Virtual PCR. - Matej Lexa; J. Horak; Bretislav Brzobohaty (Bioinform., 2001)

PRIMEX: rapid identification of oligonucleotide matches in whole genomes. - Matej Lexa; Giorgio Valle (Bioinform., 2003)

RAP: a new computer program for de novo identification of repeated sequences in whole genomes. - Davide Campagna; Chiara Romualdi; Nicola Vitulo; Micky Del Favero; Matej Lexa; Nicola Cannata; Giorgio Valle (Bioinform., 2005)

A Flexible Technique for the Automatic Design of Approximate String Matching Architectures. - Tomás Martínek; Jan Korenek; Otto Fucík; Matej Lexa (DDECS, 2006)

Automatic Generation of Circuits for Approximate String Matching. - Tomás Martínek; Otto Fucík; Patrik Beck; Matej Lexa (DDECS, 2007)

Hardware acceleration of approximate palindromes searching. - Tomás Martínek; Matej Lexa (FPT, 2008)

Architecture model for approximate palindrome detection. - Tomás Martínek; Jan Vozenilek; Matej Lexa (DDECS, 2009)

Data-Mining Protein Structure by Clustering, Segmentation and Evolutionary Algorithms. - Matej Lexa; Václav Snásel; Ivan Zelinka (Foundations of Computational Intelligence (4), 2009)

Hardware Acceleration of Approximate Tandem Repeat Detection. - Tomás Martínek; Matej Lexa (FCCM, 2010)

Clustering of Protein Substructures for Discovery of a Novel Class of Sequence-Structure Fragments. - Ivana Rudolfova; Jaroslav Zendulka; Matej Lexa (ITBAM, 2010)

Architecture model for approximate tandem repeat detection. - Tomás Martínek; Matej Lexa (ASAP, 2011)

A dynamic programming algorithm for identification of triplex-forming sequences. - Matej Lexa; Tomás Martínek; Ivana Burgetova; Daniel Kopecek; Marie Brázdová (Bioinform., 2011)

cswHMM: A Novel Context Switching Hidden Markov Model for Biological Sequence Analysis. - Vojtech Bystrý; Matej Lexa (BIOINFORMATICS, 2012)

Prediction of Significant Cruciform Structures from Sequence in Topologically Constrained DNA - A Probabilistic Modelling Approach. - Matej Lexa; Lucie Navrátilová; Karel Nejedlý; Marie Brázdová (BIOINFORMATICS, 2012)

Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. - Jirí Hon; Tomás Martínek; Kamil Rajdl; Matej Lexa (Bioinform., 2013)

Uneven Distribution of Potential Triplex Sequences in the Human Genome - In Silico Study using the R/Bioconductor Package Triplex. - Matej Lexa; Tomás Martínek; Marie Brázdová (BIOINFORMATICS, 2014)

The Possibilities of Filtering Pairs of SNPs in GWAS Studies - Exploratory Study on Public Protein-interaction and Pathway Data. - Matej Lexa; Stanislav Stefanic (BIOINFORMATICS, 2014)

A Flexible Denormalization Technique for Data Analysis above a Deeply-Structured Relational Database: Biomedical Applications. - Stanislav Stefanic; Matej Lexa (IWBBIO (1), 2015)

Semi-automatic mining of correlated data from a complex database: Correlation network visualization. - Matej Lexa; Radovan Lapar (ICCABS, 2016)

Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. - Adam Krejci; Ted R. Hupp; Matej Lexa; Borivoj Vojtesek; Petr Müller (Bioinform., 2016)

pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. - Jirí Hon; Tomás Martínek; Jaroslav Zendulka; Matej Lexa (Bioinform., 2017)

TE-nester: a recursive software tool for structure-based discovery of nested transposable elements. - Matej Lexa; Radovan Lapar; Pavel Jedlicka; Ivan Vanat; Michal Cervenanský; Eduard Kejnovský (BIBM, 2018)

pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. - Dominika Labudová; Jirí Hon; Matej Lexa (Bioinform., 2020)

TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. - Matej Lexa; Pavel Jedlicka; Ivan Vanat; Michal Cervenanský; Eduard Kejnovský (Bioinform., 2020)

SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. - Pratik Goswami; Martin Bartas; Matej Lexa; Natália Bohálová; Adriana Volná; Jirí Cerven; Veronika Cervenová; Petr Pecinka; Vladimír Spunda; Miroslav Fojta; Václav Brázda (Briefings Bioinform., 2021)

HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization. - Matej Lexa; Monika Cechova; Son Hoang Nguyen; Pavel Jedlicka; Viktor Tokan; Zdenek Kubat; Roman Hobza; Eduard Kejnovský (Bioinform., 2022)

A perspective on genetic and polygenic risk scores - advances and limitations and overview of associated tools. - Jana Schwarzerova; Martin Hurta; Vojtech Barton; Matej Lexa; Dirk Walther 001; Valentine Provazník; Wolfram Weckwerth (Briefings Bioinform., 2024)

Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning. - Jakub Horvath; Pavel Jedlicka; Marie Kratka; Zdenek Kubat; Eduard Kejnovský; Matej Lexa (BioData Min., 2024)

Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning. - Jakub Horvath; Pavel Jedlicka; Marie Kratka; Zdenek Kubat; Eduard Kejnovský; Matej Lexa (BioData Min., 2024)