Tomáš Martínek

2021

PUTEROVÁ Janka and MARTÍNEK Tomáš. digIS: Towards detecting distant and putative novel insertion sequences in prokaryotic genomes. BMC Bioinformatics, vol. 22, no. 258, 2021, pp. 1-20. ISSN 1471-2105.
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HON Jiří, MARUŠIAK Martin, MARTÍNEK Tomáš, KUNKA Antonín, ZENDULKA Jaroslav, BEDNÁŘ David and DAMBORSKÝ Jiří. SoluProt: prediction of soluble protein expression in Escherichia coli. Bioinformatics, vol. 37, no. 1, 2021, pp. 23-28. ISSN 1367-4803.
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2020

HON Jiří, BORKO Simeon, ŠTOURAČ Jan, PROKOP Zbyněk, BEDNÁŘ David, ZENDULKA Jaroslav, MARTÍNEK Tomáš and DAMBORSKÝ Jiří. EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic Acids Research, vol. 48, no. 1, 2020, pp. 104-109. ISSN 1362-4962.
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2019

HON Jiří, BORKO Simeon, MARUŠIAK Martin, MARTÍNEK Tomáš, BEDNÁŘ David and DAMBORSKÝ Jiří. EnzymeMiner: Web Server for Automated Mining and Annotation of Soluble Enzymes in Genomic Databases. ISMB/ECCB 2019. Basilej, 2019.
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2018

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

MUSIL Miloš, ŠTOURAČ Jan, BENDL Jaroslav, BREZOVSKÝ Jan, PROKOP Zbyněk, ZENDULKA Jaroslav, MARTÍNEK Tomáš, BEDNÁŘ David and DAMBORSKÝ Jiří. FireProt: web server for automated design of thermostable proteins. Nucleic Acids Research, vol. 45, no. 1, 2017, pp. 393-399. ISSN 1362-4962.
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HON Jiří, MARTÍNEK Tomáš, ZENDULKA Jaroslav and LEXA Matej. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics, vol. 33, no. 21, 2017, pp. 3373-3379. ISSN 1367-4803.
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HON Jiří, LEXA Matej, MARTÍNEK Tomáš and ZENDULKA Jaroslav. pqsfinder: imperfection-tolerant identification of potential quadruplex-forming sequences in R. ISMB/ECCB 2017. Praha, 2017.
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PUTEROVÁ Janka, RAZUMOVA Olga, MARTÍNEK Tomáš, ALEXANDROV Oleg, DIVASHUK Mikhail, KUBÁT Zdeněk, HOBZA Roman, KARLOV Gennady and KEJNOVSKÝ Eduard. Satellite DNA and Transposable Elements in Seabuckthorn ( Hippophae rhamnoides ), a Dioecious Plant with Small Y and Large X Chromosomes. Genome Biology and Evolution, vol. 9, no. 1, 2017, pp. 197-212. ISSN 1759-6653.
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2016

BRÁZDOVÁ Marie, TICHÝ Vlastimil, HELMA Robert, BAŽANTOVÁ Pavla, POLÁŠKOVÁ Alena, KREJČÍ Aneta, PETR Marek, NAVRÁTILOVÁ Lucie, TICHÁ Olga, NEJEDLÝ Karel, BENNINK Martin L., SUBRAMANIAM Vinod, BÁBKOVÁ Zuzana, MARTÍNEK Tomáš, LEXA Matej and ADÁMIK Matej. p53 Specifically Binds Triplex DNA In Vitro and in Cells. PLoS ONE, vol. 11, no. 12, 2016, pp. 1-25. ISSN 1932-6203.
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2014

