Leguizamon-Robayo, Alexander; Jiménez-Pastor, Antonio; Tribastone, Micro; Tschaikowski, Max; Vandin, Andrea Approximate constrained lumping of polynomial differential equations. (English) Zbl 07810887 Pang, Jun (ed.) et al., Computational methods in systems biology. 21st international conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 14137, 106-123 (2023). MSC: 92C42 34C60 PDFBibTeX XMLCite \textit{A. Leguizamon-Robayo} et al., Lect. Notes Comput. Sci. 14137, 106--123 (2023; Zbl 07810887) Full Text: DOI
Hemery, Mathieu; Fages, François On estimating derivatives of input signals in biochemistry. (English) Zbl 07810885 Pang, Jun (ed.) et al., Computational methods in systems biology. 21st international conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 14137, 78-96 (2023). MSC: 92C40 92C42 PDFBibTeX XMLCite \textit{M. Hemery} and \textit{F. Fages}, Lect. Notes Comput. Sci. 14137, 78--96 (2023; Zbl 07810885) Full Text: DOI arXiv
Julien, David; Cantin, Guillaume; Delahaye, Benoît End-to-end statistical model checking for parametric ODE models. (English) Zbl 1522.68325 Ábrahám, Erika (ed.) et al., Quantitative evaluation of systems. 19th international conference, QEST 2022, Warsaw, Poland, September 12–16, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13479, 85-106 (2022). MSC: 68Q60 65L05 92-10 PDFBibTeX XMLCite \textit{D. Julien} et al., Lect. Notes Comput. Sci. 13479, 85--106 (2022; Zbl 1522.68325) Full Text: DOI
Helfrich, Martin; Češka, Milan; Křetínský, Jan; Martiček, Štefan Abstraction-based segmental simulation of chemical reaction networks. (English) Zbl 1505.92074 Petre, Ion (ed.) et al., Computational methods in systems biology. 20th international conference, CMSB 2022, Bucharest, Romania, September 14–16, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13447, 41-60 (2022). MSC: 92C42 92C40 PDFBibTeX XMLCite \textit{M. Helfrich} et al., Lect. Notes Comput. Sci. 13447, 41--60 (2022; Zbl 1505.92074) Full Text: DOI arXiv
Yuan, Youyang; Lv, Hui; Zhang, Qiang Molecular device design based on chemical reaction networks: state feedback controller, static pre-filter, addition gate control system and full-dimensional state observer. (English) Zbl 1492.92165 J. Math. Chem. 60, No. 5, 915-935 (2022). MSC: 92E20 92C42 93B52 93C05 PDFBibTeX XMLCite \textit{Y. Yuan} et al., J. Math. Chem. 60, No. 5, 915--935 (2022; Zbl 1492.92165) Full Text: DOI
Doty, David; Severson, Eric ppsim: a software package for efficiently simulating and visualizing population protocols. (English) Zbl 1489.92003 Cinquemani, Eugenio (ed.) et al., Computational methods in systems biology. 19th international conference, CMSB 2021, Bordeaux, France, September 22–24, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12881, 245-253 (2021). MSC: 92-04 92C42 92C40 PDFBibTeX XMLCite \textit{D. Doty} and \textit{E. Severson}, Lect. Notes Comput. Sci. 12881, 245--253 (2021; Zbl 1489.92003) Full Text: DOI arXiv
Turpin, Baptiste; Bijman, Eline Y.; Kaltenbach, Hans-Michael; Stelling, Jörg Population design for synthetic gene circuits. (English) Zbl 1491.92066 Cinquemani, Eugenio (ed.) et al., Computational methods in systems biology. 19th international conference, CMSB 2021, Bordeaux, France, September 22–24, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12881, 181-197 (2021). MSC: 92C42 92D25 34C60 92-08 PDFBibTeX XMLCite \textit{B. Turpin} et al., Lect. Notes Comput. Sci. 12881, 181--197 (2021; Zbl 1491.92066) Full Text: DOI
