Publications

• 2021

  PUTEROVÁ, J.; MARTÍNEK, T. digIS: Towards detecting distant and putative novel insertion sequences in prokaryotic genomes. BMC BIOINFORMATICS, 2021, vol. 22, no. 258, p. 1-20. ISSN: 1471-2105.
  Detail | WWW

  HON, J.; MARUŠIAK, M.; MARTÍNEK, T.; KUNKA, A.; ZENDULKA, J.; BEDNÁŘ, D.; DAMBORSKÝ, J. SoluProt: prediction of soluble protein expression in Escherichia coli. BIOINFORMATICS, 2021, vol. 37, no. 1, p. 23-28. ISSN: 1367-4803.
  Detail | WWW

• 2020

  HON, J.; BORKO, S.; ŠTOURAČ, J.; PROKOP, Z.; BEDNÁŘ, D.; ZENDULKA, J.; MARTÍNEK, T.; DAMBORSKÝ, J. EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic Acids Research, 2020, vol. 48, no. 1, p. 104-109. ISSN: 1362-4962.
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• 2019

  SUMBALOVÁ, L.; MARTÍNEK, T.; BEDNÁŘ, D.; DAMBORSKÝ, J. Prediction of Critical Residues in Protein Structures using Amino Acid Networks. ISMB/ECCB 2019. Basilej: 2019. p. 0-0.
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  HON, J.; BORKO, S.; MARUŠIAK, M.; MARTÍNEK, T.; BEDNÁŘ, D.; DAMBORSKÝ, J. EnzymeMiner: Web Server for Automated Mining and Annotation of Soluble Enzymes in Genomic Databases. ISMB/ECCB 2019. Basilej: 2019. p. 0-0.
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• 2018

  PUTEROVÁ, J.; MARTÍNEK, T. digIS: automated pipeline for detecting distant, novel insertion sequence elements in prokaryotes. Data & Knowledge 2018. Brno: Brno University of Technology, 2018. p. 1-5. ISBN: 978-80-214-5679-2.
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  HON, J.; MARUŠIAK, M.; MARTÍNEK, T.; ZENDULKA, J.; BEDNÁŘ, D.; DAMBORSKÝ, J. SoluProt: Prediction of Protein Solubility. DAZ & WIKT 2018 Proceedings. Brno: Brno University of Technology, 2018. p. 261-265. ISBN: 978-80-214-5679-2.
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  SUMBALOVÁ, L.; ŠTOURAČ, J.; MARTÍNEK, T.; BEDNÁŘ, D.; DAMBORSKÝ, J. HotSpot Wizard 3.0: Web Server for Automated Design of Mutations and Smart Libraries based on Sequence Input Information. Nucleic Acids Research, 2018, vol. 46, no. 1, p. 356-362. ISSN: 1362-4962.
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  MUSIL, M.; MARTÍNEK, T.; ZENDULKA, J. FireProt: web server for automated design of thermostable proteins. DAZ & WIKT 2018 Proceedings. Brno: 2018. p. 1-4.
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• 2017

  KUPKOVÁ, K.; PROVAZNÍK, I.; SEDLÁŘ, K.; HON, J.; MARTÍNEK, T.; ZENDULKA, J. Visualization of Nanopore Sequencing Data in Metagenomics. Praha: 2017. p. 1 (1 s.).
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  PUTEROVÁ, J.; RAZUMOVA, O.; MARTÍNEK, T.; ALEXANDROV, O.; DIVASHUK, M.; KUBÁT, Z.; HOBZA, R.; KARLOV, G.; KEJNOVSKÝ, E. Satellite DNA and Transposable Elements in Seabuckthorn ( Hippophae rhamnoides ), a Dioecious Plant with Small Y and Large X Chromosomes. GENOME BIOL EVOL, 2017, vol. 9, no. 1, p. 197-212. ISSN: 1759-6653.
  Detail | WWW | Full text in the Digital Library

  MUSIL, M.; ŠTOURAČ, J.; BENDL, J.; BREZOVSKÝ, J.; PROKOP, Z.; ZENDULKA, J.; MARTÍNEK, T.; BEDNÁŘ, D.; DAMBORSKÝ, J. FireProt: web server for automated design of thermostable proteins. Nucleic Acids Research, 2017, vol. 45, no. 1, p. 393-399. ISSN: 1362-4962.
  Detail | WWW

  HON, J.; LEXA, M.; MARTÍNEK, T.; ZENDULKA, J. pqsfinder: imperfection-tolerant identification of potential quadruplex-forming sequences in R. ISMB/ECCB 2017. Praha: 2017. p. 0-0.
  Detail

  HON, J.; MARTÍNEK, T.; ZENDULKA, J.; LEXA, M. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. BIOINFORMATICS, 2017, vol. 33, no. 21, p. 3373-3379. ISSN: 1367-4803.
  Detail | WWW