LEXA Matej, ŠTEFLOVÁ Pavlína, MARTÍNEK Tomáš, VORLÍČKOVÁ Michaela, VYSKOT Boris and KEJNOVSKÝ Eduard. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics, vol. 15, no. 1032, 2014, pp. 1-12. ISSN 1471-2164.
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POLČÁK Libor, HRANICKÝ Radek and MARTÍNEK Tomáš. On Identities in Modern Networks. The Journal of Digital Forensics, Security and Law, vol. 2014, no. 2, pp. 9-22. ISSN 1558-7215.
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LEXA Matej, MARTÍNEK Tomáš and BRÁZDOVÁ Marie. 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, pp. 80-88. ISBN 978-989-758-012-3.
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POLČÁK Libor, MARTÍNEK Tomáš, HRANICKÝ Radek, BÁRTA Stanislav, HOLKOVIČ Martin, FRANKOVÁ Barbora and KRAMOLIŠ Petr. Zákonné odposlechy v moderních sítích - Shrnutí výsledků skupiny pro zákonné odposlechy projektu Moderní prostředky pro boj s kybernetickou kriminalitou na Internetu nové generace. FIT-TR-2014-07, Brno: Faculty of Information Technology BUT, 2014.
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2013

BRÁZDOVÁ Marie, MARTÍNEK Tomáš and LEXA Matej. In silico search for secondary structures in p53 target genes using R/Bioconductor. In: ITAT 2013: Information Technologies - Applications and Theory. Donovaly: CreativeSpace Independent Publishing Platform, 2013, pp. 42-46. ISBN 978-1-4909-5208-6.
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HON Jiří, MARTÍNEK Tomáš, RAJDL Kamil and LEXA Matej. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. Bioinformatics, vol. 29, no. 15, 2013, pp. 1900-1901. ISSN 1367-4803.
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2012

MARTÍNEK Tomáš, KRAMOLIŠ Petr, HOLKOVIČ Martin and POLČÁK Libor. Dynamická identifikace uživatelů v prostředí sítí IPv4 a IPv6. FIT-TR-2012-006, Brno: Faculty of Information Technology BUT, 2012.
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2011

LEXA Matej, MARTÍNEK Tomáš, BURGETOVÁ Ivana, KOPEČEK Daniel and BRÁZDOVÁ Marie. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics, vol. 27, no. 18, 2011, pp. 2510-2517. ISSN 1367-4803.
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MARTÍNEK Tomáš and LEXA Matej. Architecture Model for Approximate Tandem Repeat Detection. In: 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors. Santa Monica, California: IEEE Computer Society, 2011, pp. 239-242. ISBN 978-1-4577-1290-6.
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POLČÁK Libor, KRAMOLIŠ Petr, KAJAN Michal and MARTÍNEK Tomáš. Architektura systému pro zákonné odposlechy. FIT-TR-2011-008, Brno: Faculty of Information Technology BUT, 2011.
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2010

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

MARTÍNEK Tomáš, LEXA Matej and VOŽENÍLEK Jan. Architecture model for approximate palindrome detection. In: 2009 IEEE Symposium on Design and Diagnostics of Electronic Circuits and Systems. Liberec: IEEE Computer Society, 2009, pp. 90-95. ISBN 978-1-4244-3339-1.
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MARTÍNEK Tomáš. Architektura sběrnice PCI, PCI-X a PCI Express. In: Sborník příspěvků 35. konference Europen. Plzeň: Czech Open Systems User's Group, 2009, pp. 37-50. ISBN 978-80-86583-17-4.
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2008

MÁLEK Tomáš, MARTÍNEK Tomáš and KOŘENEK Jan. GICS: Generic Interconnection System. In: 2008 International Conference on Field Programmable Logic and Applications. Heidelberg: IEEE Computer Society, 2008, pp. 263-268. ISBN 978-1-4244-1960-9.
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MARTÍNEK Tomáš and LEXA Matej. Hardware Acceleration of Approximate Palindromes Searching. In: The International Conference on Field-Programmable Technology. Taipei: IEEE Computer Society, 2008, pp. 65-72. ISBN 978-1-4244-2796-3.
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MARTÍNEK Tomáš and KOŠEK Martin. 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, pp. 219-224. ISBN 978-1-4244-2276-0.
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2007

