Výpis publikací

VESELÝ, Vojtěch; Eva ŠMIJÁKOVÁ; Samuel PASTVA; Nikola BENEŠ a David ŠAFRÁNEK. AEON 2025: Robust Control of Partially-Specified Boolean Networks. Online. In Fages, Francois and Peres, Sabine. International Conference on Computational Methods in Systems Biology, CMSB 2025. Cham: Springer Nature Switzerland, 2026, s. 61-68. ISBN 978-3-032-01435-1. Dostupné z: https://doi.org/10.1007/978-3-032-01436-8_4.

HUVAR, Ondřej; Nikola BENEŠ; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Sketchbook: logical model inference from Boolean network sketches. BIOINFORMATICS ADVANCES. OXFORD: OXFORD UNIV PRESS, 2026, roč. 6, č. 1, s. 1-5. ISSN 2635-0041. Dostupné z: https://doi.org/10.1093/bioadv/vbag014.

BENEŠ, Nikola; Luboš BRIM; Ondřej HUVAR; Samuel PASTVA a David ŠAFRÁNEK. Symbolic Model Checking of Hybrid CTL on Coloured Kripke Structures. Online. In Akshay, S. and Niemetz, Aina and Sankaranarayanan, Sriram. International Symposium on Automated Technology for Verification and Analysis, ATVA 2024. Cham: Springer Nature Switzerland, 2025, s. 212-233. ISBN 978-3-031-78749-2. Dostupné z: https://doi.org/10.1007/978-3-031-78750-8_11.

HELFRICH, Martin; Roman ANDRIUSHCHENKO; Milan ČEŠKA; Jan KŘETÍNSKÝ; Štefan MARTIČEK a David ŠAFRÁNEK. Abstraction-based segmental simulation of reaction networks using adaptive memoization. BMC Bioinformatics. 2024, roč. 25, č. 350, s. 1-24. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-024-05966-5.

BENEŠ, Nikola; Luboš BRIM; Ondřej HUVAR; Samuel PASTVA a David ŠAFRÁNEK. BNClassifier: Classifying Boolean Models by Dynamic Properties. Online. In Gori, Roberta; Milazzo, Paolo; Tribastone, Mirco. Computational Methods in Systems Biology. Cham: Springer, 2024, s. 19-26. ISBN 978-3-031-71670-6. Dostupné z: https://doi.org/10.1007/978-3-031-71671-3_2.

BENEŠ, Nikola; Luboš BRIM; Ondřej HUVAR; Samuel PASTVA a David ŠAFRÁNEK. Boolean network sketches: a unifying framework for logical model inference. Bioinformatics. 2023, roč. 39, č. 4, s. "btad158", 8 s. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btad158.

KLEIN, Julia; Huy PHUNG; Matej HAJNAL; David ŠAFRÁNEK a Tatjana PETROV. Combining formal methods and Bayesian approach for inferring discrete-state stochastic models from steady-state data. Plos one. San Francisco: Public Library of Science, 2023, roč. 18, č. 11, s. 1-26. ISSN 1932-6203. Dostupné z: https://doi.org/10.1371/journal.pone.0291151.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA; David ŠAFRÁNEK a Eva ŠMIJÁKOVÁ. Phenotype Control of Partially Specified Boolean Networks. In Jun Pang, Joachim Niehren. Computational Methods in Systems Biology. Luxembourg City, Luxembourg: Springer Cham, 2023, s. 18-35. ISBN 978-3-031-42696-4. Dostupné z: https://doi.org/10.1007/978-3-031-42697-1_2.

TROJÁK, Matej; David ŠAFRÁNEK; Samuel PASTVA a Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. Biosystems. Elsevier, 2023, roč. 225, č. 104843, s. 1-15. ISSN 0303-2647. Dostupné z: https://doi.org/10.1016/j.biosystems.2023.104843.

BRIM, Luboš; Samuel PASTVA; David ŠAFRÁNEK a Eva ŠMIJÁKOVÁ. Temporary and Permanent Control of Partially Specified Boolean Networks. BIOSYSTEMS. Elsevier, 2023, roč. 223, JAN, s. 104795-104808. ISSN 0303-2647. Dostupné z: https://doi.org/10.1016/j.biosystems.2022.104795.

BENEŠ, Nikola; Luboš BRIM; Ondřej HUVAR; Samuel PASTVA; David ŠAFRÁNEK a Eva ŠMIJÁKOVÁ. AEON.py: Python library for attractor analysis in asynchronous Boolean networks. BIOINFORMATICS. UK: OXFORD UNIV PRESS, 2022, roč. 38, č. 21, s. 4978-4980. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btac624.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. BDD-Based Algorithm for SCC Decomposition of Edge-Coloured Graphs. Logical Methods in Computer Science. Episciences, 2022, roč. 18, č. 1, s. 1-27. ISSN 1860-5974. Dostupné z: https://doi.org/10.46298/LMCS-18(1:38)2022.

