Publication Records

ULLAH, Sajid, Klára PANZAROVÁ, Martin TRTÍLEK, Matej LEXA, Vojtěch MÁČALA, Thomas ALTMANN, Kerstin NEUMANN, Jan HEJÁTKO, Markéta PERNISOVÁ and Evgeny GLADILIN. High-throughput spike detection in greenhouse cultivated grain crops with attention mechanisms based deep learning models. Plant Phenomics. AAAS, 2024. ISSN 2643-6515. Available from: https://dx.doi.org/10.34133/plantphenomics.0155.

LEXA, Matej and Hedvig HEGYI. Alternatives to classical HiC data analysis. In Workshop on Bioinformatics and Computational Biology (WBCB 2023). 2023, p. 14-14.

HORVÁTH, Jakub and Matej LEXA. Analysis and classification of long terminal repeat sequences from plant LTR-retrotransposons. Online. In Workshop on Bioinformatics and Computational Biology (WBCB 2023). 2023, p. 10-10.

BREJOVÁ, Bronislava, Lucie CIENCIALOVÁ, Martin HOLEŇA, Róbert JAJCAY, Tatiana JAJCAYOVÁ, Matej LEXA, František MRÁZ, Dana PARDUBSKÁ and Martin PLÁTEK. ITAT’23: Information technologies – Applications and Theory, September 22–26, 2023, Tatranské Matliare, Slovakia. 2023.

JEDLIČKA, Pavel, Ivan VANÁT, Matej LEXA, Marie KRÁTKÁ and Eduard KEJNOVSKÝ. TE-greedy-nester: a tool for reconstruction of transposable elements in plant genomes. Online. In Workshop on Bioinformatics and Computational Biology (WBCB 2023). 2023, p. 12-12.

LEXA, Matej, Monika ČECHOVÁ, Son Hoang NGUYEN, Pavel JEDLIČKA, Viktor TOKAN, Zdeněk KUBÁT, Roman HOBZA and Eduard KEJNOVSKÝ. HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization. BIOINFORMATICS. ENGLAND: OXFORD UNIV PRESS, 2022, vol. 38, No 16, p. 4030-4032. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btac442.

HRALA, Matěj, Juraj BOSÁK, Lenka MICENKOVÁ, Jitka KŘENOVÁ, Matej LEXA, Viktória PIRKOVÁ, Zuzana TOMASTIKOVA, Ivana KOLÁČKOVÁ and David ŠMAJS. Escherichia coli Strains Producing Selected Bacteriocins Inhibit Porcine Enterotoxigenic Escherichia coli (ETEC) under both In Vitro and In Vivo Conditions. Applied and Environmental Microbiology. WASHINGTON, DC (USA): AMER SOC MICROBIOLOGY, 2021, vol. 87, No 14, p. 1-12. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.03121-20.

BARTAS, Martin, Pratik GOSWAMI, Matej LEXA, Jiří ČERVEŇ, Adriana VOLNÁ, Miroslav FOJTA, Vaclav BRAZDA and Petr PEČINKA. Letter to the Editor: Significant mutation enrichment in inverted repeat sites of new SARS-CoV-2 strains. Briefings in Bioinformatics. Oxford University Press, 2021, vol. 22, No 5, p. "bbab129", 17 pp. ISSN 1467-5463. Available from: https://dx.doi.org/10.1093/bib/bbab129.

BOSÁK, Juraj, Matej LEXA, Kristýna FIEDOROVÁ, Darshak Chandulal GADARA, Lenka MICENKOVÁ, Zdeněk SPÁČIL, Jiří LITZMAN, Tomáš FREIBERGER and David ŠMAJS. Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates. Frontiers in Immunology. LAUSANNE: FRONTIERS MEDIA SA, 2021, vol. 12, May 2021, p. 1-13. ISSN 1664-3224. Available from: https://dx.doi.org/10.3389/fimmu.2021.671239.

GOSWAMI, Pratik, Martin BARTAS, Matej LEXA, Natália BOHÁLOVÁ, Adriana VOLNÁ, Jiří ČERVEŇ, Veronika ČERVEŇOVÁ, Petr PEČINKA, Vladimír ŠPUNDA, Miroslav FOJTA and Václav BRÁZDA. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. Briefings in Bioinformatics. Oxford: Oxford University Press, 2021, vol. 22, No 2, p. 1338-1345. ISSN 1467-5463. Available from: https://dx.doi.org/10.1093/bib/bbaa385.

LABUDOVÁ, Dominika, Jiří HON and Matej LEXA. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics. Oxford: Oxford University Press, 2020, vol. 36, No 8, p. 2584-2586. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz928.

LEXA, Matej, Pavel JEDLICKA, Ivan VANÁT, Michal ČERVEŇANSKÝ and Eduard KEJNOVSKÝ. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. Bioinformatics. OXFORD: OXFORD UNIV PRESS, 2020, vol. 36, No 20, p. 4991-4999. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btaa632.

JEDLICKA, Pavel, Matej LEXA and Eduard KEJNOVSKÝ. What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination? Frontiers in Plant Science. Lausanne (Switzerland): Frontiers Media SA, 2020, vol. 11, No 644, p. 1-15. ISSN 1664-462X. Available from: https://dx.doi.org/10.3389/fpls.2020.00644.

