Výpis publikací

VETEŠNÍKOVÁ ŠIMKOVÁ, Andrea; Md Mehedi Hasan FUAD; Markéta ONDRAČKOVÁ; Tomáš TICHOPÁD; Kristína KŘÍŽOVÁ; Mária SEIFERTOVÁ; Kristýna VOŘÍŠKOVÁ; Martin DEMKO a Lukáš VETEŠNÍK. Diplostomum pseudospathaceum (Trematoda) inducing differential immune geneexpression in asexual and sexual gibel carp (Carassius gibelio). In XV. Slovak and Czech Parasitological Days, http://www.paradni2024.sav.sk. 2024. ISBN 978-80-972239-1-5.

ŠÁMALOVÁ, Markéta; Alesia MELNIKAVA; Kareem ELSAYAD; Alexis PEAUCELLE; Evelína GAHUROVÁ; Jaromír GUMULEC; Ioannis SPYROGLOU; Elena V ZEMLYANSKAYA; Elena V UBOGOEVA; Darina BALKOVÁ; Martin DEMKO; Nicolas BLAVET; Panagiotis ALEXIOU; Vladimir BENES; Gregory MOUILLE a Jan HEJÁTKO. Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth. Plant Physiology. CARY: OXFORD UNIV PRESS INC, 2024, roč. 194, č. 1, s. 209-228. ISSN 0032-0889. Dostupné z: https://doi.org/10.1093/plphys/kiad228.

JACQUES, Florian; Tomáš TICHOPÁD; Martin DEMKO; Vojtěch BYSTRÝ; Kristína KŘÍŽOVÁ; Mária SEIFERTOVÁ; Kristýna VOŘÍŠKOVÁ; Md Mehedi Hasan FUAD; Lukáš VETEŠNÍK a Andrea VETEŠNÍKOVÁ ŠIMKOVÁ. Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction. BMC Genomics. London: BioMed Central Ltd, 2024, roč. 25, č. 1, s. 1-22. ISSN 1471-2164. Dostupné z: https://doi.org/10.1186/s12864-024-10462-4.

LYČKA, Martin; Michal BUBENÍK; Michal ZÁVODNÍK; Vratislav PESKA; Petr FAJKUS; Martin DEMKO; Jiří FAJKUS a Miloslava FOJTOVÁ. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Research. Oxford: Oxford University Press, 2024, roč. 52, D1, s. "D311"-"D321", 11 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkad672.