TROJÁK, Matej; David ŠAFRÁNEK; Branislav BROZMANN a Luboš BRIM. eBCSgen 2.0: Modelling and Analysis of Regulated Rule-Based Systems. Online. In I. Petre, A. Păun. 20th International Conference on Computational Methods in Systems Biology. LNBI 13447. Neuveden: Springer, 2022, s. 302-309. ISBN 978-3-031-15033-3. Dostupné z: https://doi.org/10.1007/978-3-031-15034-0_17.

BENEŠ, Nikola; Luboš BRIM; Jakub KADLECAJ; Samuel PASTVA a David ŠAFRÁNEK. Exploring attractor bifurcations in Boolean networks. BMC Bioinformatics. 2022, roč. 23, č. 173, s. 1-18. ISSN 1471-2105. Dostupné z: https://doi.org/10.1186/s12859-022-04708-9.

PETROV, Tatjana; Matej HAJNAL; Julia KLEIN; David ŠAFRÁNEK a Morgane NOUVIAN. Extracting individual characteristics from population data reveals a negative social effect during honeybee defence. Plos Computational Biology. 2022, roč. 18, č. 9, s. 1-20. ISSN 1553-734X. Dostupné z: https://doi.org/10.1371/journal.pcbi.1010305.

OBRUČA, Stanislav; Pavel DVOŘÁK; Petr SEDLÁČEK; Martin KOLLER; Karel SEDLÁŘ; Iva PERNICOVÁ a David ŠAFRÁNEK. Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics. Biotechnology Advances. Elsevier, 2022, roč. 58, September, s. 1-28. ISSN 0734-9750. Dostupné z: https://doi.org/10.1016/j.biotechadv.2022.107906.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Aeon 2021: Bifurcation Decision Trees in Boolean Networks. In Cinquemani et al. International Conference on Computational Methods in Systems Biology (CMSB 2021). Cham: Springer, 2021, s. 230-237. ISBN 978-3-030-85632-8. Dostupné z: https://doi.org/10.1007/978-3-030-85633-5_14.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Computing Bottom SCCs Symbolically Using Transition Guided Reduction. Online. In Alexandra Silva, K. Rustan, M. Leino. Computer Aided Verification - 33rd International Conference, CAV 2021. Neuveden: Springer Nature, 2021, s. 505-528. ISBN 978-3-030-81684-1. Dostupné z: https://doi.org/10.1007/978-3-030-81685-8_24.

HAJNAL, Matej; Tatjana PETROV a David ŠAFRÁNEK. DiPS: A Tool for Data-Informed Parameter Synthesis for Markov Chains from Multiple-Property Specifications. In Ballarini et al. Performance Engineering and Stochastic Modeling. Cham: Springer, 2021, s. 79-95. ISBN 978-3-030-91824-8. Dostupné z: https://doi.org/10.1007/978-3-030-91825-5_5.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Symbolic Coloured SCC Decomposition. Online. In Jan Friso Groote, Kim Larsen. Tools and Algorithms for the Construction and Analysis of Systems, 27th International Conference, TACAS 2021. Neuveden: Springer Nature, 2021, s. 64-83. ISBN 978-3-030-72012-4. Dostupné z: https://doi.org/10.1007/978-3-030-72013-1_4.

BENEŠ, Nikola; Luboš BRIM; Jakub KADLECAJ; Samuel PASTVA a David ŠAFRÁNEK. AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks. In Shuvendu K. Lahiri and Chao Wang. Computer Aided Verification. CAV 2020. LNCS 12224. Cham: Springer, Cham, 2020, s. 569-581. ISBN 978-3-030-53287-1. Dostupné z: https://doi.org/10.1007/978-3-030-53288-8_28.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Digital Bifurcation Analysis of Internet Congestion Control Protocols. International Journal of Bifurcation and Chaos. 2020, roč. 30, č. 13, s. 2030038-2030055. ISSN 0218-1274. Dostupné z: https://doi.org/10.1142/S0218127420300384.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a Luboš BRIM. eBCSgen: A Software Tool for Biochemical Space Language. Online. In Abate A., Petrov T., Wolf V. 18th International Conference on Computational Methods in Systems Biology, CMSB 2020. LNBI 12314. Neuveden: Springer, 2020, s. 356-361. ISBN 978-3-030-60326-7. Dostupné z: https://doi.org/10.1007/978-3-030-60327-4_20.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. PLOS ONE. Public Library of Science, 2020, roč. 15, č. 9, s. 1-23, 24 s. ISSN 1932-6203. Dostupné z: https://doi.org/10.1371/journal.pone.0238838.

