti; Alexandru I. Tomescu; Francesco Vezzi (J. Comput. Syst. Sci., 2012)

Infinity, in short. - Eugenio G. Omodeo; Alberto Policriti; Alexandru I. Tomescu (J. Log. Comput., 2012)

Sets as graphs. - Alexandru Ioan Tomescu (2012)

A Proof-checking Experiment on Representing Graphs as Membership Digraphs. - Pierpaolo Calligaris; Eugenio G. Omodeo; Alexandru I. Tomescu (CILC, 2013)

Indexes for Jumbled Pattern Matching in Strings, Trees and Graphs. - Ferdinando Cicalese; Travis Gagie; Emanuele Giaquinta; Eduardo Sany Laber; Zsuzsanna Lipták; Romeo Rizzi; Alexandru I. Tomescu (SPIRE, 2013)

A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. - Alexandru I. Tomescu; Anna Kuosmanen; Romeo Rizzi; Veli Mäkinen (WABI, 2013)

Markov chain algorithms for generating sets uniformly at random. - Alberto Policriti; Alexandru I. Tomescu (Ars Math. Contemp., 2013)

A novel min-cost flow method for estimating transcript expression with RNA-Seq. - Alexandru I. Tomescu; Anna Kuosmanen; Romeo Rizzi; Veli Mäkinen (BMC Bioinform., 2013)

Enumeration of the adjunctive hierarchy of hereditarily finite sets. - Giorgio Audrito; Alexandru I. Tomescu (CoRR, 2013)

Floating-point arithmetic for approximate counting and random generation problems. - Romeo Rizzi; Alexandru I. Tomescu (CoRR, 2013)

Set graphs. I. Hereditarily finite sets and extensional acyclic orientations. - Martin Milanic; Alexandru I. Tomescu (Discret. Appl. Math., 2013)

Well-quasi-ordering hereditarily finite sets. - Alberto Policriti; Alexandru I. Tomescu (Int. J. Comput. Math., 2013)

Ranking, unranking and random generation of extensional acyclic digraphs. - Romeo Rizzi; Alexandru I. Tomescu (Inf. Process. Lett., 2013)

The Representation of Boolean Algebras in the Spotlight of a Proof Checker. - Rodica Ceterchi; Eugenio G. Omodeo; Alexandru I. Tomescu (CILC, 2014)

Hyper-Extensionality and One-Node Elimination on Membership Graphs. - Eugenio G. Omodeo; Carla Piazza; Alberto Policriti; Alexandru I. Tomescu (CILC, 2014)

On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly. - Romeo Rizzi; Alexandru I. Tomescu; Veli Mäkinen (BMC Bioinform., 2014)

Set graphs. IV. Further connections with claw-freeness. - Martin Milanic; Alexandru I. Tomescu (Discret. Appl. Math., 2014)

Set Graphs. III. Proof Pearl: Claw-Free Graphs Mirrored into Transitive Hereditarily Finite Sets. - Eugenio G. Omodeo; Alexandru I. Tomescu (J. Autom. Reason., 2014)

Motif matching using gapped patterns. - Emanuele Giaquinta; Kimmo Fredriksson; Szymon Grabowski; Alexandru I. Tomescu; Esko Ukkonen (Theor. Comput. Sci., 2014)

Set graphs. II. Complexity of set graph recognition and similar problems. - Martin Milanic; Romeo Rizzi; Alexandru I. Tomescu (Theor. Comput. Sci., 2014)

Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing. - Veli Mäkinen; Djamal Belazzougui; Fabio Cunial; Alexandru I. Tomescu (Cambridge University Press, 2015)

Finding a Perfect Phylogeny from Mixed Tumor Samples. - Ademir Hujdurovic; Ursa Kacar; Martin Milanic; Bernard Ries; Alexandru I. Tomescu (WABI, 2015)

SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP. - Karen E. van Rens; Veli Mäkinen; Alexandru I. Tomescu (Bioinform., 2015)

Interval scheduling maximizing minimum coverage. - Veli Mäkinen; Valeria Staneva; Alexandru I. Tomescu; Daniel Valenzuela 001 (CoRR, 2015)

Mapping Sets and Hypersets into Numbers. - Giovanna D'Agostino; Eugenio G. Omodeo; Alberto Policriti; Alexandru I. Tomescu (Fundam. Informaticae, 2015)

Enumeration of the adjunctive hierarchy of hereditarily finite sets. - Giorgio Audrito; Alexandru I. Tomescu; Stephan G. Wagner (J. Log. Comput., 2015)