ABUEG, Linelle Ann L.; Enis AFGAN; Olivier ALLART; Ahmed H. A. WAN; W. Endi A. BACON; Dannon BAKER; Madeline BASSETTI; Berenice BATUT; Matthias BERNT; Daniel BLANKENBERG; Aureliano BOMBARELY; Anthony BRETAUDEAU; Catherine J. BROMHEAD; Melissa L. BURKE; Patrick K. CAPON; Martin CECH; Maria CHAVERO-DIEZ; John M. CHILTON; Tyler J. COLLINS; Frederik COPPENS; Nate CORAOR; Gianmauro CUCCURU; Fabio CUMBO; John DAVIS; F. Paul DE GEEST; Willem DE KONING; Martin DEMKO; Assunta DESANTO; Jose Manuel Dominguez BEGINES; Maria A. DOYLE; Bert DROESBEKE; Anika ERXLEBEN-EGGENHOFER; Melanie C. FOLL; Giulio FORMENTI; Anne FOUILLOUX; Rendani GANGAZHE; Tanguy GENTHON; Jeremy GOECKS; Alejandra N. Gonzalez BELTRAN; Nuwan A. GOONASEKERA; Nadia GOUE; Timothy J. GRIFFIN; Bjorn A. GRUNING; Aysam GUERLER; Sveinung GUNDERSEN; Ove Johan Ragnar GUSTAFSSON; Christina HALL; Thomas W. HARROP; Helge HECHT; Alireza HEIDARI; Tillman HEISNER; Florian HEYL; Saskia HILTEMANN; Hans-Rudolf HOTZ; Cameron J. HYDE; Pratik D. JAGTAP; Julia JAKIELA; James E. JOHNSON; Jayadev JOSHI; Marie JOSSE; Khaled JUM'AH; Matus KALAS; Katarzyna KAMIENIECKA; Tunc KAYIKCIOGLU; Markus KONKOL; Leonid KOSTRYKIN; Natalie KUCHER; Anup KUMAR; Mira KUNTZ; Delphine LARIVIERE; Ross LAZARUS; Yvan LE BRAS; Gildas LE CORGUILLE; Justin LEE; Simone LEO; Leandro LIBORIO; Romane LIBOUBAN; David Lopez TABERNERO; Lucille LOPEZ-DELISLE; Laila S. LOS; Alexandru MAHMOUD; Igor MAKUNIN; Pierre MARIN; Subina MEHTA; Winnie MOK; Pablo A. MORENO; Francois MORIER-GENOUD; Stephen MOSHER; Teresa MUELLER; Engy NASR; Anton NEKRUTENKO; Tiffanie M. NELSON; Asime J. OBA; Alexander OSTROVSKY; Polina V. POLUNINA; Krzysztof POTERLOWICZ; Elliott James PRICE; Gareth R. PRICE; Helena RASCHE; Bryan RAUBENOLT; Coline ROYAUX; Luke SARGENT; Michelle T. SAVAGE; Volodymyr SAVCHENKO; Denys SAVCHENKO; Michael C. SCHATZ; Pauline SEGUINEAU; Beatriz SERRANO-SOLANO; Nicola SORANZO; Sanjay Kumar SRIKAKULAM; Keith SUDERMAN; Anna E. SYME; Marco Antonio TANGARO; Jonathan A. T. EDDS; Mehmet T. EKMAN; Wai Cheng THANG; Anil S. THANKI; Michael UHL; Marius VAN DEN BEEK; Deepti VARSHNEY; Jenn VESSIO; Pavankumar VIDEM; Von Kuster GREG; Gregory R. WATSON; Natalie WHITAKER-ALLEN; Uwe WINTER; Martin WOLSTENCROFT; Federico ZAMBELLI; Paul ZIEREP a Rand ZOABI. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic acids research. Oxford: Oxford University Press, 2024, roč. 52, W1, s. "W83"-"W94", 12 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkae410.

MACHELOVÁ, Adéla; Martina NEŠPOR DADEJOVÁ; Michal FRANEK; Guillaume MOUGEOT; Lauriane SIMON; Samuel LE GOFF; Celine DUC; Jasmin BASSLER; Martin DEMKO; Jana SCHWARZEROVA; Sophie DESSET; Aline V PROBST a Martina DVOŘÁČKOVÁ. The histone chaperones ASF1 and HIRA are required for telomere length and 45S rDNA copy number homeostasis. Plant Journal. Hoboken: Wiley, 2024, roč. 120, č. 3, s. 1125-1141. ISSN 0960-7412. Dostupné z: https://doi.org/10.1111/tpj.17041.

VETEŠNÍKOVÁ ŠIMKOVÁ, Andrea; Md Mehedi Hasan FUAD; Tomáš TICHOPÁD; Markéta ONDRAČKOVÁ; Kristína KŘÍŽOVÁ; Mária SEIFERTOVÁ; Kristýna VOŘÍŠKOVÁ; Martin DEMKO a Lukáš VETEŠNÍK. Trematode Diplostomum pseudospathaceum inducing differential immune gene expression in sexual and gynogenetic gibel carp (Carassius gibelio), an invasive freshwater fish. In The XIV European Multicolloquium of Parasitology, Wrocław, Poland, August 26–30, 2024. 2024. ISSN 2300-6706.

FUAD, Md Mehedi Hasan; Tomas TICHOPAD; Marketa ONDRACKOVA; Kristína KŘÍŽOVÁ; Mária SEIFERTOVÁ; Kristýna VOŘÍŠKOVÁ; Martin DEMKO; Lukáš VETEŠNÍK a Andrea VETEŠNÍKOVÁ ŠIMKOVÁ. Trematode Diplostomum pseudospathaceum inducing differential immune gene expression in sexual and gynogenetic gibel carp (Carassius gibelio): parasites facilitating the coexistence of two reproductive forms of the invasive species. Frontiers in immunology. LAUSANNE: Frontiers Media S.A., 2024, roč. 15, June, s. "1392569", 16 s. ISSN 1664-3224. Dostupné z: https://doi.org/10.3389/fimmu.2024.1392569.