TROJÁK, Matej; David ŠAFRÁNEK; Luboš BRIM; Jakub ŠALAGOVIČ a Jan ČERVENÝ. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. Online. In Ankit Gupta, Tatjana Petrov. 9th International Workshop on Static Analysis and Systems Biology (SASB). ENTCS 350. Amsterdam: Elsevier, 2020, s. 91-116. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2020.06.006.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. In 7th Workshop on Hybrid Systems and Biology. 2020.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Parallel parameter synthesis algorithm for hybrid CTL. Science of Computer Programming. 2020, roč. 185, č. 102321, s. 1-19. ISSN 0167-6423. Dostupné z: https://doi.org/10.1016/j.scico.2019.102321.

ŠMIJÁKOVÁ, Eva; Samuel PASTVA; David ŠAFRÁNEK a Luboš BRIM. Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications. Online. In Abate A., Petrov T., Wolf V. Computational Methods in Systems Biology. CMSB 2020. Lecture Notes in Computer Science, vol 12314. Cham: Springer, Cham, 2020, s. 280-297. ISBN 978-3-030-60326-7. Dostupné z: https://doi.org/10.1007/978-3-030-60327-4_15.

TROJÁK, Matej; David ŠAFRÁNEK; Lukrécia MERTOVÁ a Luboš BRIM. Parameter Synthesis and Robustness Analysis of Rule-Based Models. In Ritchie Lee, Susmit Jha, Anastasia Mavridou. 12th International Symposium on NASA Formal Methods, NFM 2020. LNCS 12229. Moffett Field, CA, USA: Springer, 2020, s. 41-59. ISBN 978-3-030-55753-9. Dostupné z: https://doi.org/10.1007/978-3-030-55754-6_3.

HOLLMANN, Susanne; Andreas KREMER; Špela BAEBLER; Christophe TREFOIS; Kristina GRUDEN; Witold RUDNICKY; Weida TONG; Alexandra GRUCA; Erik BONGCAM-RUDLOFF; Chris EVELO; Alina NECHYPORENKO; Marcus FROHME; David ŠAFRÁNEK; Babette REGIERER a Domenica D'ELIA. The need for standardisation in life science research - an approach to excellence and trust. F1000Research. 2020, roč. 9, č. 1398, s. 1-9. ISSN 2046-1402. Dostupné z: https://doi.org/10.12688/f1000research.27500.2.

BENEŠ, Nikola; Luboš BRIM; Martin GELETKA; Samuel PASTVA a David ŠAFRÁNEK. Accelerating Parameter Synthesis Using Semi-algebraic Constraints. Online. In Ahrendt, Wolfgang and Tapia Tarifa, Silvia Lizeth. Integrated Formal Methods. LNCS 11918. Cham: Springer International Publishing, 2019, s. 27-45. ISBN 978-3-030-34967-7. Dostupné z: https://doi.org/10.1007/978-3-030-34968-4_2.

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.

TROJÁK, Matej; David ŠAFRÁNEK; Jan ČERVENÝ; Marek HAVLÍK; Lukrécia MERTOVÁ; Matej HAJNAL; Jakub HRABEC a Jakub ŠALAGOVIČ. Comprehensive Modelling Platform. In 6th Workshop on Hybrid Systems & Biology. 2019.

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.

HAJNAL, Matej; Nouvian MORGANE; Tatjana PETROV a David ŠAFRÁNEK. Data-Informed Parameter Synthesis for Population Markov Chains. In Bortolussi, L. and Sanguinetti, G. 17th International Conference on Computational Methods in Systems Biology (CMSB 2019). LNBI 11773. Neuveden: Springer Nature, 2019, s. 383-386. ISBN 978-3-030-31303-6. Dostupné z: https://doi.org/10.1007/978-3-030-31304-3_32.

HAJNAL, Matej; Morgan NOUVIAN; David ŠAFRÁNEK a Tatjana PETROV. Data-Informed Parameter Synthesis for Population Markov Chains. In Ceska, M et al. Hybrid Systems Biology (HSB 2019). LNCS 11705. Cham: Springer International Publishing, 2019, s. 147-164. ISBN 978-3-030-28041-3. Dostupné z: https://doi.org/10.1007/978-3-030-28042-0_10.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Digital Bifurcation Analysis of TCP Dynamics. In Tomáš Vojnar and Lijun Zhang. Tools and Algorithms for the Construction and Analysis of Systems. TACAS 2019. LNCS, volume 11428. Cham: Springer International Publishing, 2019, s. 339-356. ISBN 978-3-030-17464-4. Dostupné z: https://doi.org/10.1007/978-3-030-17465-1_19.

BENEŠ, Nikola; Luboš BRIM; Jana DRAŽANOVÁ; Samuel PASTVA a David ŠAFRÁNEK. Facetal Abstraction for Non-linear Dynamical Systems Based on delta-decidable SMT. In Proceedings of the 22Nd ACM International Conference on Hybrid Systems: Computation and Control. New York, NY, USA: ACM, 2019, s. 99-108. ISBN 978-1-4503-6282-5. Dostupné z: https://doi.org/10.1145/3302504.3311793.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA; Jakub POLÁČEK a David ŠAFRÁNEK. Formal Analysis of Qualitative Long-Term Behaviour in Parametrised Boolean Networks. In Ait Ameur et al. Formal Methods and Software Engineering - 21st International Conference on Formal Engineering Methods, ICFEM 2019, Shenzhen, China, November 5-9, 2019, Proceedings. Heidelberg: Springer, 2019, s. 353-369. ISBN 978-3-030-32408-7. Dostupné z: https://doi.org/10.1007/978-3-030-32409-4_22.