Set Graphs. V. On representing graphs as membership digraphs. - Eugenio G. Omodeo; Alexandru I. Tomescu (J. Log. Comput., 2015)

Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly. - Alexandru I. Tomescu; Travis Gagie; Alexandru Popa 001; Romeo Rizzi; Anna Kuosmanen; Veli Mäkinen (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy. - Anna Kuosmanen; Ahmed Sobih; Romeo Rizzi; Veli Mäkinen; Alexandru I. Tomescu (BIOINFORMATICS, 2016)

MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows. - Ahmed Sobih; Alexandru I. Tomescu; Veli Mäkinen (RECOMB, 2016)

Safe and Complete Contig Assembly Via Omnitigs. - Alexandru I. Tomescu; Paul Medvedev (RECOMB, 2016)

Gap Filling as Exact Path Length Problem. - Leena Salmela; Kristoffer Sahlin; Veli Mäkinen; Alexandru I. Tomescu (J. Comput. Biol., 2016)

Graph operations on parity games and polynomial-time algorithms. - Christoph Dittmann; Stephan Kreutzer; Alexandru I. Tomescu (Theor. Comput. Sci., 2016)

On Sets and Graphs: Perspectives on Logic and Combinatorics - Eugenio G. Omodeo; Alberto Policriti; Alexandru I. Tomescu (Springer, 2017)

Optimal Omnitig Listing for Safe and Complete Contig Assembly. - Massimo Cairo; Paul Medvedev; Nidia Obscura Acosta; Romeo Rizzi; Alexandru I. Tomescu (CPM, 2017)

The Minimum Conflict-Free Row Split Problem Revisited. - Ademir Hujdurovic; Edin Husic; Martin Milanic; Romeo Rizzi; Alexandru I. Tomescu (WG, 2017)

The minimum conflict-free row split problem revisited: a branching formulation and (in)approximability issues. - Ademir Hujdurovic; Edin Husic; Martin Milanic; Romeo Rizzi; Alexandru I. Tomescu (CoRR, 2017)

Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. - Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi; Alexandru I. Tomescu; Veli Mäkinen (CoRR, 2017)

Interval scheduling maximizing minimum coverage. - Veli Mäkinen; Valeria Staneva; Alexandru I. Tomescu; Daniel Valenzuela 001; Sebastian Wilzbach (Discret. Appl. Math., 2017)

Safe and Complete Contig Assembly Through Omnitigs. - Alexandru I. Tomescu; Paul Medvedev (J. Comput. Biol., 2017)

Set-syllogistics meet combinatorics. - Eugenio G. Omodeo; Alberto Policriti; Alexandru I. Tomescu (Math. Struct. Comput. Sci., 2017)

Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. - Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi; Alexandru I. Tomescu; Veli Mäkinen (RECOMB, 2018)

A safe and complete algorithm for metagenomic assembly. - Nidia Obscura Acosta; Veli Mäkinen; Alexandru I. Tomescu (Algorithms Mol. Biol., 2018)

Perfect Phylogenies via Branchings in Acyclic Digraphs and a Generalization of Dilworth's Theorem. - Ademir Hujdurovic; Edin Husic; Martin Milanic; Romeo Rizzi; Alexandru I. Tomescu (ACM Trans. Algorithms, 2018)

Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples. - Ademir Hujdurovic; Ursa Kacar; Martin Milanic; Bernard Ries; Alexandru I. Tomescu (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. - Niko Kiirala; Leena Salmela; Alexandru I. Tomescu (CPM, 2019)

MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP. - Edin Husic; Xinyue Li; Ademir Hujdurovic; Miika Mehine; Romeo Rizzi; Veli Mäkinen; Martin Milanic; Alexandru I. Tomescu (Bioinform., 2019)

On the Complexity of Exact Pattern Matching in Graphs: Determinism and Zig-Zag Matching. - Massimo Equi; Roberto Grossi; Alexandru I. Tomescu; Veli Mäkinen (CoRR, 2019)

Faster FPTASes for counting and random generation of Knapsack solutions. - Romeo Rizzi; Alexandru I. Tomescu (Inf. Comput., 2019)

An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph. - Massimo Cairo; Paul Medvedev; Nidia Obscura Acosta; Romeo Rizzi; Alexandru I. Tomescu (ACM Trans. Algorithms, 2019)