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Juraj BOSÁK, Hana GROMBIŘÍKOVÁ, Eva NĚMCOVÁ, Pavlína KRÁLÍČKOVÁ, Michaela ČERNOCHOVÁ, Iva KOTÁSKOVÁ, Matej LEXA, Jiří LITZMAN, David ŠMAJS and Tomáš FREIBERGER. Bacterial and fungal gut microbiota analysis in common variable immunodeficiency (CVID) disorders: paired case-control study. In 2nd ESID Focused Meeting, Brussels. 2019.

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Juraj BOSÁK, Hana GROMBIŘÍKOVÁ, Eva NĚMCOVÁ, Pavlina KRÁLÍČKOVÁ, Michaela ČERNOCHOVÁ, Iva KOTÁSKOVÁ, Matej LEXA, Jiří LITZMAN, David ŠMAJS and Tomáš FREIBERGER. Bacterial but Not Fungal Gut Microbiota Alterations Are Associated With Common Variable Immunodeficiency (CVID) Phenotype. Frontiers in Immunology. LAUSANNE: FRONTIERS MEDIA SA, 2019, vol. 10, No 1914, p. 1-14. ISSN 1664-3224. Available from: https://dx.doi.org/10.3389/fimmu.2019.01914.

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Pavlína KRÁLÍČKOVÁ, Michaela ČERNOCHOVÁ, Eva NĚMCOVÁ, Hana GROMBIŘÍKOVÁ, Juraj BOSÁK, Matej LEXA, David ŠMAJS, Jiří LITZMAN and Tomáš FREIBERGER. Gut microbiome analysis in common variable immunodeficiency (CVID) patients and paired healthy controls sharing the same household. In 29th European Congress of Clinical Microbiology & Infectious Diseases. 2019.

SOUČEK, Přemysl, Kamila RÉBLOVÁ, Michal KRAMÁREK, Lenka RADOVÁ, Tereza GRYMOVÁ, Pavla HUJOVÁ, Tatiana KOVÁČOVÁ, Matej LEXA, Lucie GRODECKÁ and Tomáš FREIBERGER. High-throughput analysis revealed mutations' diverging effects on SMN1 exon 7 splicing. RNA BIOLOGY. PHILADELPHIA: TAYLOR & FRANCIS INC, 2019, vol. 16, No 10, p. 1364-1376. ISSN 1547-6286. Available from: https://dx.doi.org/10.1080/15476286.2019.1630796.

JEDLIČKA, Pavel, Matej LEXA, Ivan VANÁT, Eduard KEJNOVSKÝ and Roman HOBZA. Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. Mobile DNA. 2019, vol. 10, No 1, p. 1-14. ISSN 1759-8753. Available from: https://dx.doi.org/10.1186/s13100-019-0186-z.

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Eva NĚMCOVÁ, Hana GROMBIŘÍKOVÁ, Juraj BOSÁK, Michaela ČERNOCHOVÁ, Matej LEXA, David ŠMAJS and Tomáš FREIBERGER. The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery. Frontiers in Microbiology. Lausanne: Frontiers Media SA, 2019, vol. 10, No 821, p. 1-11. ISSN 1664-302X. Available from: https://dx.doi.org/10.3389/fmicb.2019.00821.

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Hana GROMBIŘÍKOVÁ, Eva NĚMCOVÁ, Juraj BOSÁK, Matej LEXA, David ŠMAJS and Tomáš FREIBERGER. Artificial fungal community (fMOCK) as a control of sequencing process in mycobiome research. In In 6th World Congress on Targeting Microbiota, Porto. 2018.

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Martina VANĚRKOVÁ, Hana GROMBIŘÍKOVÁ, Matej LEXA and Tomáš FREIBERGER. Dynamics of human gut microbiome in healthy volunteers from the Czech Republic. In In 7th International Human Microbiome Consortium Meeting, Killarney. 2018.

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Králíčková PAVLÍNA, Černochová MICHAELA, Eva NĚMCOVÁ, Hana GROMBIŘÍKOVÁ, Juraj BOSÁK, Matej LEXA, David ŠMAJS, Jiří LITZMAN and Tomáš FREIBERGER. Gut microbiome analysis in common variable immunodeficiency (CVID) patients. In 18th Biennial meeting of the European Society for immunodeficiencies, Lisbon. 2018.

TOKAN, Viktor, Janka PUTEROVÁ, Matej LEXA and Eduard KEJNOVSKÝ. Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast. BMC Genomics. BioMed Central, 2018, vol. 19, 06 03 2018, p. 184-194. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-018-4563-7.

LEXA, Matej, Radovan LAPÁR, Pavel JEDLIČKA, Ivan VANÁT, Michal ČERVEŇANSKÝ and Eduard KEJNOVSKÝ. TE-nester: a recursive software tool for structure-based discovery of nested transposable elements. Online. In Zheng Huiru. Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Neuveden: IEEE, 2018, p. 2776-2778. ISBN 978-1-5386-5488-0. Available from: https://dx.doi.org/10.1109/BIBM.2018.8621071.

FIEDOROVÁ, Kristýna, Juraj BOSÁK, Barbora ZWINSOVÁ, Matej LEXA, Jiří LITZMAN, Tomáš FREIBERGER and David ŠMAJS. Gastrointestinal microbiome in patients with primary immune deficiencies. In Food, Microbiota and Immunity, Třešť. 2017.