BENEŠ, Nikola; Luboš BRIM; Samuel PASTVA a David ŠAFRÁNEK. Model Checking Approach to the Analysis of Biological Systems. Online. In Pietro Liò, Paolo Zuliani. Automated Reasoning for Systems Biology and Medicine. Cham: Springer, Cham, 2019, s. 3-35. Computational Biology. ISBN 978-3-030-17296-1. Dostupné z: https://doi.org/10.1007/978-3-030-17297-8_1.

KOLČÁK, Juraj; David ŠAFRÁNEK; Stefan HAAR a Loïc PAULEVÉ. Parameter space abstraction and unfolding semantics of discrete regulatory networks. Theoretical Computer Science. Elsevier, 2019, roč. 765, April, s. 120-144. ISSN 0304-3975. Dostupné z: https://doi.org/10.1016/j.tcs.2018.03.009.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Jan ČERVENÝ; Matej HAJNAL; Lukrécia MERTOVÁ; Katarína PALUBOVÁ a Marek HAVLÍK. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In 16th International Conference on Computational Methods in Systems Biology. 2018.

BENEŠ, Nikola; Luboš BRIM; Jan ČERVENÝ; Samuel PASTVA; David ŠAFRÁNEK; Jakub ŠALAGOVIČ a Matej TROJÁK. Fully Automated Attractor Analysis of Cyanobacteria Models. In Marian Barbu, Răzvan Şolea, Adrian Filipescu. 22nd International Conference on System Theory, Control and Computing. Neuveden: IEEE, 2018, s. 354-359. ISBN 978-1-5386-4444-7. Dostupné z: https://doi.org/10.1109/ICSTCC.2018.8540762.

ČERVENÝ, Jan; Jakub ŠALAGOVIČ; František MUZIKA; David ŠAFRÁNEK a Igor SCHREIBER. Influence of circadian clocks on optimal regime of central C-N metabolism of cyanobacteria. Online. In Mishra, A. K.; Tiwari, D.; Rai, A. N. Cyanobacteria: From Basic Science to Applications. 1st ed. Neuveden: Academic Press, 2018, s. 193-206. ISBN 978-0-12-814667-5. Dostupné z: https://doi.org/10.1016/B978-0-12-814667-5.00009-X.

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

KOLČÁK, Juraj; David ŠAFRÁNEK; Paulevé LOIC a Stefan HAAR. Unfolding of Parametric Boolean Networks. Electronic Notes in Theoretical Computer Science. Elsevier Science, 2018, roč. 335, Duben 2018, s. 67-90. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2018.03.009.

ŠAFRÁNEK, David a Guido SANGUINETTI. 7th International Workshop on Static Analysis and Systems Biology (SASB 2016). In 7th International Workshop on Static Analysis and Systems Biology (SASB 2016). Neuveden: Elsevier, 2018, 130 s. ISSN 1571-0661.

TROJÁK, Matej; David ŠAFRÁNEK a Jakub ŠALAGOVIČ. BCSgen: Biochemical Space language software tool. 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ a Matej HAJNAL. Biochemical Space: A framework for formal description and annotation of complex biological processes. In Computational Modeling in Biology Network meeting (COMBINE 2017). 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ a Matej HAJNAL. Biochemical Space: A Framework for Formal Description and Annotation of Complex Biological Processes. In The 8th International Workshop on Static Analysis for Systems Biology. 2017.

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.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ; Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In International Conference on Systems Biology 2017. 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ; Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In The Biomania Student Scientific Meeting 2017. 2017.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ; Matej HAJNAL a Jan ČERVENÝ. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 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.

TROJÁK, Matej; Tadeáš DĚD; David ŠAFRÁNEK; Matej KLEMENT; Jan ČERVENÝ a Františka ROMANOVSKÁ. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. In MEMICS 2016. 2016.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Jan ČERVENÝ a Matej HAJNAL. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. 2016.

TROJÁK, Matej; David ŠAFRÁNEK; Jakub HRABEC; Jakub ŠALAGOVIČ; Františka ROMANOVSKÁ a Jan ČERVENÝ. E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In Ezio Bartocci et al. Computational Methods in Systems Biology. CMSB 2016. Heidelberg: Springer, 2016, s. 316-322. ISBN 978-3-319-45176-3. Dostupné z: https://doi.org/10.1007/978-3-319-45177-0_20.

DĚD, Tadeáš; David ŠAFRÁNEK; Matej TROJÁK; Matej KLEMENT; Jakub ŠALAGOVIČ a Luboš BRIM. Formal Biochemical Space with Semantics in Kappa and BNGL. Online. In Loic Pauleve et al. The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015. ENTCS 326. Neuveden: Elsevier, 2016, s. 27-49. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2016.09.017.