• 2016

  BRÁZDOVÁ, M.; TICHÝ, V.; HELMA, R.; BAŽANTOVÁ, P.; POLÁŠKOVÁ, A.; KREJČÍ, A.; PETR, M.; NAVRÁTILOVÁ, L.; TICHÁ, O.; NEJEDLÝ, K.; BENNINK, M.; SUBRAMANIAM, V.; BÁBKOVÁ, Z.; MARTÍNEK, T.; LEXA, M.; ADÁMIK, M. p53 Specifically Binds Triplex DNA In Vitro and in Cells. PLOS ONE, 2016, vol. 11, no. 12, p. 1-25. ISSN: 1932-6203.
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• 2014

  LEXA, M.; ŠTEFLOVÁ, P.; MARTÍNEK, T.; VORLÍČKOVÁ, M.; VYSKOT, B.; KEJNOVSKÝ, E. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC GENOMICS, 2014, vol. 15, no. 1032, p. 1-12. ISSN: 1471-2164.
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  POLČÁK, L.; HRANICKÝ, R.; MARTÍNEK, T. On Identities in Modern Networks. The Journal of Digital Forensics, Security and Law, 2014, vol. 2014, no. 2, p. 9-22. ISSN: 1558-7215.
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  LEXA, M.; MARTÍNEK, T.; BRÁZDOVÁ, M. Uneven distribution of potential triplex sequences in the human genome: In silico study using the R/Bioconductor package triplex. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Angers: SciTePress - Science and Technology Publications, 2014. p. 80-88. ISBN: 978-989-758-012-3.
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• 2013

  BRÁZDOVÁ, M.; MARTÍNEK, T.; LEXA, M. In silico search for secondary structures in p53 target genes using R/Bioconductor. ITAT 2013: Information Technologies - Applications and Theory. Donovaly: CreativeSpace Independent Publishing Platform, 2013. p. 42-46. ISBN: 978-1-4909-5208-6.
  Detail

  HON, J.; MARTÍNEK, T.; RAJDL, K.; LEXA, M. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. BIOINFORMATICS, 2013, vol. 29, no. 15, p. 1900-1901. ISSN: 1367-4803.
  Detail

• 2011

  MARTÍNEK, T.; LEXA, M. Architecture Model for Approximate Tandem Repeat Detection. 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors. Santa Monica, California: IEEE Computer Society, 2011. p. 239-242. ISBN: 978-1-4577-1290-6.
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  LEXA, M.; MARTÍNEK, T.; BURGETOVÁ, I.; KOPEČEK, D.; BRÁZDOVÁ, M. A dynamic programming algorithm for identification of triplex-forming sequences. BIOINFORMATICS, 2011, vol. 27, no. 18, p. 2510-2517. ISSN: 1367-4803.
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• 2010

  MARTÍNEK, T.; LEXA, M. Hardware Acceleration of Approximate Tandem Repeat Detection. IEEE Symposium on Field-Programmable Custom Computing Machines. Charlotte: IEEE Computer Society, 2010. p. 79-86. ISBN: 978-0-7695-4056-6.
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  MARTÍNEK, T. Evaluation of Biological Sequence Similarity Using FPGA Technology. Information Sciences and Technologies Bulletin of the ACM Slovakia, 2010, vol. 2, no. 2, p. 93-102. ISSN: 1338-1237.
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  MARTÍNEK, T.; ŽÁDNÍK, M. Precise Timestamp Generation Module and its Applications in Flow Monitoring. In Networking Studies IV, Selected Technical Reports. Praha: CESNET National Research and Education Network, 2010. p. 45-56. ISBN: 978-80-904173-8-0.
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• 2009

  MARTÍNEK, T. Architektura sběrnice PCI, PCI-X a PCI Express. Sborník příspěvků 35. konference Europen. Plzeň: Česká společnost uživatelů otevřených systémů EurOpen.CZ, 2009. p. 37-50. ISBN: 978-80-86583-17-4.
  Detail

  MARTÍNEK, T.; LEXA, M.; VOŽENÍLEK, J. 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.
  Detail | WWW

• 2008

  MARTÍNEK, T.; KOŠEK, M. NetCOPE: Platform for Rapid Development of Network Applications. In Proc. of 2008 IEEE Design and Diagnostics of Electronic Circuits and Systems Workshop. Bratislava: IEEE Computer Society, 2008. p. 219-224. ISBN: 978-1-4244-2276-0.
  Detail

  MARTÍNEK, T.; LEXA, M. 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.
  Detail | WWW

  MÁLEK, T.; MARTÍNEK, T.; KOŘENEK, J. GICS: Generic Interconnection System. 2008 International Conference on Field Programmable Logic and Applications. Heidelberg: IEEE Computer Society, 2008. p. 263-268. ISBN: 978-1-4244-1960-9.
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• 2007