JEDLIČKOVÁ, Veronika; Václav HEJRET; Martin DEMKO; Pavel JEDLIČKA; Marie ŠTEFKOVÁ a Helene ROBERT BOISIVON. Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus. BMC Genomics. London: BioMed Central Ltd, 2023, roč. 24, č. 1, s. 1-15. ISSN 1471-2164. Dostupné z: https://doi.org/10.1186/s12864-023-09316-2.

VETEŠNÍKOVÁ ŠIMKOVÁ, Andrea; Kristína KŘÍŽOVÁ; Kristýna VOŘÍŠKOVÁ; Lukáš VETEŠNÍK; Vojtěch BYSTRÝ a Martin DEMKO. Transcriptome Profile Analyses of Head Kidney in Roach (Rutilus rutilus), Common Bream (Abramis brama) and Their Hybrids: Does Infection by Monogenean Parasites in Freshwater Fish Reveal Differences in Fish Vigour among Parental Species and Their Hybrids? Biology. Basel: MDPI, 2023, roč. 12, č. 9, s. 1-29. ISSN 2079-7737. Dostupné z: https://doi.org/10.3390/biology12091199.

CAVALLIN, Ivana; Marek BARTOŠOVIČ; Tomáš SKALICKÝ; Praveenkumar RENGARAJ; Martin DEMKO; Martina Christina SCHMIDT-DENGLER; Aleksej DRINO; Mark HELM a Štěpánka VAŇÁČOVÁ. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs. RNA. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2022, roč. 28, č. 12, s. 1568-1581. ISSN 1355-8382. Dostupné z: https://doi.org/10.1261/rna.079421.122.

BYSTRÝ, Vojtěch; Viktor MAŠÍČEK; Nicolas MOKRIŠ a Martin DEMKO. SeqUIa: Softwarová platforma pro zpracování sekvenování nové generace skrze grafické rozhraní. 2022.

LYČKA, Martin; Vratislav PEŠKA; Martin DEMKO; Ioannis SPYROGLOU; Agata Magdalena KILAR; Jiří FAJKUS a Miloslava FOJTOVÁ. WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis. BMC Bioinformatics. London: BioMed Central, 2021, roč. 22, č. 1, s. "145", 14 s. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-021-04064-0.

ŠAFRÁNEK, David; Matej TROJÁK; Vojtěch BRŮŽA; Tomáš VEJPUSTEK; Jan PAPOUŠEK; Martin DEMKO; Samuel PASTVA; Aleš PEJZNOCH a Luboš BRIM. Barbaric Robustness Monitoring Revisited for STL* in Parasim. In Bortolussi L., Sanguinetti G. Computational Methods in Systems Biology (CMSB 2019). LNBI 11773. Neuveden: Springer, 2019, s. 356-359. ISBN 978-3-030-31303-6. Dostupné z: https://doi.org/10.1007/978-3-030-31304-3_26.

DEMKO, Martin; Lukáš CHRÁST; Pavel DVOŘÁK; Jiří DAMBORSKÝ a David ŠAFRÁNEK. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms. Basel: MDPI, 2019, roč. 7, č. 11, s. 553-581. ISSN 2076-2607. Dostupné z: https://doi.org/10.3390/microorganisms7110553.

DEMKO, Martin; Samuel PASTVA; David ŠAFRÁNEK; Nikola BENEŠ a Luboš BRIM. PITHYA. 2018.

JANKŮJOVÁ, Marie; David POTĚŠIL; Zbyněk ZDRÁHAL; Martin DEMKO; Jan OPPELT; Martin KAŠNÝ a Jaroslav VADLEJCH. Analysis of gene expression and protein synthesis related to hypobiosis of Teladorsagia circumcincta. In The 26th International Conference of the World Association for the Advancement of Veterinary Parasitology. 2017.