MARTÍNEK Tomáš, LEXA Matej, BECK Patrik and FUČÍK Otto. Automatic Generation of Circuits for Approximate String Matching. In: 2007 IEEE Design and Diagnostics of Electronic Circuits and Systems. Krakow: IEEE Computer Society, 2007, pp. 203-208. ISBN 1-4244-1161-0.
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MARTÍNEK Tomáš. Automatizované Mapování architektur s proměnným počtem výpočetních elementů Automatizované mapování architektur s proměnným počtem výpočetních elementů. In: Počítačové architektury a diagnostika 2007. Česko-slovenský seminář pro studenty doktorandského studia. Plzeň: University of West Bohemia in Pilsen, 2007, pp. 77-83. ISBN 978-80-7043-605-9.
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SEKANINA Lukáš and MARTÍNEK Tomáš. Evolving Image Operators Directly in Hardware. 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, pp. 93-112. ISBN 978-977-454-001-1.
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LEXA Matej, MARTÍNEK Tomáš, BECK Patrik, FUČÍK Otto, VALLE Giorgio and ZARA Ivano. 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, pp. 333-338. ISBN 978-0-9553018-2-7.
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DEDEK Tomáš, MAREK Tomáš and MARTÍNEK Tomáš. 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, pp. 648-651. ISBN 1-4244-1060-6.
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TOBOLA Jiří, KOTÁSEK Zdeněk, KOŘENEK Jan, MARTÍNEK Tomáš and STRAKA Martin. 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, pp. 676-679. ISBN 0-7695-2978-X.
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2006

MARTÍNEK Tomáš, LEXA Matej, KOŘENEK Jan and FUČÍK Otto. 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, pp. 83-84. ISBN 1-4244-0184-4.
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SEKANINA Lukáš, MARTÍNEK Tomáš and GAJDA Zbyšek. Extrinsic and Intrinsic Evolution of Multifunctional Combinational Modules. In: 2006 IEEE World Congress on Computational Intelligence. CA: IEEE Computational Intelligence Society, 2006, pp. 9676-9683. ISBN 0-7803-9489-5.
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ČERNÝ Stanislav, STRUŽKA Petr, KOŘENEK Jan, MARTÍNEK Tomáš and KOTÁSEK Zdeněk. FPGA Components in Simulink. In: Proceedings of XXVIIIth International Autumn Colloquium ASIS 2006. Ostrava, 2006, pp. 158-163. ISBN 80-86840-26-3.
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MARTÍNEK Tomáš, KOŘENEK Jan and NOVOTNÝ Jiří. 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, pp. 143-151. ISBN 978-80-239-6533-9.
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2005

MARTÍNEK Tomáš and SEKANINA Lukáš. An Evolvable Image Filter: Experimental Evaluation of a Complete Hardware Implementation in FPGA. In: Evolvable Systems: From Biology to Hardware. Lecture Notes in Computer Science, vol. 3637. Berlin: Springer Verlag, 2005, pp. 76-85. ISBN 978-3-540-28736-0.
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MARTÍNEK Tomáš. Analýza datových toků s využitím sebe-rekonfigurovatelných automatů. In: Sborník příspěvků ze semináře Počítačové Architektury a Diagnostika. Praha: Faculty of Electrical Engineering, Czech Technical University, 2005, pp. 119-124. ISBN 80-01-03298-1.
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MARTÍNEK Tomáš, ZEMČÍK Pavel and KOŘENEK Jan. 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, pp. 194-197. ISBN 963-9364-48-7.
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2004

MARTÍNEK Tomáš, KOŘENEK Jan and NOVOTNÝ Jiří. Passive network monitoring adapter intended for 10Gbps technology. In: Sborník příspěvků z XXV. konference Europen. Plzeň: Czech Open Systems User's Group, 2004, pp. 55-63. ISBN 80-86583-07-4.
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2002

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