Indexing Factors in DNA/RNA Sequences. - Tomás Flouri; Costas S. Iliopoulos; Mohammad Sohel Rahman; Ladislav Vagner; Michal Vorácek (BIRD, 2008)

Subtree matching by deterministic pushdown automata. - Tomás Flouri; Borivoj Melichar; Jan Janousek (IMCSIT, 2009)

An algorithm for mapping short reads to a dynamically changing genomic sequence. - Tomás Flouri; Jan Holub 001; Costas S. Iliopoulos; Solon P. Pissis (BIBM, 2010)

Aho-Corasick like multiple subtree matching by pushdown automata. - Tomás Flouri; Borivoj Melichar; Jan Janousek (SAC, 2010)

Subtree matching by pushdown automata. - Tomás Flouri; Jan Janousek; Borivoj Melichar (Comput. Sci. Inf. Syst., 2010)

DynMap: mapping short reads to multiple related genomes. - Tomás Flouri; Costas S. Iliopoulos; Solon P. Pissis (BCB, 2011)

Approximate string-matching with a single gap for sequence alignment. - Tomás Flouri; Kunsoo Park; Kimon Frousios; Solon P. Pissis; Costas S. Iliopoulos; German Tischler (BCB, 2011)

Tree Indexing by Pushdown Automata and Repeats of Subtrees. - Tomás Flouri; Jan Janousek; Borivoj Melichar; Costas S. Iliopoulos; Solon P. Pissis (FedCSIS, 2011)

Computing All Subtree Repeats in Ordered Ranked Trees. - Michalis Christou; Maxime Crochemore; Tomás Flouri; Costas S. Iliopoulos; Jan Janousek; Borivoj Melichar; Solon P. Pissis (SPIRE, 2011)

Libgapmis: An ultrafast library for short-read single-gap alignment. - Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (BIBM Workshops, 2012)

GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures. - Tomás Flouri; Costas S. Iliopoulos; Kunsoo Park; Solon P. Pissis (AIAI (2), 2012)

New and Efficient Approaches to the Quasiperiodic Characterisation of a String. - Tomás Flouri; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Simon J. Puglisi; William F. Smyth; Wojciech Tyczynski (Stringology, 2012)

Computing all subtree repeats in ordered trees. - Michalis Christou; Maxime Crochemore; Tomás Flouri; Costas S. Iliopoulos; Jan Janousek; Borivoj Melichar; Solon P. Pissis (Inf. Process. Lett., 2012)

Tree template matching in ranked ordered trees by pushdown automata. - Tomás Flouri; Costas S. Iliopoulos; Jan Janousek; Borivoj Melichar; Solon P. Pissis (J. Discrete Algorithms, 2012)

Arbology: Trees and pushdown automata. - Borivoj Melichar; Jan Janousek; Tomás Flouri (Kybernetika, 2012)

GapsMis: flexible sequence alignment with a bounded number of gaps. - Carl Barton; Tomás Flouri; Costas S. Iliopoulos; Solon P. Pissis (BCB, 2013)

Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library. - Diego Darriba; Andre J. Aberer; Tomás Flouri; Tracy A. Heath; Fernando Izquierdo-Carrasco; Alexandros Stamatakis (IPDPS Workshops, 2013)

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library. - Fernando Izquierdo-Carrasco; Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (IPDPS Workshops, 2013)

An Optimal Algorithm for Computing All Subtree Repeats in Trees. - Tomás Flouri; Kassian Kobert; Solon P. Pissis; Alexandros Stamatakis (IWOCA, 2013)

libgapmis: extending short-read alignments. - Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (BMC Bioinform., 2013)

Tree template matching in unranked ordered trees. - Michalis Christou; Tomás Flouri; Costas S. Iliopoulos; Jan Janousek; Borivoj Melichar; Solon P. Pissis; Jan Zdárek (J. Discrete Algorithms, 2013)

Enhanced string covering. - Tomás Flouri; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Simon J. Puglisi; W. F. Smyth; Wojciech Tyczynski (Theor. Comput. Sci., 2013)

The Divisible Load Balance Problem and Its Application to Phylogenetic Inference. - Kassian Kobert; Tomás Flouri; Andre J. Aberer; Alexandros Stamatakis (WABI, 2014)

PEAR: a fast and accurate Illumina Paired-End reAd mergeR. - Jiajie Zhang; Kassian Kobert; Tomás Flouri; Alexandros Stamatakis (Bioinform., 2014)

Longest common substrings with k mismatches. - Tomás Flouri; Emanuele Giaquinta; Kassian Kobert; Esko Ukkonen (Inf. Process. Lett., 2015)

Global and local sequence alignment with a bounded number of gaps. - Carl Barton; Tomás Flouri; Costas S. Iliopoulos; Solon P. Pissis (Theor. Comput. Sci., 2015)

The Divisible Load Balance Problem with Shared Cost and Its Application to Phylogenetic Inference. - Constantin Scholl; Kassian Kobert; Tomás Flouri; Alexandros Stamatakis (IPDPS Workshops, 2016)

A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation. - Diep Thi Hoang; Le Sy Vinh; Tomás Flouri; Alexandros Stamatakis; Arndt von Haeseler; Bui Quang Minh (KSE, 2016)

An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties. - Tomás Flouri; Jiajie Zhang; Lucas Czech; Kassian Kobert; Alexandros Stamatakis (Algorithms for Next-Generation Sequencing Data, 2017)

A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic Inference Using Site Repeats. - Benoit Morel; Tomás Flouri; Alexandros Stamatakis (HPCC/SmartCity/DSS, 2017)

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. - Paschalia Kapli; Sarah Lutteropp; Jiajie Zhang; Kassian Kobert; Pavlos Pavlidis; Alexandros Stamatakis; Tomás Flouri (Bioinform., 2017)

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. - Alexey M. Kozlov; Diego Darriba; Tomás Flouri; Benoit Morel; Alexandros Stamatakis (Bioinform., 2019)