doc. Ing. Matej Lexa, Ph.D.

Curriculum vitae

Name, first names, scientific degrees

• Matej Lexa
  Born Sep 2, 1966 in Bratislava, Czechoslovakia
  Married

Department/Faculty/University

• Masaryk University Brno
  Faculty of Informatics
  Department of Information Technology
  Botanická 68a
  60200 Brno
  Czech Republic

Function, current position

• associate professor

Education and academic qualifications

• 1999: university, Plant Biology, PhD, "The effect of the site of nitrogen assimilation on plant growth.", University of Illinois at Champaign-Urbana, USA
• 1995: university, Plant Biology, MS, University of Illinois at Champaign-Urbana, USA
• 1988: university, agronomy, Ing., "Modelling the winter wheat production process as influenced by N, P and K utilization.:, VŠP Nitra, Czechoslovakia
• 1984: secondary, Gymnázium A. Markuša, ČA 18, Bratislava, Czechoslovakia
• 1980: elementary

Professional experience

• 2004->: Masaryk University Brno, Faculty of Informatics, assistant professor
• 1998-2004: Masaryk University Brno, Faculty of Science, scientist
• 1992-1997: University of Illinois at Champaign-Urbana, USA, teaching and research assistant
• 1990-1998: Irrigation Research Institute, Bratislava, scientist
• 1988-1990: Research Institute of Soil Science and Plant Nutrition, Bratislava, scientist

Teaching activities

• 2005->: Bioinformatics I and II
• 2004: Bioinformatics Seminar
• 2000-2003: Laboratory of Plant Genomics
• 2000-2002: Thesis
• 1992-1995: Plant Biology 100

Research activities

• 2008: GACR, "In vitro and in silico identification of non-canonical DNA structures in genomic sequences"
• 2002: University of Padova, "Virtual PCR - simulation of the PCR reaction using genomic sequences as templates"
• 1999: GACR, "The role of nitrate-inducible bacterial response regulator homologs in Arabidopsis thaliana"
• 1998: USDA, "Nitrate regulated processes in Arabidopsis thaliana.", (John M. Cheeseman)
• 1991: JDC International Developmenmt Program, "A greenhouse tomato management decision model.", (Beni Bar-Yosef)

Professional stays abroad

• 2006: University of Ljubljana, Ljubljana, Slovenia, machine learning and bioinformatics
• 2002-2004: University of Padova, Padova, Italy, developing bioinformatic tools for molecular biology, genomics and proteomics
• 2000: University of Illinois, Champaign-Urbana, IL, USA, characterization of nitrate-reductase transformants
• 1999: Oxford University, Oxford, UK, screening for insertional mutants in Arabidopsis
• 1991: Soil & Water Institute, ARO, Bet-Dagan, Israel, modelling of drip irrigation
• 1990: Horticulture Research International, Wellesbourne, UK, modelling of crop growth
• 1990: University of Helsinki, modelling of crop growth

Non-university activities

• 2006->: International Society of Computational Biology, member
• 2005->: FOBIA, section of the Czech Society for Biochemistry and Mol. Biology, member
• 2002-2003: SigmaXi, member
• 1993-1998: American Society of Plant Physiologists, member

Most significant professional accomplishments

• 1998, John R. Laughnan Award
• ECMS 2007, Simulation in Molecular Biology track, programming chair
• FOBIA 2006 Annual Meeting, chair