Sparse Dynamic Programming on DAGs with Small Width. - Veli Mäkinen; Alexandru I. Tomescu; Anna Kuosmanen; Topi Paavilainen; Travis Gagie; Rayan Chikhi (ACM Trans. Algorithms, 2019)

Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics. - Romeo Rizzi; Massimo Cairo; Veli Mäkinen; Alexandru I. Tomescu; Daniel Valenzuela 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Safely Filling Gaps with Partial Solutions Common to All Solutions. - Leena Salmela; Alexandru I. Tomescu (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Linear Time Construction of Indexable Founder Block Graphs. - Veli Mäkinen; Bastien Cazaux; Massimo Equi; Tuukka Norri; Alexandru I. Tomescu (WABI, 2020)

Conditional Indexing Lower Bounds Through Self-Reducibility. - Massimo Equi; Veli Mäkinen; Alexandru I. Tomescu (CoRR, 2020)

From omnitigs to macrotigs: a linear-time algorithm for safe walks - common to all closed arc-coverings of a directed graph. - Massimo Cairo; Romeo Rizzi; Alexandru I. Tomescu; Elia C. Zirondelli (CoRR, 2020)

Computing all s-t bridges and articulation points simplified. - Massimo Cairo; Shahbaz Khan 004; Romeo Rizzi; Sebastian S. Schmidt; Alexandru I. Tomescu; Elia C. Zirondelli (CoRR, 2020)

On the parameterized complexity of the Minimum Path Cover problem in DAGs. - Manuel Cáceres; Massimo Cairo; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu (CoRR, 2020)

Genome assembly, a universal theoretical framework: unifying and generalizing the safe and complete algorithms. - Massimo Cairo; Shahbaz Khan 004; Romeo Rizzi; Sebastian S. Schmidt; Alexandru I. Tomescu; Elia C. Zirondelli (CoRR, 2020)

Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time. - Massimo Cairo; Romeo Rizzi; Alexandru I. Tomescu; Elia C. Zirondelli (ICALP, 2021)

Algorithms and Complexity on Indexing Elastic Founder Graphs. - Massimo Equi; Tuukka Norri; Jarno Alanko; Bastien Cazaux; Alexandru I. Tomescu; Veli Mäkinen (ISAAC, 2021)

A Linear-Time Parameterized Algorithm for Computing the Width of a DAG. - Manuel Cáceres; Massimo Cairo; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu (WG, 2021)

Safety of Flow Decompositions in DAGs. - Shahbaz Khan 004; Alexandru I. Tomescu (CoRR, 2021)

The Labeled Direct Product Optimally Solves String Problems on Graphs. - Nicola Rizzo 001; Alexandru I. Tomescu; Alberto Policriti (CoRR, 2021)

A simplified algorithm computing all s-t bridges and articulation points. - Massimo Cairo; Shahbaz Khan 004; Romeo Rizzi; Sebastian S. Schmidt; Alexandru I. Tomescu; Elia C. Zirondelli (Discret. Appl. Math., 2021)

Optimizing Safe Flow Decompositions in DAGs. - Shahbaz Khan 004; Alexandru I. Tomescu (ESA, 2022)

Fast, Flexible, and Exact Minimum Flow Decompositions via ILP. - Fernando H. C. Dias; Lucia Williams; Brendan Mumey; Alexandru I. Tomescu (RECOMB, 2022)

Safety and Completeness in Flow Decompositions for RNA Assembly. - Shahbaz Khan 004; Milla Kortelainen; Manuel Cáceres; Lucia Williams; Alexandru I. Tomescu (RECOMB, 2022)

Sparsifying, Shrinking and Splicing for Minimum Path Cover in Parameterized Linear Time. - Manuel Cáceres; Massimo Cairo; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu (SODA, 2022)

Safety in s-t Paths, Trails and Walks. - Massimo Cairo; Shahbaz Khan 004; Romeo Rizzi; Sebastian S. Schmidt; Alexandru I. Tomescu (Algorithmica, 2022)

Solving String Problems on Graphs Using the Labeled Direct Product. - Nicola Rizzo 001; Alexandru I. Tomescu; Alberto Policriti (Algorithmica, 2022)

Minimum Flow Decomposition in Graphs with Cycles using Integer Linear Programming. - Fernando H. C. Dias; Lucia Williams; Brendan Mumey; Alexandru I. Tomescu (CoRR, 2022)

Minimum Path Cover in Parameterized Linear Time. - Manuel Cáceres; Massimo Cairo; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu (CoRR, 2022)