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.

TROJÁK, Matej; Tadeáš DĚD; David ŠAFRÁNEK; Matej KLEMENT; Jan ČERVENÝ a Luboš BRIM. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. In 13th Conference on Computational Methods in Systems Biology. 2015.

TROJÁK, Matej; David ŠAFRÁNEK; Matej KLEMENT; Tadeáš DĚD; Jan ČERVENÝ a Luboš BRIM. Biochemical Space: A Language for Formal Description and Annotation of Complex Biological Processes. In Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. 2015.

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; Juraj NIŽNAN a David ŠAFRÁNEK. Compact Representation of Photosynthesis Dynamics by Rule-based Models. Online. In 5th International Workshop on Static Analysis and Systems Biology (SASB 2014). 316. vyd. Neuveden: Elsevier, 2015, s. 17-27. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2015.06.008.

ČERVENÝ, Jan; Stefan MUELLER a David ŠAFRÁNEK. CyanoNetwork workshop - Cyanobacterium in silico 2015. 2015.

KLEMENT, Matej; David ŠAFRÁNEK; Jan ČERVENÝ; Tadeáš DĚD; Matej TROJÁK; Luboš BRIM a Stefan MUELLER. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. In Fourth International Workshop on Hybrid Systems Biology. 2015.

ABATE, Alessandro a David ŠAFRÁNEK. Fourth International Workshop on Hybrid Systems Biology. 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.

ALESSANDRO, Abate a David ŠAFRÁNEK. Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. In Lecture Notes in Bioinformatics. Springer International Publishing, 2015, 263 s. ISBN 978-3-319-26915-3. Dostupné z: https://doi.org/10.1007/978-3-319-26916-0.

ŠAFRÁNEK, David. Parameter Synthesis by Model Checking in Formal Biochemical Space. In IST Austria Henzinger Group Seminar. 2015.

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.

ŠAFRÁNEK, David. PC Member of HSB 2015. Fourth International Workshop on Hybrid Systems Biology (HSB 2015), 2015.

ŠAFRÁNEK, David. PC Member of SASB 2015. The Sixth International Workshop on Static Analysis and Systems Biology (SASB 2015), 2015.

ČEŠKA, Milan; Caroline SCHNEIDER; Abate ALESSANDRO; David ŠAFRÁNEK; Louis MAHADEVAN a Marta KWIATKOWSKA. Stochastic Modelling of the Interface between Regulatory Enzymes and Transcription Initiation at Inducible Genes. In Fourth International Workshop on Hybrid Systems Biology. 2015.

KLEMENT, Matej; Tadeáš DĚD; David ŠAFRÁNEK; Jan ČERVENÝ; Stefan MUELLER a Ralf STEUER. Biochemical Space: A Framework for Systemic Annotation of Biological Models. Online. In Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14). Amsterdam: Elsevier, 2014, s. 31-44. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2014.06.013.

KLEMENT, Matej; David ŠAFRÁNEK; Jan ČERVENÝ; Tadeáš DĚD; Stefan MUELLER a Ralf STEUER. E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria. 2014.

ŠAFRÁNEK, David. From Formal Methods to Systems Biology. In Modeling and Simulation Seminar, Saarland University. 2014.

ŠAFRÁNEK, David. Model Checking in Systems Biology. In LACS Seminar, University of Luxembourg. 2014.

ŠAFRÁNEK, David. PC Member of HSB 2014. Third International Workshop on Hybrid Systems Biology (HSB 2014), 2014.

ŠAFRÁNEK, David. PC Member of MEMICS 2014. Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2014), 2014.

ŠAFRÁNEK, David. PC Member of SASB 2014. The Fifth International Workshop on Static Analysis and Systems Biology (SASB 2014), 2014.

ČEŠKA, Milan; David ŠAFRÁNEK; Sven DRAŽAN a Luboš BRIM. Robustness Analysis of Stochastic Biochemical Systems. Plos One. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2014, roč. 9, č. 4, s. 1-23. ISSN 1932-6203. Dostupné z: https://doi.org/10.1371/journal.pone.0094553.

BRIM, Luboš; Petr DLUHOŠ; David ŠAFRÁNEK a Tomáš VEJPUSTEK. STL*: Extending signal temporal logic with signal-value freezing operator. Information and computation. Academic Press, 2014, roč. 236, January, s. 52-67. ISSN 0890-5401. Dostupné z: https://doi.org/10.1016/j.ic.2014.01.012.

ČEŠKA, Milan; Caroline SCHNEIDER; Alessandro ABATE; David ŠAFRÁNEK; Louis MAHADEVAN a Marta KWIATKOWSKA. Stochastic Modelling of the Interface between Regulatory Enzymes and Transcription Initiation at Inducible Genes. In CMSB 2014. 2014.