Major publications

• SCHWARZEROVÁ, Jana, Martin HURTA, Vojtěch BARTOŇ, Matej LEXA, Dirk WALTHER, Valentine PROVAZNÍK a Wolfram WECKWERTH. A perspective on genetic and polygenic risk scores - advances and limitations and overview of associated tools. Briefings in Bioinformatics. OXFORD: Oxford University Press, 2024, roč. 25, č. 3, s. 1-11. ISSN 1467-5463. Dostupné z: https://dx.doi.org/10.1093/bib/bbae240. URL info
• HORVÁTH, Jakub, Pavel JEDLIČKA, Marie KRÁTKÁ, Zdeněk KUBÁT, Eduard KEJNOVSKÝ a Matej LEXA. Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning. BIODATA MINING. ENGLAND: SpringerNature, 2024, roč. 17, č. 1, s. 57-82. ISSN 1756-0381. Dostupné z: https://dx.doi.org/10.1186/s13040-024-00410-z. URL info
• BREJOVÁ, Bronislava, Lucie CIENCIALOVÁ, Martin HOLEŇA, Róbert JAJCAY, Tatiana JAJCAYOVÁ, Matej LEXA, František MRÁZ, Dana PARDUBSKÁ a Martin PLÁTEK. ITAT’23: Information technologies – Applications and Theory, September 22–26, 2023, Tatranské Matliare, Slovakia. 2023. URL info
• LEXA, Matej, Monika ČECHOVÁ, Son Hoang NGUYEN, Pavel JEDLIČKA, Viktor TOKAN, Zdeněk KUBÁT, Roman HOBZA a 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, roč. 38, č. 16, s. 4030-4032. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btac442. URL info
• LABUDOVÁ, Dominika, Jiří HON a Matej LEXA. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics. Oxford: Oxford University Press, 2020, roč. 36, č. 8, s. 2584-2586. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btz928. URL info
• LEXA, Matej, Pavel JEDLICKA, Ivan VANÁT, Michal ČERVEŇANSKÝ a Eduard KEJNOVSKÝ. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. Bioinformatics. OXFORD: OXFORD UNIV PRESS, 2020, roč. 36, č. 20, s. 4991-4999. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btaa632. URL info
• JEDLIČKA, Pavel, Matej LEXA, Ivan VANÁT, Eduard KEJNOVSKÝ a 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, roč. 10, č. 1, s. 1-14. ISSN 1759-8753. Dostupné z: https://dx.doi.org/10.1186/s13100-019-0186-z. URL info
• TOKAN, Viktor, Janka PUTEROVÁ, Matej LEXA a 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, roč. 19, 06 03 2018, s. 184-194. ISSN 1471-2164. Dostupné z: https://dx.doi.org/10.1186/s12864-018-4563-7. URL info
• LEXA, Matej, Radovan LAPÁR, Pavel JEDLIČKA, Ivan VANÁT, Michal ČERVEŇANSKÝ a 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, s. 2776-2778. ISBN 978-1-5386-5488-0. Dostupné z: https://dx.doi.org/10.1109/BIBM.2018.8621071. info
• HON, Jiří, Tomáš MARTÍNEK, Jaroslav ZENDULKA a Matej LEXA. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics. Oxford: Oxford University Press, 2017, roč. 33, č. 21, s. 3373-3379. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btx413. Hon et al. (2017) info
• KREJČÍ, Adam, TR HUPP, Matej LEXA, Bořivoj VOJTĚŠEK a 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, roč. 32, č. 1, s. 9-16. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btv522. info
• 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 a Matej ADÁMIK. p53 Specifically Binds Triplex DNA In Vitro and in Cells. PLOS ONE. Public Library of Science, 2016, roč. 11, č. 12, s. "e0167439", 25 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0167439. URL URL info
• KEJNOVSKÝ, Eduard, Viktor TOKAN a Matej LEXA. Transposable elements and G-quadruplexes. Chromosome Research. Springer Netherlands, 2015, roč. 23, č. 3, s. 615-623. ISSN 0967-3849. Dostupné z: https://dx.doi.org/10.1007/s10577-015-9491-7. URL info
• LEXA, Matej, Eduard KEJNOVSKÝ, Pavlína ŠTEFLOVÁ, Helena KONVALINOVÁ, Michaela VORLÍČKOVÁ a Boris VYSKOT. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons. Nucleic Acids Research. Oxford: Oxford University Press, 2014, roč. 42, č. 2, s. 968-978. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkt893. URL info
• LEXA, Matej a 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, s. 259-264. ISBN 978-989-758-012-3. Dostupné z: https://dx.doi.org/10.5220/0004915002590264. URL info
• LEXA, Matej, Tomáš MARTÍNEK a 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, s. 80-88. ISBN 978-989-758-012-3. Dostupné z: https://dx.doi.org/10.5220/0004824100800088. URL info
• KEJNOVSKÝ, Eduard a Matej LEXA. Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators. Mobile Genetic Elements. Landes Bioscience, 2014, roč. 4, č. 1, s. "e28084", 4 s. ISSN 2159-256X. Dostupné z: https://dx.doi.org/10.4161/mge.28084. URL info
• LEXA, Matej, Pavlina STEFLOVA, Tomáš MARTÍNEK, Michaela VORLÍČKOVÁ, Boris VYSKOT a Eduard KEJNOVSKÝ. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics. London: BioMed Central Ltd, 2014, roč. 15, č. 1, s. 1032-1043. ISSN 1471-2164. Dostupné z: https://dx.doi.org/10.1186/1471-2164-15-1032. URL info
• HON, Jiří, Tomáš MARTÍNEK, Kamil RAJDL a 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, roč. 29, č. 15, s. 1900-1901. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btt299. URL info