BYSTRÝ, Vojtěch; Tomáš REIGL; Adam KREJČÍ; Martin DEMKO; Barbora HANÁKOVÁ; Andrea GRIONI; Henrik KNECHT; Max SCHLITT; Peter DREGER; Leopold SELLNER; Dietrich HERRMANN; Marine PINGEON; Myriam BOUDJOGHRA; Jos RIJNTJES; Christiane POTT; Anton W. LANGERAK; Patricia J. T. A. GROENEN; Frederic DAVI; Monika BRUGGEMANN a Nikos DARZENTAS. ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data. Bioinformatics. Oxford: Oxford University Press, 2017, roč. 33, č. 3, s. 435-437. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btw634.

BRIM, Luboš; Jiří BARNAT; David ŠAFRÁNEK; Nikola BENEŠ; Martin DEMKO; Samuel PASTVA a Matej HAJNAL. Detecting Attractors in Biological Models with Uncertain Parameters. In Jérôme Feret and Heinz Koeppl. Computational Methods in Systems Biology. CMSB 2017. LNCS 10545. Cham: Springer International Publishing, 2017, s. 40-56. ISBN 978-3-319-67470-4. Dostupné z: https://doi.org/10.1007/978-3-319-67471-1_3.

BENEŠ, Nikola; Luboš BRIM; Martin DEMKO; Matej HAJNAL; Samuel PASTVA a David ŠAFRÁNEK. Discrete Bifurcation Analysis with Pithya. In Feret J. et al. 15th International Conference on Computational Methods in Systems Biology (CMSB). LNCS 10545. Cham: Springer, 2017, s. 319-320. ISBN 978-3-319-67470-4.

PÁL, Karol; Vojtěch BYSTRÝ; Tomáš REIGL; Martin DEMKO; Adam KREJČÍ; T. TOULOUMENIDOU; E. STALIKA; Boris TICHÝ; P. GHIA; K. STAMATOPOULOS; Šárka POSPÍŠILOVÁ; Jitka MALČÍKOVÁ a Nikos DARZENTAS. GLASS. 2017.

PÁL, Karol; Vojtěch BYSTRÝ; Tomáš REIGL; Martin DEMKO; Adam KREJČÍ; T. TOULOUMENIDOU; E. STALIKA; Boris TICHÝ; P. GHIA; K. STAMATOPOULOS; Šárka POSPÍŠILOVÁ; Jitka MALČÍKOVÁ a Nikos DARZENTAS. GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data. Bioinformatics. Oxford: Oxford University Press, 2017, roč. 33, č. 23, s. 3802-3804. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btx423.

PÁL, Karol; Vojtěch BYSTRÝ; Tomáš REIGL; Martin DEMKO; Adam KREJČÍ; Boris TICHÝ; Šárka POSPÍŠILOVÁ; Jitka MALČÍKOVÁ a Nikos DARZENTAS. GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data. In CEITEC PHD RETREAT II, Telč. 2017.

PÁL, Karol; Vojtěch BYSTRÝ; Tomáš REIGL; Martin DEMKO; Adam KREJČÍ; Boris TICHÝ; Šárka POSPÍŠILOVÁ; Jitka MALČÍKOVÁ a Nikos DARZENTAS. GLASS:assisted and standardized assessment of gene variations from Sanger sequence trace data. In Curie-Pasteur-CEITEC joint young scientist retreat. 2017.

BENEŠ, Nikola; Luboš BRIM; Martin DEMKO; David ŠAFRÁNEK; Samuel PASTVA a Matej HAJNAL. Model Checking Approach to Discrete Bifurcation Analysis. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2017.

BRIM, Luboš; David ŠAFRÁNEK; Nikola BENEŠ; Martin DEMKO; Samuel PASTVA a Matej HAJNAL. Parameter Synthesis of Biological Models by Model Checking: A Case Study. In 4th International Synthetic & Systems Biology Summer School. SSBSS 2017. 2017.