Efficient Minimum Flow Decomposition via Integer Linear Programming. - Fernando H. C. Dias; Lucia Williams; Brendan Mumey; Alexandru I. Tomescu (J. Comput. Biol., 2022)

Improving RNA Assembly via Safety and Completeness in Flow Decompositions. - Shahbaz Khan 004; Milla Kortelainen; Manuel Cáceres; Lucia Williams; Alexandru I. Tomescu (J. Comput. Biol., 2022)

Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG. - Manuel Cáceres; Brendan Mumey; Edin Husic; Romeo Rizzi; Massimo Cairo; Kristoffer Sahlin; Alexandru I. Tomescu (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Genome-Scale Algorithm Design: Bioinformatics in the Era of High-Throughput Sequencing (2nd edition). - Veli Mäkinen; Djamal Belazzougui; Fabio Cunial; Alexandru I. Tomescu (Cambridge University Press, 2023)

Cut Paths and Their Remainder Structure, with Applications. - Massimo Cairo; Shahbaz Khan 004; Romeo Rizzi; Sebastian S. Schmidt; Alexandru I. Tomescu; Elia C. Zirondelli (STACS, 2023)

Minimum Path Cover: The Power of Parameterization. - Manuel Cáceres; Brendan Mumey; Santeri Toivonen; Alexandru I. Tomescu (CoRR, 2023)

Flow Decomposition With Subpath Constraints. - Lucia Williams; Alexandru I. Tomescu; Brendan Mumey (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Algorithms and Complexity on Indexing Founder Graphs. - Massimo Equi; Tuukka Norri; Jarno Alanko; Bastien Cazaux; Alexandru I. Tomescu; Veli Mäkinen (Algorithmica, 2023)

On the Complexity of String Matching for Graphs. - Massimo Equi; Veli Mäkinen; Alexandru I. Tomescu; Roberto Grossi (ACM Trans. Algorithms, 2023)

Chaining for accurate alignment of erroneous long reads to acyclic variation graphs. - Jun Ma; Manuel Cáceres; Leena Salmela; Veli Mäkinen; Alexandru I. Tomescu (Bioinform., 2023)

A safety framework for flow decomposition problems via integer linear programming. - Fernando H. C. Dias; Manuel Cáceres; Lucia Williams; Brendan Mumey; Alexandru I. Tomescu (Bioinform., 2023)

Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails. - Massimo Equi; Veli Mäkinen; Alexandru I. Tomescu (Theor. Comput. Sci., 2023)

Applying the Safe-And-Complete Framework to Practical Genome Assembly. - Sebastian S. Schmidt; Santeri Toivonen; Paul Medvedev; Alexandru I. Tomescu (WABI, 2024)

Practical Minimum Path Cover. - Manuel Cáceres; Brendan Mumey; Santeri Toivonen; Alexandru I. Tomescu (SEA, 2024)

Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions. - Andreas Grigorjew; Fernando H. C. Dias; Andrea Cracco; Romeo Rizzi; Alexandru I. Tomescu (SEA, 2024)

Parameterised Approximation and Complexity of Minimum Flow Decompositions. - Andreas Grigorjew; Wanchote Jiamjitrak; Brendan Mumey; Alexandru I. Tomescu (CoRR, 2024)

Safe Paths and Sequences for Scalable ILPs in RNA Transcript Assembly Problems. - Francisco Sena; Alexandru I. Tomescu (CoRR, 2024)

Accurate Flow Decomposition via Robust Integer Linear Programming. - Fernando H. C. Dias; Alexandru I. Tomescu (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Simplicity in Eulerian circuits: Uniqueness and safety. - Nidia Obscura Acosta; Alexandru I. Tomescu (Inf. Process. Lett., 2024)

Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time. - Massimo Cairo; Romeo Rizzi; Alexandru I. Tomescu; Elia C. Zirondelli (ACM Trans. Algorithms, 2024)

Width Helps and Hinders Splitting Flows. - Manuel Cáceres; Massimo Cairo; Andreas Grigorjew; Shahbaz Khan 004; Brendan Mumey; Romeo Rizzi; Alexandru I. Tomescu; Lucia Williams (ACM Trans. Algorithms, 2024)

Maximum Coverage k-Antichains and Chains: A Greedy Approach. - Manuel Cáceres; Andreas Grigorjew; Wanchote Po Jiamjitrak; Alexandru I. Tomescu (CoRR, 2025)