HON, Jiří, Tomáš MARTÍNEK, Jaroslav ZENDULKA and Matej LEXA. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics. Oxford: Oxford University Press, 2017, vol. 33, No 21, p. 3373-3379. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx413.

HON, Jiří, Matej LEXA, Tomáš MARTÍNEK and Jaroslav ZENDULKA. pqsfinder: identification of potential quadruplex forming sequences. 2017. Available from: https://dx.doi.org/10.18129/B9.bioc.pqsfinder.

KAŠPAROVSKÁ, Jitka, Martina ZAPLETALOVÁ, Kateřina DADÁKOVÁ, Ludmila KŘÍŽOVÁ, Sylvie HADROVÁ, Matej LEXA, Jan LOCHMAN and Tomáš KAŠPAROVSKÝ. Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows. Plos one. San Francisco: Public Library of Science, 2016, vol. 11, No 4, p. "nestrankovano", 17 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0154642.

KREJČÍ, Adam, TR HUPP, Matej LEXA, Bořivoj VOJTĚŠEK and Petr MÜLLER. Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. Bioinformatics. Oxford: Oxford University Press, 2016, vol. 32, No 1, p. 9-16. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btv522.

BRÁZDOVÁ, Marie, Vlastimil TICHÝ, Robert HELMA, Pavla BAŽANTOVÁ, Alena POLÁŠKOVÁ, Aneta KREJČÍ, Marek PETR, Lucie NAVRÁTILOVÁ, Olga TICHÁ, Karel NEJEDLÝ, Martin L BENNINK, Vinod SUBRAMANIAM, Zuzana BÁBKOVÁ, Tomáš MARTÍNEK, Matej LEXA and Matej ADÁMIK. p53 Specifically Binds Triplex DNA In Vitro and in Cells. PLOS ONE. Public Library of Science, 2016, vol. 11, No 12, p. "e0167439", 25 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0167439.

LEXA, Matej and Radovan LAPÁR. Semi-automatic mining of correlated data from a complex database: Correlation network visualization. Online. In Computational Advances in Bio and Medical Sciences (ICCABS), 2016 IEEE 6th International Conference on. New York: IEEE, 2016, p. 1-2. ISBN 978-1-5090-4199-2. Available from: https://dx.doi.org/10.1109/ICCABS.2016.7802783.

ŠTEFANIČ, Stanislav and Matej LEXA. A flexible denormalization technique for data analysis above a deeply-structured relational database: biomedical applications. In Ortuño, Francisco and Rojas, Ignacio. Lecture Notes in Computer Science 9043, Bioinformatics and Biomedical Engineering, Third International Conference, IWBBIO 2015, Granada, Spain, April 15-17 2015, Proceedings, Part I. Cham: Springer International Publishing, 2015, p. 120-133. ISBN 978-3-319-16482-3. Available from: https://dx.doi.org/10.1007/978-3-319-16483-0_12.

KEJNOVSKÝ, Eduard, Viktor TOKAN and Matej LEXA. Transposable elements and G-quadruplexes. Chromosome Research. Springer Netherlands, 2015, vol. 23, No 3, p. 615-623. ISSN 0967-3849. Available from: https://dx.doi.org/10.1007/s10577-015-9491-7.

LEXA, Matej, Lenka RADOVÁ, Martin LYSÁK, Tomáš MARTÍNEK, Nikola TOM, Karol PÁL, Alexandru POPA and Jana KAPUSTOVÁ. Bioinformatics Summer School 2014: Theoretical and practical aspects of processing and analysis of sequencing data. 2014. Available from: https://dx.doi.org/10.13140/RG.2.1.4517.0721.

LEXA, Matej, Pavlina STEFLOVA, Tomáš MARTÍNEK, Michaela VORLÍČKOVÁ, Boris VYSKOT and Eduard KEJNOVSKÝ. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics. London: BioMed Central Ltd, 2014, vol. 15, No 1, p. 1032-1043. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/1471-2164-15-1032.

KEJNOVSKÝ, Eduard and Matej LEXA. Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators. Mobile Genetic Elements. Landes Bioscience, 2014, vol. 4, No 1, p. "e28084", 4 pp. ISSN 2159-256X. Available from: https://dx.doi.org/10.4161/mge.28084.

LEXA, Matej, Eduard KEJNOVSKÝ, Pavlína ŠTEFLOVÁ, Helena KONVALINOVÁ, Michaela VORLÍČKOVÁ and Boris VYSKOT. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons. Nucleic Acids Research. Oxford: Oxford University Press, 2014, vol. 42, No 2, p. 968-978. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkt893.

LEXA, Matej and Stanislav ŠTEFANIČ. The Possibilities of Filtering Pairs of SNPs in GWAS Studies Exploratory Study on Public Protein-interaction and Pathway Data. In Pastor, O Sinoquet, C Plantier, G Schultz, T Fred, A Gamboa, H. BIOINFORMATICS 2014: PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON BIOINFORMATICS MODELS, METHODS AND ALGORITHMS. SETUBAL: SCITEPRESS, 2014, p. 259-264. ISBN 978-989-758-012-3.