BENEŠ, Nikola; Luboš BRIM; Martin DEMKO; Samuel PASTVA a David ŠAFRÁNEK. Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-Affine Dynamical Systems. In Rupak Majumdar and Viktor Kunčak. Computer Aided Verification. CAV 2017. LNCS 10426. Cham: Springer International Publishing, 2017, s. 591-598. ISBN 978-3-319-63386-2. Dostupné z: https://doi.org/10.1007/978-3-319-63387-9_29.

BRIM, Luboš; Nikola BENEŠ; David ŠAFRÁNEK; Martin DEMKO; Samuel PASTVA a Matej HAJNAL. PITHYA: High-Performance Parameter Synthesis for Biological Models. In Intelligent Systems for Molecular Biology and European Conference on Computational Biology. ISMB/ECCB 2017. 2017.

BENEŠ, Nikola; Luboš BRIM; Martin DEMKO; Samuel PASTVA a David ŠAFRÁNEK. A Model Checking Approach to Discrete Bifurcation Analysis. In John S. Fitzgerald et al. Formal Methods. FM 2016. LNCS 9995. Neuveden: Springer International Publishing, 2016, s. 85-101. ISBN 978-3-319-48988-9. Dostupné z: https://doi.org/10.1007/978-3-319-48989-6_6.

ŠKORPÍKOVÁ, Lucie; Jana ILGOVÁ; David POTĚŠIL; Zbyněk ZDRÁHAL; Martin DEMKO; Jan OPPELT; Milan GELNAR a Martin KAŠNÝ. Deep insight into secretome and transcriptome of Trichinella spiralis and Trichinela pseudospiralis. In EMOP XII – the 12th European Multicolloquium of Parasitology. 2016.

DEMKO, Martin; Nikola BENEŠ; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. In Ezio Bartocci et al. Computational Methods in Systems Biology. CMSB 2016. LNBI 9859. Neuveden: Springer International Publishing, 2016, s. 82-97. ISBN 978-3-319-45176-3. Dostupné z: https://doi.org/10.1007/978-3-319-45177-0_6.

BENEŠ, Nikola; Luboš BRIM; Martin DEMKO; Samuel PASTVA a David ŠAFRÁNEK. Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-Affine Systems. In Cyrille Artho et al. Automated Technology for Verification and Analysis. ATVA 2016. LNCS 9938. Neuveden: Springer International Publishing, 2016, s. 192-208. ISBN 978-3-319-46519-7. Dostupné z: https://doi.org/10.1007/978-3-319-46520-3_13.

HAJNAL, Matej; David ŠAFRÁNEK; Martin DEMKO; Samuel PASTVA; Pavel KREJČÍ a Luboš BRIM. Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways. In Eugenio Cinquemani. Hybrid Systems Biology. HSB 2016. LNBI 9957. Neuveden: Springer International Publishing, 2016, s. 57-66. ISBN 978-3-319-47150-1. Dostupné z: https://doi.org/10.1007/978-3-319-47151-8_4.

BRIM, Luboš; Martin DEMKO; Samuel PASTVA a David ŠAFRÁNEK. Coloured Model Checking Approach to Parameter Synthesis for Executable Models in Synthetic Biology. In Verification of Engineered Molecular Devices and Programs. 2015.

BRIM, Luboš; Martin DEMKO; Samuel PASTVA a David ŠAFRÁNEK. High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. In Alessandro Abate, David Šafránek. Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. LNCS 9271. Neuveden: Springer International Publishing, 2015, s. 58-74. ISBN 978-3-319-26915-3. Dostupné z: https://doi.org/10.1007/978-3-319-26916-0_4.

BRIM, Luboš; Milan ČEŠKA; Martin DEMKO; Samuel PASTVA a David ŠAFRÁNEK. Parameter Synthesis by Parallel Coloured CTL Model Checking. In Roux, Olivier and Bourdon, Jérémie. Computational Methods in Systems Biology. Neuveden: Springer International Publishing, 2015, s. 251-263. ISBN 978-3-319-23400-7. Dostupné z: https://doi.org/10.1007/978-3-319-23401-4_21.