KLEMENT, Matej; David ŠAFRÁNEK; Tadeáš DĚD; Aleš PEJZNOCH; Ladislav NEDBAL; Ralf STEUER; Jan ČERVENÝ a Stefan MUELLER. A Comprehensive Web-based Platform For Domain-Specific Biological Models. Online. In Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13). Neuveden: Elsevier, 2013, s. 61-67. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2013.11.006.

STRECK, Adam; Juraj KOLČÁK; Heike SIEBERT a David ŠAFRÁNEK. Esther: Introducing an Online Platform for Parameter Identification of Boolean Networks. In A. Gupta. Computational Methods in Systems Biology 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, Proceedings. Heidelberg: Springer, 2013, s. 257-258. ISBN 978-3-642-40707-9.

BRIM, Luboš; Milan ČEŠKA; Sven DRAŽAN a David ŠAFRÁNEK. Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. In 25th International Conference, CAV 2013, Saint Petersburg, Russia, July 13-19, 2013. Proceedings. Berlin: Springer Berlin Heidelberg, 2013, s. 107-123. ISBN 978-3-642-39798-1. Dostupné z: https://doi.org/10.1007/978-3-642-39799-8_7.

BRIM, Luboš; Milan ČEŠKA a David ŠAFRÁNEK. Model Checking of Biological Systems. In Marco Bernardo. Formal Methods for Dynamical Systems. Neuveden: Springer, 2013, s. 63-112. ISBN 978-3-642-38873-6. Dostupné z: https://doi.org/10.1007/978-3-642-38874-3_3.

BRIM, Luboš; Vilém DĚD a David ŠAFRÁNEK. Qualitative modelling and analysis of Photosystem II. Online. In CEUR Workshop Proceedings. Aachen: Neuveden, 2013, s. 17-29. ISSN 1613-0073.

BRIM, Luboš; Tomáš VEJPUSTEK; David ŠAFRÁNEK a Jana FABRIKOVÁ. Robustness Analysis for Value-Freezing Signal Temporal Logic. Online. In Proceedings HSB 2013. Neuveden: Neuveden, 2013, s. 20-36. ISSN 2075-2180. Dostupné z: https://doi.org/10.4204/EPTCS.125.

BRIM, Luboš; Milan ČEŠKA; Sven DRAŽAN a David ŠAFRÁNEK. Robustness Analysis of Stochastic Systems. Online. In Electronic Proceedings in Theoretical Computer Science, Volume 116. Turku: Open Publishing Association, 2013, s. 33-34. ISSN 2075-2180. Dostupné z: https://doi.org/10.4204/EPTCS.116.5.

VAN GOETHEM, Simon; Jean-Marie JACQUET; Luboš BRIM a David ŠAFRÁNEK. Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. Online. In Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12). Neuveden: Elsevier, 2013, s. 67-81. ISSN 1571-0661. Dostupné z: https://doi.org/10.1016/j.entcs.2013.02.019.

BRIM, Luboš; Jana FABRIKOVÁ; Sven DRAŽAN a David ŠAFRÁNEK. On Approximative Reachability Analysis of Biochemical Dynamical Systems. In Corrado Priami et al. Transactions on Computational Systems Biology XIV. Heidelberg: Springer, 2012, s. 77-101. ISBN 978-3-642-35523-3. Dostupné z: https://doi.org/10.1007/978-3-642-35524-0_4.

DLUHOŠ, Petr; Luboš BRIM a David ŠAFRÁNEK. On Expressing and Monitoring Oscillatory Dynamics. Electronic Proceedings in Theoretical Computer Science. Newcastle Upon Tyne: EPTCS, 2012, roč. 2012, č. 92, s. 73-87. ISSN 2075-2180. Dostupné z: https://doi.org/10.4204/EPTCS.92.

BARNAT, Jiří; Luboš BRIM; Adam KREJČÍ; Adam STRECK; David ŠAFRÁNEK; Martin VEJNÁR a Tomáš VEJPUSTEK. On Parameter Synthesis by Parallel Model Checking. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Los Alamitos: IEEE Computer Society, 2012, roč. 9, č. 3, s. 693-705. ISSN 1545-5963. Dostupné z: https://doi.org/10.1109/TCBB.2011.110.

KLARNER, Hannes; Adam STRECK; David ŠAFRÁNEK; Juraj KOLČÁK a Heike SIEBERT. Parameter Identification and Model Ranking of Thomas Networks. In Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings. Berlin: Springer, 2012, s. 207-226. ISBN 978-3-642-33635-5. Dostupné z: https://doi.org/10.1007/978-3-642-33636-2_13.

COLLINS, Pieter; Luc HABETS; Jan VAN SCHUPPEN; Ivana ČERNÁ; Jana FABRIKOVÁ a David ŠAFRÁNEK. Abstraction of Biochemical Reaction Systems on Polytopes. In Proceedings of the 18th IFAC World Congress. Milano: IFAC, 2011, s. 14869-14875. ISBN 978-1-1234-7890-2.