Innocentini, Guilherme C. P.; Hodgkinson, Arran; Antoneli, Fernando; Debussche, Arnaud; Radulescu, Ovidiu Push-forward method for piecewise deterministic biochemical simulations. (English) Zbl 1518.92066 Theor. Comput. Sci. 893, 17-40 (2021). MSC: 92C40 92C42 60H30 35Q92 PDFBibTeX XMLCite \textit{G. C. P. Innocentini} et al., Theor. Comput. Sci. 893, 17--40 (2021; Zbl 1518.92066) Full Text: DOI arXiv
Gharesi, Niloofar; Arefi, Mohammad Mehdi; Khayatian, Alireza; Bahrami, Zahra Extended state observer-based control of heartbeat described by heterogeneous coupled oscillator model. (English) Zbl 1467.92106 Commun. Nonlinear Sci. Numer. Simul. 101, Article ID 105884, 15 p. (2021). MSC: 92C55 93B53 93C15 93D25 PDFBibTeX XMLCite \textit{N. Gharesi} et al., Commun. Nonlinear Sci. Numer. Simul. 101, Article ID 105884, 15 p. (2021; Zbl 1467.92106) Full Text: DOI
Bhattacharyya, Arnab; Gupta, Ashutosh; Kuppusamy, Lakshmanan; Mani, Somya; Shukla, Ankit; Srivas, Mandayam; Thattai, Mukund A formal methods approach to predicting new features of the eukaryotic vesicle traffic system. (English) Zbl 1512.92022 Acta Inf. 58, No. 1-2, 57-93 (2021). MSC: 92C37 05C90 68T20 PDFBibTeX XMLCite \textit{A. Bhattacharyya} et al., Acta Inf. 58, No. 1--2, 57--93 (2021; Zbl 1512.92022) Full Text: DOI
Condon, Anne; Hajiaghayi, Monir; Kirkpatrick, David; Maňuch, Ján Approximate majority analyses using tri-molecular chemical reaction networks. (English) Zbl 07802747 Nat. Comput. 19, No. 1, 249-270 (2020). MSC: 68Q07 92C40 92C42 PDFBibTeX XMLCite \textit{A. Condon} et al., Nat. Comput. 19, No. 1, 249--270 (2020; Zbl 07802747) Full Text: DOI
Cavallo, James C.; Scholpp, Steffen; Flegg, Mark B. Delay-driven oscillations via axin2 feedback in the Wnt/\(\beta\)-catenin signalling pathway. (English) Zbl 1455.92056 J. Theor. Biol. 507, Article ID 110458, 20 p. (2020). MSC: 92C42 92C45 PDFBibTeX XMLCite \textit{J. C. Cavallo} et al., J. Theor. Biol. 507, Article ID 110458, 20 p. (2020; Zbl 1455.92056) Full Text: DOI
Gomes Paulino, Nuno Miguel; Foo, Mathias; Kim, Jongmin; Bates, Declan G. On the stability of nucleic acid feedback control systems. (English) Zbl 1451.92125 Automatica 119, Article ID 109103, 9 p. (2020). MSC: 92C40 92C42 93B52 93C10 PDFBibTeX XMLCite \textit{N. M. Gomes Paulino} et al., Automatica 119, Article ID 109103, 9 p. (2020; Zbl 1451.92125) Full Text: DOI arXiv
Chang, Jing; Carbó-Dorca, Ramon Fuzzy hypercubes and their time-like evolution. (English) Zbl 1454.05079 J. Math. Chem. 58, No. 7, 1337-1344 (2020). Reviewer: Weiping Li (Stillwater) MSC: 05C65 62E86 05C90 92E20 PDFBibTeX XMLCite \textit{J. Chang} and \textit{R. Carbó-Dorca}, J. Math. Chem. 58, No. 7, 1337--1344 (2020; Zbl 1454.05079) Full Text: DOI
Sunkara, Vikram Algebraic expressions of conditional expectations in gene regulatory networks. (English) Zbl 07121167 J. Math. Biol. 79, No. 5, 1779-1829 (2019). MSC: 65C40 60G20 92B05 PDFBibTeX XMLCite \textit{V. Sunkara}, J. Math. Biol. 79, No. 5, 1779--1829 (2019; Zbl 07121167) Full Text: DOI
Chu, Dominique Performance limits and trade-offs in entropy-driven biochemical computers. (English) Zbl 1397.92009 J. Theor. Biol. 443, 1-9 (2018). MSC: 92-08 92C40 PDFBibTeX XMLCite \textit{D. Chu}, J. Theor. Biol. 443, 1--9 (2018; Zbl 1397.92009) Full Text: DOI arXiv Link