LEXA, Matej and Stanislav ŠTEFANIČ. The possibilities of using biological knowledge for filtering pairs of SNPs in GWAS studies: an exploratory study on public protein-interaction and pathway data. In Oscar Pastor, Christine Sinoquet, Guy Plantier, Tanja Schultz, Ana L. N. Fred, Hugo Gamboa. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Angers, France: SciTePress, 2014, p. 259-264. ISBN 978-989-758-012-3. Available from: https://dx.doi.org/10.5220/0004915002590264.

LEXA, Matej, Tomáš MARTÍNEK and Marie BRÁZDOVÁ. Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex. In Oscar Pastor, Christine Sinoquet, Guy Plantier, Tanja Schultz, Ana L. N. Fred, Hugo Gamboa. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Angers, France: SciTePress, 2014, p. 80-88. ISBN 978-989-758-012-3. Available from: https://dx.doi.org/10.5220/0004824100800088.

LEXA, Matej. Bioinformatika v štúdiu genómov a proteómov (ITAT 2013) (Bioinformatics in genomics and proteomics (ITAT 2013)). 2013.

ŠTEFLOVÁ, Pavlína, Viktor TOKAN, Ivan VOGEL, Matej LEXA, Jiří MACAS, Petr NOVAK, Roman HOBZA, Boris VYSKOT and Eduard KEJNOVSKÝ. Contrasting Patterns of Transposable Element and Satellite Distribution on Sex Chromosomes (XY1Y2) in the Dioecious Plant Rumex acetosa. GENOME BIOLOGY AND EVOLUTION. Oxford, UK: Oxford Univ Press, 2013, vol. 5, No 4, p. 769-782. ISSN 1759-6653. Available from: https://dx.doi.org/10.1093/gbe/evt049.

KOSINA, Marcel, Ivana MAŠLAŇOVÁ, Andrea VÁVROVÁ PASCUTTI, Ondrej ŠEDO, Matej LEXA, Pavel ŠVEC and Ivo SEDLÁČEK. Description of Pseudomonas jessenii subsp. pseudoputida subsp. nov., amended description of Pseudomonas jessenii and description of Pseudomonas jessenii subsp. jessenii subsp. nov. Folia Microbiologica. Praha: Czechoslovak Society for Microbiology, 2013, vol. 58, No 6, p. 631-639. ISSN 0015-5632. Available from: https://dx.doi.org/10.1007/s12223-013-0236-8.

ŠTEFANIČ, Stanislav and Matej LEXA. Generovanie simulovaných testovacích dát pre genómové asociačné štúdie (Generating simulated testing data for genome-wide association studies). In Tomáš Vinař, Martin Holeňa, Matej Lexa, Ladislav Peška, Peter Vojtáš. ITAT 2013: Information Technologies - Applications and Theory (Workshops, Posters, and Tutorials). Neuvedeno: CreateSpace Independent Publishing Platform, 2013, p. 64-68. ISBN 1-4909-5208-X.

BRÁZDOVÁ, Marie, Tomáš MARTÍNEK and Matej LEXA. In silico search for secondary structures in p53 target genes using R/Bioconductor. In Tomáš Vinař, Martin Holeňa, Matej Lexa, Ladislav Peška, Peter Vojtáš. ITAT 2013: Information Technologies - Applications and Theory (Workshops, Posters, and Tutorials). Neuvedeno: CreateSpace Independent Publishing Platform, 2013, p. 42-46. ISBN 1-4909-5208-X.

VINAŘ, Tomáš, Martin HOLEŇA, Matej LEXA, Ladislav PEŠKA and Peter VOJTÁŠ. ITAT 2013: Information Technologies - Applications and Theory (Workshops, Posters, and Tutorials). Neuvedeno: CreateSpace Independent Publishing Platform, 2013, 142 pp. ISBN 1-4909-5208-X.

BRÁZDOVÁ, Marie, Lucie NAVRATILOVA, Vlastimil TICHÝ, Kateřina NĚMCOVÁ, Matej LEXA, Roman HRSTKA, Petr PECINKA, Matej ADÁMIK, Bořivoj VOJTĚŠEK, Emil PALECEK, Wolfgang DEPPERT and Miroslav FOJTA. Preferential Binding of Hot Spot Mutant p53 Proteins to Supercoiled DNA In Vitro and in Cells. Plos One. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2013, vol. 8, No 3, p. "e59567", 17 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0059567.

KOSINA, Marcel, Miloš BARTÁK, Ivana MAŠLAŇOVÁ, Andrea VÁVROVÁ PASCUTTI, Ondrej ŠEDO, Matej LEXA and Ivo SEDLÁČEK. Pseudomonas prosekii sp. nov., a Novel Psychrotrophic Bacterium from Antarctica. Current Microbiology. Springer US, 2013, vol. 67, No 6, p. 637-646. ISSN 0343-8651. Available from: https://dx.doi.org/10.1007/s00284-013-0406-6.

HON, Jiří, Matej LEXA, Tomáš MARTÍNEK and Kamil RAJDL. R/Bioconductor package for identification of triplex-forming sequences. 2013.

HON, Jiří, Tomáš MARTÍNEK, Kamil RAJDL and Matej LEXA. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. Bioinformatics. Oxford: Oxford University Press, 2013, vol. 29, No 15, p. 1900-1901. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btt299.

KOSINA, Marcel, Miloš BARTÁK, Ivana MAŠLAŇOVÁ, Andrea PASCUTTI, Ondrej ŠEDO, Matej LEXA and Ivo SEDLÁČEK. Classification of Pseudomonas spp. isolated from Antarctic samples. In Planet Under Pressure. 2012.

