User profiles for Alexandru I. Tomescu

Alexandru I. Tomescu

Department of Computer Science, University of Helsinki
Verified email at helsinki.fi
Cited by 1601

[BOOK][B] Genome-scale algorithm design

V Mäkinen, D Belazzougui, F Cunial, AI Tomescu - 2015 - books.google.com
High-throughput sequencing has revolutionised the field of biological sequence analysis. Its
application has enabled researchers to address important biological questions, often for the …

[HTML][HTML] Unicyclic and bicyclic graphs having minimum degree distance

AI Tomescu - Discrete applied mathematics, 2008 - Elsevier
In this paper characterizations of connected unicyclic and bicyclic graphs in terms of the
degree sequence, as well as the graphs in these classes minimal with respect to the degree …

[HTML][HTML] A novel min-cost flow method for estimating transcript expression with RNA-Seq

AI Tomescu, A Kuosmanen, R Rizzi, V Mäkinen - BMC bioinformatics, 2013 - Springer
Background Through transcription and alternative splicing, a gene can be transcribed into
different RNA sequences (isoforms), depending on the individual, on the tissue the cell is in, …

Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT

A Cracco, AI Tomescu - Genome Research, 2023 - genome.cshlp.org
Compacted de Bruijn graphs are one of the most fundamental data structures in computational
genomics. Colored compacted de Bruijn graphs are a variant built on a collection of …

On the complexity of string matching for graphs

…, R Grossi, V Mäkinen, AI Tomescu - … Colloquium on Automata …, 2019 - drops.dagstuhl.de
Exact string matching in labeled graphs is the problem of searching paths of a graph G=(V, E)
such that the concatenation of their node labels is equal to the given pattern string P [1.. m]…

Sparsifying, shrinking and splicing for minimum path cover in parameterized linear time

…, M Cairo, B Mumey, R Rizzi, AI Tomescu - Proceedings of the 2022 …, 2022 - SIAM
A minimum path cover (MPC) of a directed acyclic graph (DAG) G = (V, E) is a minimum-size
set of paths that together cover all the vertices of the DAG. Computing an MPC is a basic …

[HTML][HTML] Graphs cannot be indexed in polynomial time for sub-quadratic time string matching, unless SETH fails

M Equi, V Mäkinen, AI Tomescu - Theoretical Computer Science, 2023 - Elsevier
The string matching problem on a node-labeled graph G = ( V , E ) asks whether a given
pattern string P equals the concatenation of node labels of some path in G. This is a basic …

Sparse dynamic programming on DAGs with small width

V Mäkinen, AI Tomescu, A Kuosmanen… - ACM Transactions on …, 2019 - dl.acm.org
The minimum path cover problem asks us to find a minimum-cardinality set of paths that
cover all the nodes of a directed acyclic graph (DAG). We study the case when the size k of a …

rNA: a fast and accurate short reads numerical aligner

F Vezzi, C Del Fabbro, AI Tomescu, A Policriti - Bioinformatics, 2012 - academic.oup.com
The advent of high-throughput sequencers (HTS) introduced the need of new tools in order
to analyse the large amount of data that those machines are able to produce. The mandatory …

Flow decomposition with subpath constraints

L Williams, AI Tomescu… - IEEE/ACM Transactions on …, 2022 - ieeexplore.ieee.org
Flow network decomposition is a natural model for problems where we are given a flow
network arising from superimposing a set of weighted paths and would like to recover the …