  TOBOLA, J.; KOTÁSEK, Z.; KOŘENEK, J.; MARTÍNEK, T.; STRAKA, M. Online Protocol Testing for FPGA Based Fault Tolerant Systems. In 10th EUROMICRO Conference on Digital System Design DSD 2007. Lubeck, Germany: IEEE Computer Society, 2007. p. 676-679. ISBN: 0-7695-2978- X.
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  DEDEK, T.; MAREK, T.; MARTÍNEK, T. High Level Abstraction Language as an Alternative to Embeded Processors for Internet Packet Processing in FPGA. In 2007 International Conference on Field Programmable Logic and Applications. Amsterdam: IEEE Computer Society, 2007. p. 648-651. ISBN: 1-4244-1060- 6.
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  SEKANINA, L.; MARTÍNEK, T. Evolving Image Operators Directly in Hardware. In Genetic and Evolutionary Computation for Image Processing and Analysis. EURASIP Book Series on Signal Processing and Communications, Volume 8. New York: Hindawi Publishing Corporation, 2007. p. 93-112. ISBN: 978-977-454-001- 1.
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  MARTÍNEK, T.; LEXA, M.; BECK, P.; FUČÍK, O. Automatic Generation of Circuits for Approximate String Matching. In 2007 IEEE Design and Diagnostics of Electronic Circuits and Systems. Krakow: IEEE Computer Society, 2007. p. 203-208. ISBN: 1-4244-1161- 0.
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  LEXA, M.; MARTÍNEK, T.; BECK, P.; FUČÍK, O.; VALLE, G.; ZARA, I. Genomic PCR simulation with hardware- accelerated approximate sequence matching. In 21st European Conference on Modelling and Simulation. Praha: European Council for Modelling and Simulation, 2007. p. 333-338. ISBN: 978-0-9553018-2- 7.
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  MARTÍNEK, T. Automatizované mapování architektur s proměnným počtem výpočetních elementů. In Počítačové architektury a diagnostika 2007. Česko- slovenský seminář pro studenty doktorandského studia. Plzeň: Západočeská univerzita v Plzni, 2007. p. 77-83. ISBN: 978-80-7043-605- 9.
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• 2006

  MARTÍNEK, T.; LEXA, M.; KOŘENEK, J.; FUČÍK, O. A flexible technique for the automatic design of approximate string matching architectures. In Proc. of 2006 IEEE Design and Diagnostics of Electronic Circuits and Systems Workshop. Praha: IEEE Computer Society, 2006. p. 83-84. ISBN: 1-4244-0184- 4.
  Detail

  ČERNÝ, S.; STRUŽKA, P.; KOŘENEK, J.; MARTÍNEK, T.; KOTÁSEK, Z. FPGA Components in Simulink. In Proceedings of XXVIIIth International Autumn Colloquium ASIS 2006. Ostrava: 2006. p. 158-163. ISBN: 80-86840-26- 3.
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  SEKANINA, L.; MARTÍNEK, T.; GAJDA, Z. Extrinsic and Intrinsic Evolution of Multifunctional Combinational Modules. In 2006 IEEE World Congress on Computational Intelligence. CA: IEEE Computational Intelligence Society, 2006. p. 9676-9683. ISBN: 0-7803-9489- 5.
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  MARTÍNEK, T.; KOŘENEK, J.; NOVOTNÝ, J. Network Monitoring Adaptor for 10Gbps Technology using FPGA. In CESNET Conference 2006 Proceedings. Prague : CESNET, z. s. p. o.: CESNET National Research and Education Network, 2006. p. 143-151. ISBN: 978-80-239-6533- 9.
  Detail

• 2005

  MARTÍNEK, T., SEKANINA, L. An Evolvable Image Filter: Experimental Evaluation of a Complete Hardware Implementation in FPGA. In Evolvable Systems: From Biology to Hardware. LNCS 3637. Berlin: Springer Verlag, 2005. p. 76-85. ISBN: 978-3-540-28736- 0.
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  MARTÍNEK, T. Analýza datových toků s využitím sebe- rekonfigurovatelných automatů. In Sborník příspěvků ze semináře Počítačové Architektury a Diagnostika. Praha: Fakulta elektrotechniky ČVUT, 2005. p. 119-124. ISBN: 80-01-03298- 1.
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  MARTÍNEK, T., ZEMČÍK, P., KOŘENEK, J. FPGA-Based Platform for Network Applications. In Proc. of 8th IEEE Design and Diagnostic of Electronic Circuits and Systems Workshop. Sopron: University of West Hungary, 2005. p. 194-197. ISBN: 9639364487.
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• 2004

  MARTÍNEK, T., KOŘENEK, J., NOVOTNÝ, J. Passive network monitoring adapter intended for 10Gbps technology. In Sborník příspěvků z XXV. konference Europen. Plzeň: Czech Open Systems User' s Group, 2004. p. 55-63. ISBN: 80-86583-07- 4.
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• 2002

  MARTÍNEK, T. Deterministic parallel LR parsing. Proceedings of 8th conference and competition STUDENT EEICT 2002. Brno: Brno University of Technology, 2002. p. 192-194. ISBN: 80-214-2114-2.
  Detail

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