Češka, Milan; Dannenberg, Frits; Paoletti, Nicola; Kwiatkowska, Marta; Brim, Luboš Precise parameter synthesis for stochastic biochemical systems. (English) Zbl 1373.92038 Acta Inf. 54, No. 6, 589-623 (2017). MSC: 92C40 92-08 PDFBibTeX XMLCite \textit{M. Češka} et al., Acta Inf. 54, No. 6, 589--623 (2017; Zbl 1373.92038) Full Text: DOI
Chu, Dominique Limited by sensing – a minimal stochastic model of the lag-phase during diauxic growth. (English) Zbl 1369.92069 J. Theor. Biol. 414, 137-146 (2017). MSC: 92C99 PDFBibTeX XMLCite \textit{D. Chu}, J. Theor. Biol. 414, 137--146 (2017; Zbl 1369.92069) Full Text: DOI Link
Flegg, Mark B. Smoluchowski reaction kinetics for reactions of any order. (English) Zbl 1362.37162 SIAM J. Appl. Math. 76, No. 4, 1403-1432 (2016). Reviewer: Ilya A. Chernov (Petrozavodsk) MSC: 37N25 37M05 68U20 92E20 60J70 80A30 92C40 PDFBibTeX XMLCite \textit{M. B. Flegg}, SIAM J. Appl. Math. 76, No. 4, 1403--1432 (2016; Zbl 1362.37162) Full Text: DOI arXiv
Lakin, Matthew R.; Stefanovic, Darko; Phillips, Andrew Modular verification of chemical reaction network encodings via serializability analysis. (English) Zbl 1339.92105 Theor. Comput. Sci. 632, 21-42 (2016). MSC: 92E20 PDFBibTeX XMLCite \textit{M. R. Lakin} et al., Theor. Comput. Sci. 632, 21--42 (2016; Zbl 1339.92105) Full Text: DOI
Dannenberg, Frits; Hahn, Ernst Moritz; Kwiatkowska, Marta Computing cumulative rewards using fast adaptive uniformization. (English) Zbl 1369.65014 ACM Trans. Model. Comput. Simul. 25, No. 2, Article No. 9, 23 p. (2015). MSC: 65C40 60J28 65C20 68Q60 92D20 92E20 PDFBibTeX XMLCite \textit{F. Dannenberg} et al., ACM Trans. Model. Comput. Simul. 25, No. 2, Article No. 9, 23 p. (2015; Zbl 1369.65014) Full Text: DOI
Boemo, Michael A.; Turberfield, Andrew J.; Cardelli, Luca Automated design and verification of localized DNA computation circuits. (English) Zbl 1404.68076 Phillips, Andrew (ed.) et al., DNA computing and molecular programming. 21st international conference, DNA 21, Boston and Cambridge, MA, USA, August 17–21, 2015. Proceedings. Cham: Springer (ISBN 978-3-319-21998-1/pbk; 978-3-319-21999-8/ebook). Lecture Notes in Computer Science 9211, 168-180 (2015). MSC: 68Q60 68Q05 92D20 PDFBibTeX XMLCite \textit{M. A. Boemo} et al., Lect. Notes Comput. Sci. 9211, 168--180 (2015; Zbl 1404.68076) Full Text: DOI
Ballarini, Paolo; Duflot, Marie Applications of an expressive statistical model checking approach to the analysis of genetic circuits. (English) Zbl 1337.92138 Theor. Comput. Sci. 599, 4-33 (2015). MSC: 92D10 92C42 68Q60 PDFBibTeX XMLCite \textit{P. Ballarini} and \textit{M. Duflot}, Theor. Comput. Sci. 599, 4--33 (2015; Zbl 1337.92138) Full Text: DOI
Ito, Sohei; Ichinose, Takuma; Shimakawa, Masaya; Izumi, Naoko; Hagihara, Shigeki; Yonezaki, Naoki Qualitative analysis of gene regulatory networks by temporal logic. (English) Zbl 1329.92049 Theor. Comput. Sci. 594, 151-179 (2015). MSC: 92C42 03B44 68Q60 PDFBibTeX XMLCite \textit{S. Ito} et al., Theor. Comput. Sci. 594, 151--179 (2015; Zbl 1329.92049) Full Text: DOI
Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea Component identification in biochemical pathways. (English) Zbl 1327.68163 Theor. Comput. Sci. 587, 104-124 (2015). MSC: 68Q60 92C40 PDFBibTeX XMLCite \textit{G. Pardini} et al., Theor. Comput. Sci. 587, 104--124 (2015; Zbl 1327.68163) Full Text: DOI