BYSTRÝ, Vojtěch and Matej LEXA. cswHMM: a novel context switching hidden Markov model for biological sequence analysis. In Jan Schier, Carlos Correia, Ana Fred and Hugo Gamboa. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Neuveden: SciTePress, 2012, p. 208-213. ISBN 978-989-8425-90-4. Available from: https://dx.doi.org/10.5220/0003780902080213.

LEXA, Matej, Karel NEJEDLÝ, Lucie NAVRÁTILOVÁ and Marie BRÁZDOVÁ. Prediction of significant cruciform structures from sequence in topologically constrained DNA - a probabilistic modelling approach. In Jan Schier, Carlos Correia, Ana Fred and Hugo Gamboa. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Neuveden: SciTePress, 2012, p. 124-130. ISBN 978-989-8425-90-4. Available from: https://dx.doi.org/10.5220/0003705701240130.

LEXA, Matej, Tomáš MARTÍNEK, Ivana BURGETOVÁ, Daniel KOPEČEK and Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics. Oxford: Oxford University Press, 2011, vol. 27, No 18, p. 2510-2517. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btr439.

MARTÍNEK, Tomáš and Matej LEXA. Architecture Model for Approximate Tandem Repeat Detection. In 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors. Santa Monica, California, US: IEEE CS, 2011, p. 239-242. ISBN 978-1-4577-1290-6. Available from: https://dx.doi.org/10.1109/FCCM.2010.21.

RUDOLFOVÁ, Ivana, Jaroslav ZENDULKA and Matej LEXA. Clustering of Protein Substructures for Discovery of a Novel Class of Sequence-Structure Fragments. In ITBAM 2010 (Information Technology in Bio- and Medical Informatics), LNCS 6266. Heidelberg, DE: Springer Verlag, 2010, p. 94-101. ISBN 978-3-642-15019-7. Available from: https://dx.doi.org/10.1007/978-3-642-15020-3_9.

BURGETOVÁ, Ivana, Jaroslav ZENDULKA and Matej LEXA. Clustering Techniques for Protein Fragments Analysis. Brno, CZ: Publishing house of Brno University of Technology VUTIUM, 2010, 102 pp. ISBN 978-80-214-4207-8.

MARTÍNEK, Tomáš and Matej LEXA. Hardware Acceleration of Approximate Tandem Repeat Detection. In 18th IEEE Symposium on Field-Programmable Custom Computing Machines. Los Alamitos, CA, USA: IEEE Computer Society, 2010, p. 79-86. ISBN 978-0-7695-4056-6.

MARTÍNEK, Tomáš and Matej LEXA. Identification of palindrome-forming sequences. 2010.

MARTÍNEK, Tomáš, Matej LEXA, Daniel KOPEČEK and Ivana BURGETOVÁ. Identification of triplex-forming sequences. 2010.

MARTÍNEK, Tomáš, Matej LEXA and Jan VOŽENÍLEK. Architecture model for approximate palindrome detection. In 2009 IEEE Symposium on Design and Diagnostics of Electronic Circuits and Systems. Liberec: IEEE Computer Society, 2009, p. 90-95. ISBN 978-1-4244-3339-1.

KOSINA, Marcel, Andrea TESHIM, Eva NĚMCOVÁ, Ivo SEDLÁČEK, Ondrej ŠEDO and Matej LEXA. CALCITE MOONMILK AND ITS BACTERIAL ASSOCIATION. In HYDROGEOCHÉMIA 09. Bratislava, Slovensko: Slovenská asociácia hydrogeológov, 2009, 191 pp. ISBN 978-80-969342-5-6.

KOSINA, Marcel, Andrea TESHIM, Eva NĚMCOVÁ, Ivo SEDLÁČEK, Ondrej ŠEDO and Matej LEXA. CALCITE MOONMILK AND ITS BACTERIAL ASSOCIATION. In 17th INTERNATIONAL KARSTOLOGICAL SCHOOL "CLASSICAL KARST" CAVE CLIMATE. 2009.

LEXA, Matej, Václav SNÁŠEL and Ivan ZELINKA. Data-mining protein structure by clustering, segmentation and evolutionary algorithms. In Data Mining: Theoretical Foundations and Applications. Germany: Springer Verlag, 2009, p. 221-248. ISBN 978-3-642-01087-3. Available from: https://dx.doi.org/10.1007/978-3-642-01088-0_10.

TICHÝ, V., Marie BRÁZDOVÁ, T. QUANTE, L. TOGEL, K. WALTER, G. LOSCHER, L. NAVRATILOVA, Matej LEXA, W. DEPPERT and G.V. TOLSTONOG. Mutp53 non-B DNA structure binding to intronic sequences modulates gene expression in U251 cells. In 34th Congress of the Federation-of-European-Biochemical-Societies Prague. 2009. ISSN 1742-464X.

NAVRATILOVA, L., Marie BRAZDOVA, V. TICHY, Miroslav FOJTA, Matej LEXA, I. KYJOVSKY, W. DEPPERT and E. PALEČEK. Recognition of non-canonical DNA structures in genomic DNA sequences by p53 proteins. In 34th Congress of the Federation-of-European-Biochemical-Societies Prague. 2009. ISSN 1742-464X.