ŠAFRÁNEK, David; Jan ČERVENÝ; Matej KLEMENT; Jana POSPÍŠILOVÁ; Luboš BRIM; Dušan LAZÁR a Ladislav NEDBAL. E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. BioSystems. Elsevier, 2011, roč. 103, č. 2, s. 115-124. ISSN 0303-2647. Dostupné z: https://doi.org/10.1016/j.biosystems.2010.10.013.

BRIM, Luboš; Jana FABRIKOVÁ; Sven DRAŽAN a David ŠAFRÁNEK. Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation. Electronic Proceedings in Theoretical Computer Science. 2011, Neuveden, č. 67, s. 97-112, 15 s. ISSN 2075-2180. Dostupné z: https://doi.org/10.4204/EPTCS.67.9.

KLEMENT, Matej; David ŠAFRÁNEK; Jan ČERVENÝ; Luboš BRIM a Ladislav NEDBAL. E-photosynthesis: web software for modeling and analysis of biological processes behind photosynthesis. 2010.

BARNAT, Jiří; Luboš BRIM a David ŠAFRÁNEK. High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings in Bioinformatics. Oxford (UK): Oxford University Press, 2010, roč. 11, č. 3, s. 301-312. ISSN 1467-5463.

BARNAT, Jiří; Luboš BRIM; David ŠAFRÁNEK a Martin VEJNÁR. Parameter Scanning by Parallel Model Checking with Applications in Systems Biology. In Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology. Los Alamitos: IEEE Computer Society, 2010, s. 95-104. ISBN 978-0-7695-4265-2.

BARNAT, Jiří; Luboš BRIM; Ivana ČERNÁ; Sven DRAŽAN; Jana FABRIKOVÁ; Jan LÁNÍK; David ŠAFRÁNEK a Ma HONGWU. BioDiVinE: A Framework for Parallel Analysis of Biological Models. In Proceedings of 2nd International Workshop on Computational Models for Cell Processes. Neuveden: EPTCS, 2009, s. 31-45. ISSN 2075-2180.

BARNAT, Jiří; Luboš BRIM; Ivana ČERNÁ; Sven DRAŽAN; Jana FABRIKOVÁ; Jan LÁNÍK a David ŠAFRÁNEK. BioDiVinE: A Tool for Parallel Analysis of Multi-Affine ODE Models. In Computational Mehotds in Systems Biology: Abstract of the Posters. Pisa: University of Pisa, 2009, s. 1-5, 4 s.

BARNAT, Jiří; Luboš BRIM; Ivana ČERNÁ; Sven DRAŽAN; Jana FABRIKOVÁ a David ŠAFRÁNEK. Computational Analysis of Large-Scale Multi-Affine ODE Models. In International Workshop on High Performance Computational Systems Biology. Los Alamitos (California): IEEE Computer Society, 2009, s. 81-90. ISBN 978-0-7695-3809-9.

BARNAT, Jiří; Luboš BRIM; Ivana ČERNÁ; Sven DRAŽAN; Jana FABRIKOVÁ a David ŠAFRÁNEK. On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking. Theoretical Computer Science. 2009, roč. 2009, č. 410, s. 3128-3148, 20 s. ISSN 0304-3975.

BARNAT, Jiří; Luboš BRIM; Ivana ČERNÁ; Sven DRAŽAN a David ŠAFRÁNEK. From Simple Regulatory Motifs to Parallel Model Checking of Complex Transcriptional Networks. In Proceedings of PDMC 2008 - Parallel and Distributed Methods ins VerifiCation. Budapest: Ivana Cerna and Gerald Luettgen, 2008, s. 83-96, 15 s. ISSN 1571-0661.

BARNAT, Jiří; Luboš BRIM; Ivana ČERNÁ; Sven DRAŽAN a David ŠAFRÁNEK. Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. In Electronic Notes in Theoretical Computer Science. Vol. 194/3. Elsevier: Elsevier Science, 2008, s. 35-50, 15 s. ISSN 1571-0661.

ŠAFRÁNEK, David; Petr KOBIERSKÝ; Viktor PUŠ a Tom MÁLEK. SystemVerilog verification of VHDL design. CESNET, z.s.p.o. Praha: CESNET, z.s.p.o., 2007. CESNET Technical Reports.

SMRČKA, Aleš; Vojtěch ŘEHÁK; Tomáš VOJNAR; David ŠAFRÁNEK; Petr MATOUŠEK a Zdeněk ŘEHÁK. Verifying VHDL Designs with Multiple Clocks in SMV. In Formal Methods Applications and Technology, 11th International Workshop on Formal Methods for Industrial Critical Systems, FMICS 2006, and 5th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2006. Bonn: Springer-Verlag, 2007, s. 148-164, 16 s. ISBN 978-3-540-70951-0.