Bartocci, Ezio; Bortolussi, Luca; Nenzi, Laura; Sanguinetti, Guido System design of stochastic models using robustness of temporal properties. (English) Zbl 1327.68147 Theor. Comput. Sci. 587, 3-25 (2015). MSC: 68Q45 03B44 68Q60 68Q87 92C42 PDFBibTeX XMLCite \textit{E. Bartocci} et al., Theor. Comput. Sci. 587, 3--25 (2015; Zbl 1327.68147) Full Text: DOI
Andreychenko, Alexander; Krüger, Thilo; Spieler, David Analyzing oscillatory behavior with formal methods. (English) Zbl 1427.92016 Remke, Anne (ed.) et al., Stochastic model checking. Rigorous dependability analysis using model checking techniques for stochastic systems. International autumn school, ROCKS 2012, Vahrn, Italy, October 22–26, 2012. Advanced lectures. Berlin: Springer. Lect. Notes Comput. Sci. 8453, 1-25 (2014). MSC: 92B25 92C40 92D25 PDFBibTeX XMLCite \textit{A. Andreychenko} et al., Lect. Notes Comput. Sci. 8453, 1--25 (2014; Zbl 1427.92016) Full Text: DOI
Chen, Taolue; Diciolla, Marco; Kwiatkowska, Marta; Mereacre, Alexandru Quantitative verification of implantable cardiac pacemakers over hybrid heart models. (English) Zbl 1311.92100 Inf. Comput. 236, 87-101 (2014). MSC: 92C50 68Q45 68Q60 PDFBibTeX XMLCite \textit{T. Chen} et al., Inf. Comput. 236, 87--101 (2014; Zbl 1311.92100) Full Text: DOI
Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea An algorithm for the identification of components in biochemical pathways. (English) Zbl 1337.92066 Merelli, Emanuela (ed.) et al., Proceedings of the 4th international workshop on interactions between computer science and biology (CS2Bio’13), Florence, Italy, June 6, 2013. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 299, 69-84 (2013). MSC: 92C40 68Q45 68Q85 PDFBibTeX XMLCite \textit{G. Pardini} et al., Electron. Notes Theor. Comput. Sci. 299, 69--84 (2013; Zbl 1337.92066) Full Text: DOI
John, Mathias; Schulz, Hans-Jörg; Schumann, Heidrun; Uhrmacher, Adelinde M.; Unger, Andrea Constructing and visualizing chemical reaction networks from pi-calculus models. (English) Zbl 1298.92128 Formal Asp. Comput. 25, No. 5, 723-742 (2013). MSC: 92E20 68Q85 PDFBibTeX XMLCite \textit{M. John} et al., Formal Asp. Comput. 25, No. 5, 723--742 (2013; Zbl 1298.92128) Full Text: DOI
Brim, Luboš; Češka, Milan; Šafránek, David Model checking of biological systems. (English) Zbl 1380.92024 Bernardo, Marco (ed.) et al., Formal methods for dynamical systems. 13th international school on formal methods for the design of computer, communication, and software systems, SFM 2013, Bertinoro, Italy, June 17–22, 2013. Advanced lectures. Berlin: Springer (ISBN 978-3-642-38873-6/pbk). Lecture Notes in Computer Science 7938, 63-112 (2013). MSC: 92C42 68Q60 92-08 PDFBibTeX XMLCite \textit{L. Brim} et al., Lect. Notes Comput. Sci. 7938, 63--112 (2013; Zbl 1380.92024) Full Text: DOI
Yuan, Qixia; Trairatphisan, Panuwat; Pang, Jun; Mauw, Sjouke; Wiesinger, Monique; Sauter, Thomas Probabilistic model checking of the PDGF signaling pathway. (English) Zbl 1381.92033 Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology XIV. Special issue on computational models for cell processes. Berlin: Springer (ISBN 978-3-642-35523-3/pbk). Lecture Notes in Computer Science 7625. Lecture Notes in Bioinformatics. Journal Subline, 151-180 (2012). MSC: 92C40 92-08 PDFBibTeX XMLCite \textit{Q. Yuan} et al., Lect. Notes Comput. Sci. 7625, 151--180 (2012; Zbl 1381.92033) Full Text: DOI