MARTÍNEK, Tomáš and Matej LEXA. Hardware Acceleration of Approximate Palindromes Searching. In The International Conference on Field-Programmable Technology. Taipei: IEEE Computer Society, 2008, p. 65-72. ISBN 978-1-4244-2796-3.

TESHIM, Andrea, Ivo SEDLÁČEK, Ludmila TVRZOVÁ, Ondrej ŠEDO, Matej LEXA and Zbyněk ZDRÁHAL. THE USE OF MALDI-TOF MASS SPECTROMETRY WHOLE CELL PROTEIN/PEPTIDE PROFILES FOR IDENTIFICATION OF AEROMONAS SPECIES. In XII. Setkání biochemiků a molekulárních biologů. 2008. ISBN 978-80-210-4526-2.

MARTÍNEK, Tomáš, Matej LEXA, Patrik BECK and Otto FUČÍK. Automatic generation of circuits for approximate string matching. In Proceedings of 2007 IEEE Design and Diagnostics of Electronic Circuits and Systems. Krakow: IEEE Computer Society, 2007, p. 203-208. ISBN 1-4244-1161-0.

LEXA, Matej, Tomáš MARTÍNEK, Patrik BECK, Otto FUČÍK, Giorgio VALLE and Ivano ZARA. Genomic PCR simulation with hardware-accelerated approximate sequence matching. In Proceedings 21st European Conference on Modelling and Simulation. Praha: ECMS, 2007, p. 333-338. ISBN 978-0-9553018-2-7.

TESHIM, Andrea, Ludmila TVRZOVÁ, Ondrej ŠEDO, Matej LEXA, Ivo SEDLÁČEK, Zbyněk ZDRÁHAL and Pavel ŠVEC. The application of MALDI MS whole-cell profiles of the genus Pseudomonas. In Connections between Collections. 2007. ISBN 978-3-00-022417-1.

TESHIM, Andrea, Ludmila TVRZOVÁ, Ivo SEDLÁČEK, Ondrej ŠEDO, Zbyněk ZDRÁHAL and Matej LEXA. Využití MALDI-MS celobuněčných profilů při charakterizaci bakterií rodu Aeromonas (The application of MALDI MS whole-cell profiles of the genus Aeromonas). In Tomáškovy dny mladých mikrobiologů. 2007.

MARTÍNEK, Tomáš, Matej LEXA, Jan KOŘENEK and Otto FUČÍK. A flexible technique for the automatic design for approximate string matching architectures. In Proceedings of 2006 IEEE Design and Diagnostics of Electronic Circuits and Systems Workshop. Praha: IEEE Computer Society, 2006, p. 83-84. ISBN 1424401844.

LEXA, Matej. FOBIA. 2006.

ŠEDO, Ondrej, Andrea VÁVROVÁ, Matej LEXA, Ludmila TVRZOVÁ and Zbyněk ZDRÁHAL. Chemotaxonomic Characterisation of Pseudomonads by MALDI-TOF MS. In 17th International Mass Spectrometry Conference Abstract Book. 2006.

VÁVROVÁ, Andrea, Ludmila TVRZOVÁ, Zbyněk ZDRÁHAL, Ondrej ŠEDO, Matej LEXA and Pavel ŠVEC. Využití MALDI-MS pro identifikaci Pseudomonas spp. (The use of MALDI-MS for typing Pseudomonas spp.). In Tomáškovy dny mladých mikrobiologů. 2006.

CAMPAGNA, D, C ROMUALDI, N VITULO, Micky DEL-FAVERO, Matej LEXA, N CANNATA and G VALLE. RapH and RapD: two indexes designed for de novo identification of repeats in whole. In BITS Meeting 2005. 2005.

HUDÍK, Tomáš and Matej LEXA. Segmentation of texts and biological sequences into lexical and structural units using a machine-learning approach. In Proceedings of the 1st International Summer School on Computational Biology. Brno: L. Dušek, L., J. Hřebíček, L. Jarkovský, 2005, p. 50-56, 8 pp. ISBN 80-210-3907-8.

TOSATTO, S.C.E., O. BORTOLAMI, A. CESTARO, G. COZZA, Matej LEXA, S. TOPPO, G. VALLE and S. MORO. An Integrated Approach to the Prediction of Protein Structure and Function. In Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. 2004, p. A30.

LEXA, Matej and Giorgio VALLE. Combining rapid word searches with segment-to-segment alignment for sensitive similarity detection, domain identification and structural modelling. In BITS 2004 Bioinformatics Italian Society Meeting, March 26-27. Padova: BITS, 2004, p. S66. ISSN 1471-2105.

CAMPAGNA, Davide, Chiara ROMUALDI, Nicola VITULO, Micky DEL FAVERO, Matej LEXA, Nicola CANNATA and Giorgio VALLE. RAP: a new computer program for de novo identification of repeated sequences in whole genomes. Bioinformatics. Oxford: Oxford University Press, 2004, vol. 20, p. 582-588, 9 pp. ISSN 1367-4803.

HORÁK, Jakub and Matej LEXA. Dvoukomponentni systemy: regulatory odpovedi a prenos signalu u Arabidopsis thaliana (Two-component systems: response regulators and signal transduction in Arabidopsis thaliana). Biologické listy. Praha: ÚMG AV ČR, 2003, vol. 67, No 4, p. 297-317. ISSN 0366-0486.