ŠAFRÁNEK, David. Architectural Interoperability Checking in Visual Coordination Networks. In Combined Proceedings of the Second International Workshop on Coordination and Organization (CoOrg 2006) and the Second International Workshop on Methods and Tools for Coordinating Concurrent, Distributed and Mobile Systems (MTCoord 2006). Bologna: Elsevier Science, 2006, s. 81-96, 15 s. ISSN 1571-0661.

KRAMÁREKOVÁ, Miroslava; Daniel JAKUBÍK; Martin ŽÁDNÍK a David ŠAFRÁNEK. FlowMon Cache Simulation and Analysis of Inter-Packet Gaps. CESNET, z.s.p.o. Praha: CESNET, z.s.p.o., 2006. CESNET Technical Report Series 32/2006. Dostupné z: https://doi.org/10.1000/182.

KRATOCHVÍLA, Tomáš; Vojtěch ŘEHÁK a David ŠAFRÁNEK. Formal Verification of a FIFO Component in Design of Network Monitoring Hardware. In 10 years of CESNET - CESNET CONFERENCE 2006. Praha: CESNET, z.s.p.o., 2006, s. 151-160. ISBN 978-80-239-6533-9.

SMRČKA, Aleš; Petr HLÁVKA; David ŠAFRÁNEK; Vojtěch ŘEHÁK; Pavel ŠIMEČEK a Tomáš VOJNAR. Formal Verification of the CRC Algorithm Properties. In Proceedings of 2nd Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2006). Brno: FIT BUT, 2006, s. 55-62. ISBN 80-214-3287-X.

ŠAFRÁNEK, David. Visual Coordination Networks. Brno: Masaryk University, 2006, 218 s. PhD Thesis.

ŠAFRÁNEK, David; Vojtěch ŘEHÁK; Tomáš KRATOCHVÍLA; Pavel ŠIMEČEK; Petr HLÁVKA a Tomáš VOJNAR. CRC64 Algorithm Analysis and Verification. Brno: CESNET, z. s. p. o., 2005. Technical Report 27/2005.

ŠAFRÁNEK, David a Jiří ŠIMŠA. VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. In SOFSEM 2005: Theory and Practice of Computer Science. Heidelberg: Springer, 2005, s. 320-330, 10 s. ISBN 3-540-24302-X.

HOLEČEK, Jan; Tomáš KRATOCHVÍLA; Vojtěch ŘEHÁK; David ŠAFRÁNEK a Pavel ŠIMEČEK. How to Formalize FPGA Hardware Design. Praha: CESNET, z.s.p.o., 2004. CESNET Technical Report No. 04/2004.

HOLEČEK, Jan; Tomáš KRATOCHVÍLA; Vojtěch ŘEHÁK; David ŠAFRÁNEK a Pavel ŠIMEČEK. Verification Process of Hardware Design in Liberouter Project. Praha: CESNET z.s.p.o., 2004. CESNET Technical Report No. 05/2004.

HOLEČEK, Jan; Tomáš KRATOCHVÍLA; Vojtěch ŘEHÁK; David ŠAFRÁNEK a Pavel ŠIMEČEK. Verification Results in Liberouter Project. Praha: CESNET, z.s.p.o., 2004. CESNET Technical Report No. 03/2004.

ŠAFRÁNEK, David. Visual Coordination Diagrams. In Proceedings of the Doctoral Symposium of 7th International Conference on the Unified Modeling Language. Lisbon, Portugal: Alanen M., Cabot J., Goulao M., Saez J. and Simmonds D. (editors), 2004, s. 53-60.

ŠAFRÁNEK, David. Visual Specification of Systems with Heterogeneous Coordination Models. In Proceeding of 3rd International Workshop on Foundations of Coordination Languages and Software Architectures. London: ENTCS, 2004, s. 107-121. ISSN 1571-0661.

ŠAFRÁNEK, David. Visual Specification of Concurrent Systems. In 18th IEEE International Conference on Automated Software Engineering. Montreal, Quebec, Canada: IEEE Computer Society, 2003, s. 369-372. ISBN 0-7695-2035-9.

ŠAFRÁNEK, David. SGCCS: A Graphical Language for Real-Time Coordination. In Proceedings of 1th International Workshop on Foundations of Coordination Languages and Software Architectures. Namur, Belgium: Elsevier Science, 2002, s. 99-114. ISSN 1571-0661.

ŠAFRÁNEK, David. SGCCS: A Graphical Language for Real-Time Systems. In Proceedings SOFSEM 2002 Student Research Forum. Milovy: Mária Bieliková, 2002, s. 47-52.

CRHOVÁ, Jitka; Pavel KRČÁL; Jan STREJČEK; David ŠAFRÁNEK a Pavel ŠIMEČEK. YAHODA: verification tools database. In Proceedings of Tools Day. Brno: FI MU, 2002, s. 99-103.

ŠAFRÁNEK, David. Grafická specifikace souběžných systémů. Brno: Masarykova universita, Fakulta informatiky, 2001, 68 s. Diplomová práce.