Donaldson, Robin; Calder, Muffy Modular modelling of signalling pathways and their cross-talk. (English) Zbl 1250.92014 Theor. Comput. Sci. 456, 30-50 (2012). MSC: 92C42 92C55 92C37 PDFBibTeX XMLCite \textit{R. Donaldson} and \textit{M. Calder}, Theor. Comput. Sci. 456, 30--50 (2012; Zbl 1250.92014) Full Text: DOI
Caravagna, Giulio; Hillston, Jane Bio-PEPAd: a non-Markovian extension of Bio-PEPA. (English) Zbl 1232.68090 Theor. Comput. Sci. 419, 26-49 (2012). MSC: 68Q85 68Q87 92C42 PDFBibTeX XMLCite \textit{G. Caravagna} and \textit{J. Hillston}, Theor. Comput. Sci. 419, 26--49 (2012; Zbl 1232.68090) Full Text: DOI
Barbuti, Roberto; Levi, Francesca; Milazzo, Paolo; Scatena, Guido Probabilistic model checking of biological systems with uncertain kinetic rates. (English) Zbl 1234.92020 Theor. Comput. Sci. 419, 2-16 (2012). MSC: 92C42 68Q42 60J20 PDFBibTeX XMLCite \textit{R. Barbuti} et al., Theor. Comput. Sci. 419, 2--16 (2012; Zbl 1234.92020) Full Text: DOI
Liu, Bing; Hsu, David; Thiagarajan, P. S. Probabilistic approximations of ODEs based bio-pathway dynamics. (English) Zbl 1211.92022 Theor. Comput. Sci. 412, No. 21, 2188-2206 (2011). MSC: 92C40 92C42 34C99 65C20 60J20 PDFBibTeX XMLCite \textit{B. Liu} et al., Theor. Comput. Sci. 412, No. 21, 2188--2206 (2011; Zbl 1211.92022) Full Text: DOI
Jha, Sumit Kumar; Langmead, Christopher James Synthesis and infeasibility analysis for stochastic models of biochemical systems using statistical model checking and abstraction refinement. (English) Zbl 1211.92021 Theor. Comput. Sci. 412, No. 21, 2162-2187 (2011). MSC: 92C40 92C42 60J20 62P10 65C20 68Q99 PDFBibTeX XMLCite \textit{S. K. Jha} and \textit{C. J. Langmead}, Theor. Comput. Sci. 412, No. 21, 2162--2187 (2011; Zbl 1211.92021) Full Text: DOI
Chu, Dominique; Barnes, David J. Modeling fimbriae mediated parasite-host interactions. (English) Zbl 1406.92097 J. Theor. Biol. 264, No. 4, 1169-1176 (2010). MSC: 92C30 92C37 PDFBibTeX XMLCite \textit{D. Chu} and \textit{D. J. Barnes}, J. Theor. Biol. 264, No. 4, 1169--1176 (2010; Zbl 1406.92097) Full Text: DOI
Drábik, Peter; Maggiolo-Schettini, Andrea; Milazzo, Paolo Modular verification of interactive systems with an application to biology. (English) Zbl 1283.68204 Krivine, Jean (ed.) et al., Proceedings of the 1st international workshop on interactions between computer science and biology (CS2Bio’10), Amsterdam, The Netherlands, June 10, 2010. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 268, 61-75 (2010). MSC: 68Q60 68Q45 92C42 PDFBibTeX XMLCite \textit{P. Drábik} et al., Electron. Notes Theor. Comput. Sci. 268, 61--75 (2010; Zbl 1283.68204) Full Text: DOI
Andrei, Oana; Calder, Muffy A model and analysis of the AKAP scaffold. (English) Zbl 1283.92014 Krivine, Jean (ed.) et al., Proceedings of the 1st international workshop on interactions between computer science and biology (CS2Bio’10), Amsterdam, The Netherlands, June 10, 2010. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 268, 3-15 (2010). MSC: 92C17 68Q60 92C40 PDFBibTeX XMLCite \textit{O. Andrei} and \textit{M. Calder}, Electron. Notes Theor. Comput. Sci. 268, 3--15 (2010; Zbl 1283.92014) Full Text: DOI
Breitling, Rainer; Donaldson, Robin A.; Gilbert, David R.; Heiner, Monika Biomodel engineering – from structure to behavior. (English) Zbl 1275.92022 Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology XII. Special issue on modeling methodologies. Berlin: Springer (ISBN 978-3-642-11711-4/pbk). Lecture Notes in Computer Science 5945. Lecture Notes in Bioinformatics. Journal Subline, 1-12 (2010). MSC: 92C42 68Q85 92-08 PDFBibTeX XMLCite \textit{R. Breitling} et al., Lect. Notes Comput. Sci. 5945, 1--12 (2010; Zbl 1275.92022) Full Text: DOI