LEXA, Matej, Todor Nikolaev GENKOV, Jiří MALBECK, Ivana MACHÁČKOVÁ and Břetislav BRZOBOHATÝ. Dynamics of Endogenous Cytokinin Pools in Tobacco Seedlings: A Modelling Approach. Annals of Botany. Oxford: Oxford University Press, 2003, vol. 91, No 5, p. 585-597. ISSN 0305-7364.

HORÁK, Jakub, Břetislav BRZOBOHATÝ and Matej LEXA. Molecular and Physiological Characterisation of an Insertion Mutant in the ARR21 Putative Response Regulator Gene from Arabidopsis thaliana. Plant Biology. Stuttgart: Thieme, Georg Thieme Verlag, 2003, vol. 5, No 3, p. 249-254, 10 pp. ISSN 1435-8603.

LEXA, Matej and Giorgio VALLE. PRIMEX: rapid identification of oligonucleotide matches in whole genomes. Bioinformatics. Oxford: Oxford University Press, 2003, vol. 19, No 18, p. 2486-2488. ISSN 1367-4803.

LEXA, Matej, Ivano ZARA and Giorgio VALLE. PRIMEX 1.0 and VPCR 2.0: Processing genomic sequence data for efficient and accurate simulation of PCR reactions with genomic DNA as template. 2003.

MIRA-RODADO, Virtudes, Uta SWEERE, Matej LEXA, Jakub HORÁK, Erzsebet FEJES, Ferenc NAGY, Eberhard SCHÄFER and Klaus HARTER. A His-to-Asp phosphorelay modifies the activity of ARR4 on phytochrome signaling. In XIII International Conference on Arabidopsis Research. Sevilla, Spain: CSIC, Madrid, 2002, p. 421.

GENKOV, Todor Nikolaev, Jaroslava DUBOVÁ, Jianchun GUO, Alena REKOVÁ, Eliška NEJEDLÁ, Matej LEXA, Jan NEJEDLÍK, Jiří MALBECK, Martin VÁGNER, Ian MOORE and Břetislav BRZOBOHATÝ. Distinct responses to activation of a cytokinin biosynthesis gene, ipt, in tobacco and Arabidopsis seedling development. In 13th Congress of the Federation of European Societies of Plant Physiology, Hersonissos, Heraklion, Crete, Greece, 2-6 September 2002, Book of Abstracts. 2002.

LEXA, Matej, Todor Nikolaev GENKOV and Břetislav BRZOBOHATÝ. Inhibitory effects of elevated endogenous cytokinins on nitrate reductase in ipt-expressing tobacco are eliminated by short-term exposure to benzyladenine. PHYSIOLOGIA PLANTARUM. Copenhagen: Munksgaard, 2002, vol. 115, No 2, p. 284-290. ISSN 0031-9317.

GENKOV, Todor Nikolaev, Jaroslava DUBOVÁ, Jianchun GUO, Alena REKOVÁ, Eliška NEJEDLÁ, Matej LEXA, Jan NEJEDLÍK, Jiří MALBECK, Martin VÁGNER, Ian MOORE and Břetislav BRZOBOHATÝ. Tobacco and Arabidopsis seedling development upon activation of ipt, a cytokinin biosynthesis gene. 2002.

GOLTSEV, Vasiliij, Todor Nikolaev GENKOV, Matej LEXA and Iordanka IVANOVA. Effect of benzyladenine, 4-PU-30 and thidiazuron on millisecond delayed and prompt chlorophyll fluorescence of Dianthus caryophyllus L. axillary buds cultured in vitro. Scientia Horticulturae. Amsterdam: Elsevier, 2001, vol. 89, No 1, p. 41-55. ISSN 0304-4238.

LEXA, Matej, Jakub HORÁK, Julie Olegivna ROTKOVSKÁ and Břetislav BRZOBOHATÝ. Insertional Mutants in Arabidopsis Response Regulator Genes (Insertional Mutants in Arabidopsis Response Regulator Genes.). In 17th International Conference on Plant Growth Substances, Brno, Czech Republic, July 1-6, 2001, Abstracts. Brno: Mendel University of Agriculture and Forestry, Brno, 2001, p. 148. ISBN 80-7157-518-6.

LEXA, Matej, Todor Nikolaev GENKOV and Břetislav BRZOBOHATÝ. Nitrate Reductase Activity in ipt-Expressing Tobacco. In 17th International Conference on Plant Growth Substances, Brno, Czech Republic, July 1-6, 2001, Abstracts. Brno: Mendel University of Agriculture and Forestry, Brno, 2001, p. 189. ISBN 80-7157-518-6.

LEXA, Matej, Jakub HORÁK and Břetislav BRZOBOHATÝ. Virtual PCR. Bioinformatics. Oxford: Oxford University Press, 2001, vol. 17, No 2, p. 192-193. ISSN 1367-4803.

LEXA, Matej and Břetislav BRZOBOHATÝ. Identifikace inzerčních mutací v ARR genech dvoukomponentního systému u Arabidopsis thaliana metodami reverzní genetiky (Reverse genetic approach to identification of insertional mutants of two-component system ARR genes in Arabidopsis thaliana). In Biochemie a molekulární biologie na prahu nového tisíciletí. IV. pracovní setkání biochemiků a molekulárních biologů. Brno: Masarykova univerzita, 2000, p. 55. ISBN 80-210-2266-3.