• ŠTEFLOVÁ, Pavlína, Viktor TOKAN, Ivan VOGEL, Matej LEXA, Jiří MACAS, Petr NOVAK, Roman HOBZA, Boris VYSKOT a 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, roč. 5, č. 4, s. 769-782. ISSN 1759-6653. Dostupné z: https://dx.doi.org/10.1093/gbe/evt049. URL info
• KOSINA, Marcel, Miloš BARTÁK, Ivana MAŠLAŇOVÁ, Andrea VÁVROVÁ PASCUTTI, Ondrej ŠEDO, Matej LEXA a Ivo SEDLÁČEK. Pseudomonas prosekii sp. nov., a Novel Psychrotrophic Bacterium from Antarctica. Current Microbiology. Springer US, 2013, roč. 67, č. 6, s. 637-646. ISSN 0343-8651. Dostupné z: https://dx.doi.org/10.1007/s00284-013-0406-6. URL info
• BRÁZDOVÁ, Marie, Lucie NAVRATILOVA, Vlastimil TICHÝ, Kateřina NĚMCOVÁ, Matej LEXA, Roman HRSTKA, Petr PECINKA, Matej ADÁMIK, Bořivoj VOJTĚŠEK, Emil PALECEK, Wolfgang DEPPERT a 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, roč. 8, č. 3, s. "e59567", 17 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0059567. Brazdova et al. 2013 info
• LEXA, Matej, Tomáš MARTÍNEK, Ivana BURGETOVÁ, Daniel KOPEČEK a Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics. Oxford: Oxford University Press, 2011, roč. 27, č. 18, s. 2510-2517. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btr439. URL info
• MARTÍNEK, Tomáš a 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, s. 79-86. ISBN 978-0-7695-4056-6. info
• RUDOLFOVÁ, Ivana, Jaroslav ZENDULKA a 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, s. 94-101. ISBN 978-3-642-15019-7. Dostupné z: https://dx.doi.org/10.1007/978-3-642-15020-3_9. info
• LEXA, Matej, Václav SNÁŠEL a Ivan ZELINKA. Data-mining protein structure by clustering, segmentation and evolutionary algorithms. In Data Mining: Theoretical Foundations and Applications. Germany: Springer Verlag, 2009, s. 221-248. ISBN 978-3-642-01087-3. Dostupné z: https://dx.doi.org/10.1007/978-3-642-01088-0_10. URL info
• MARTÍNEK, Tomáš, Matej LEXA a 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, s. 90-95. ISBN 978-1-4244-3339-1. info
• MARTÍNEK, Tomáš a Matej LEXA. Hardware Acceleration of Approximate Palindromes Searching. In The International Conference on Field-Programmable Technology. Taipei: IEEE Computer Society, 2008, s. 65-72. ISBN 978-1-4244-2796-3. info
• LEXA, Matej, Tomáš MARTÍNEK, Patrik BECK, Otto FUČÍK, Giorgio VALLE a Ivano ZARA. Genomic PCR simulation with hardware-accelerated approximate sequence matching. In Proceedings 21st European Conference on Modelling and Simulation. Praha: ECMS, 2007, s. 333-338. ISBN 978-0-9553018-2-7. info
• CAMPAGNA, Davide, Chiara ROMUALDI, Nicola VITULO, Micky DEL FAVERO, Matej LEXA, Nicola CANNATA a Giorgio VALLE. RAP: a new computer program for de novo identification of repeated sequences in whole genomes. Bioinformatics. Oxford: Oxford University Press, 2004, roč. 20, s. 582-588, 9 s. ISSN 1367-4803. URL info
• HORÁK, Jakub a Matej LEXA. Dvoukomponentni systemy: regulatory odpovedi a prenos signalu u Arabidopsis thaliana. Biologické listy. Praha: ÚMG AV ČR, 2003, roč. 67, č. 4, s. 297-317. ISSN 0366-0486. info
• LEXA, Matej, Todor Nikolaev GENKOV, Jiří MALBECK, Ivana MACHÁČKOVÁ a Břetislav BRZOBOHATÝ. Dynamics of Endogenous Cytokinin Pools in Tobacco Seedlings: A Modelling Approach. Annals of Botany. Oxford: Oxford University Press, 2003, roč. 91, č. 5, s. 585-597. ISSN 0305-7364. info
• LEXA, Matej a Giorgio VALLE. PRIMEX: rapid identification of oligonucleotide matches in whole genomes. Bioinformatics. Oxford: Oxford University Press, 2003, roč. 19, č. 18, s. 2486-2488. ISSN 1367-4803. Primex server info
• LEXA, Matej, Todor Nikolaev GENKOV a 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, roč. 115, č. 2, s. 284-290. ISSN 0031-9317. info
• GOLTSEV, Vasiliij, Todor Nikolaev GENKOV, Matej LEXA a 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, roč. 89, č. 1, s. 41-55. ISSN 0304-4238. info
• LEXA, Matej, Jakub HORÁK a Břetislav BRZOBOHATÝ. Virtual PCR. Bioinformatics. Oxford: Oxford University Press, 2001, roč. 17, č. 2, s. 192-193. ISSN 1367-4803. VPCR Homepage info
• LEXA, Matej a 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, s. 59-63. ISBN 0-7923-5716-7. info
• LEXA, Matej a 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, roč. 48, č. 311, s. 1241-1250. ISSN 0022-0957. URL info
• CHEESEMAN, John M., Roberto BARREIRO a Matej LEXA. Plant growth modelling and the integration of shoot and root activities without communicating messengers: Opinion. Plant and Soil. Dordrecht: Kluwer, 1996, roč. 185, č. 1, s. 51-64. ISSN 0032-079X. info
• CHEESEMAN, John M. a Matej LEXA. Gas exchange: models and measurements. In Photosynthesis and the environment. Dordrecht: Kluwer, 1996, s. 223-240. Advances in Photosynthesis, Volume 5. ISBN 0-7923-4316-6. info
• RÚČKA, Michal a Matej LEXA. Modelovanie zmien obsahu dusíka v biomase ozimnej pšenice. Rostlinná Výroba. Praha, 1991, roč. 37, č. 11, s. 905-909. info

2023/07/03