LEXA, Matej and John M. CHEESEMAN. Příjem dusíku a růst recipročních štěpů hráchu odrůdy Juneau a mutantů A317 s nízkou aktivitou nitrátreduktázy (Nitrogen uptake and growth of reciprocal grafts of wild-type and mutant pea plants (Pisum sativum L., var. Juneau) with low nitrate reductase activity). In Biochemie a molekulární biologie na prahu nového tisíciletí. IV. pracovní setkání biochemiků a molekulárních biologů. Brno: Masarykova univerzita, 2000, p. 21. ISBN 80-210-2266-3.

LEXA, Matej and John CHEESEMAN. Studium lokalizace asimilace dusičnanů v rostlinách s využitím klasických a molekulárně biologických metod (Classical and molecular methods used in the studies of nitrate assimilation site in plants). In Biochemie a molekulární biologie na prahu nového tisíciletí. IV. pracovní setkání biochemiků a molekulárních biologů. Brno: Masarykova Univerzita, 2000, p. 20-21. ISBN 80-210-2266-3.

LEXA, Matej and John M. CHEESEMAN. Genetic manipulation of the location of nitrate reduction and its effects on plant growth. In Plant Nutrition - Molecular Biology and Genetics. Dordrecht: Kluwer Academic Publishers, 1999, p. 59-63. ISBN 0-7923-5716-7.

LEXA, Matej. The effect of the site of nitrogen assimilation on plant growth. Urbana, Illinois: University of Illinois at Champaign-Urbana, 1999, 171 pp.

LEXA, Matej and John M. CHEESEMAN. Growth and nitrogen relations in reciprocal grafts of wild-type and nitrate reductase-deficient mutants of pea (Pisum sativum L. var. Juneau). Journal of Experimental Botany. Oxford: Oxford University Press, 1997, vol. 48, No 311, p. 1241-1250. ISSN 0022-0957.

LEXA, Matej. Aktivita nitrátreduktázy počas skorej ontogenézy listov slnečnice (Helianthus annuus L.) a jej podiel na asimilácii dusíka (Nitrate reductase activity during early ontogenesis of sunflower leaves (Helianthus annuus L.) and its share on nitrate assimilation). In Vedecké práce Výskumného ústavu závlahového hospodárstva v Bratislave. Bratislava: VÚZH, 1996, p. 101-111. ISBN 80-85755-02-5.

LEXA, Matej and John M CHEESEMAN. Biomass and nitrogen partitioning in pea chimeras with different nitrate reductase activities in shoots and root. Plant Physiology. USA: American Society of Plant Physiologists, 1996, vol. 111, 2 Suppl, p. 613. ISSN 0032-0889.

CHEESEMAN, John M. and Matej LEXA. Gas exchange: models and measurements. In Photosynthesis and the environment. Dordrecht: Kluwer, 1996, p. 223-240. Advances in Photosynthesis, Volume 5. ISBN 0-7923-4316-6.

CHEESEMAN, John M., Roberto BARREIRO and Matej LEXA. Plant growth modelling and the integration of shoot and root activities without communicating messengers: Opinion. Plant and Soil. Dordrecht: Kluwer, 1996, vol. 185, No 1, p. 51-64. ISSN 0032-079X.

LEXA, Matej and John M CHEESEMAN. Biomass and nitrogen partitioning in pea chimeras with different nitrate reductase activities in shoots and roots. Plant Physiology. USA: American Society of Plant Physiologists, 1995, vol. 108, 2 Suppl, p. 149. ISSN 0032-0889.

LEXA, Matej and John M CHEESEMAN. Multimedia software for teaching photosynthesis at an introductory level. Plant Physiology. USA: American Society of Plant Physiologists, 1995, vol. 108, 2 Suppl, p. 52. ISSN 0032-0889.

LEXA, Matej and John M. CHEESEMAN. Simulačné modely fotosyntézy a ich vzťah k problémom vodného režimu rastlín (Photosynthesis simulation models and their relation to problems of plant water regime). In Vedecké práce Výskumného ústavu závlahového hospodárstva v Bratislave. Bratislava: VÚZH, 1994, p. 105-117. ISBN 80-901172-1-X.

LEXA, Matej and John M CHEESEMAN. The role of nitrate reductase in nitrogen assimilation of expanding leaves of sunflower (Helianthus annuus L.) grown on nitrate nitrogen. Plant Physiology. USA: American Society of Plant Physiologists, 1993, vol. 102, 1 Suppl, p. 56. ISSN 0032-0889.

GREENHALGH, David and Matej LEXA. Statistical software reviews: DYMO version 1.0. Applied Statistics. 1992, vol. 41, No 2, p. 434-435. ISSN 0035-9254.

RÚČKA, Michal and Matej LEXA. Modelovanie zmien obsahu dusíka v biomase ozimnej pšenice (Modelling the changes in nitrogen content in winter wheat biomass). Rostlinná Výroba. Praha, 1991, vol. 37, No 11, p. 905-909.

LEXA, Matej. Modelovanie produkčného procesu ozimnej pšenice z hľadiska utilizácie živín N, P a K (Modelling of the production process of winter wheat as affected by N, P and K utilization). Nitra: VŠP, 1988, 46 pp.