Chu, Dominique; Zabet, Nicolae Radu; Mitavskiy, Boris Models of transcription factor binding: sensitivity of activation functions to model assumptions. (English) Zbl 1400.92182 J. Theor. Biol. 257, No. 3, 419-429 (2009). MSC: 92C40 60J20 PDFBibTeX XMLCite \textit{D. Chu} et al., J. Theor. Biol. 257, No. 3, 419--429 (2009; Zbl 1400.92182) Full Text: DOI Link
Basuki, Thomas Anung; Cerone, Antonio; Milazzo, Paolo Translating stochastic CLS into Maude. (English) Zbl 1347.68340 Ciobanu, Gabriel (ed.), Proceedings of the 2nd international meeting on membrane computing and biologically inspired process calculi (MeCBIC 2008), Iaşi, Romania, September 3–4, 2008. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 227, 37-58 (2009). MSC: 68U05 68Q42 68Q60 92C40 PDFBibTeX XMLCite \textit{T. A. Basuki} et al., Electron. Notes Theor. Comput. Sci. 227, 37--58 (2009; Zbl 1347.68340) Full Text: DOI
Ballarini, Paolo; Mardare, Radu; Mura, Ivan Analysing biochemical oscillation through probabilistic model checking. (English) Zbl 1283.92023 Cannata, Nicola (ed.) et al., Proceedings of the 2nd workshop – from biology to concurrency and back (FBTC 2008), Reykjavik, Iceland, July 12, 2008. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 229, No. 1, 3-19 (2009). MSC: 92C40 68Q60 PDFBibTeX XMLCite \textit{P. Ballarini} et al., Electron. Notes Theor. Comput. Sci. 229, No. 1, 3--19 (2009; Zbl 1283.92023) Full Text: DOI
Barbuti, Roberto; Levi, Francesca; Milazzo, Paolo; Scatena, Guido Probabilistic model checking of biological systems with uncertain kinetic rates. (English) Zbl 1260.68226 Bournez, Olivier (ed.) et al., Reachability problems. 3rd international workshop, RP 2009, Palaiseau, France, September 23–25, 2009. Proceedings. Berlin: Springer (ISBN 978-3-642-04419-9/pbk). Lecture Notes in Computer Science 5797, 64-78 (2009). MSC: 68Q60 68Q87 92C42 PDFBibTeX XMLCite \textit{R. Barbuti} et al., Lect. Notes Comput. Sci. 5797, 64--78 (2009; Zbl 1260.68226) Full Text: DOI
Calder, Muffy; Hillston, Jane Process algebra modelling styles for biomolecular processes. (English) Zbl 1260.92030 Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology XI. Berlin: Springer (ISBN 978-3-642-04185-3/pbk). Lecture Notes in Computer Science 5750. Lecture Notes in Bioinformatics. Journal Subline, 1-25 (2009). MSC: 92C45 68Q85 PDFBibTeX XMLCite \textit{M. Calder} and \textit{J. Hillston}, Lect. Notes Comput. Sci. 5750, 1--25 (2009; Zbl 1260.92030) Full Text: DOI
Ciocchetta, Federica; Hillston, Jane Bio-PEPA: A framework for the modelling and analysis of biological systems. (English) Zbl 1173.68041 Theor. Comput. Sci. 410, No. 33-34, 3065-3084 (2009). MSC: 68Q85 92B05 92C40 PDFBibTeX XMLCite \textit{F. Ciocchetta} and \textit{J. Hillston}, Theor. Comput. Sci. 410, No. 33--34, 3065--3084 (2009; Zbl 1173.68041) Full Text: DOI
van Bakel, S.; Khan, I.; Vigliotti, M. G.; Heath, J. K. Modelling intracellular fate of FGF receptors with BioAmbients. (English) Zbl 1286.68360 Aldini, Alessandro (ed.) et al., Proceedings of the 6th workshop on quantitative aspects of programming languages (QAPL 2008), Budapest, Hungary, March 29–30, 2008. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 220, No. 3, 181-197 (2008). MSC: 68Q85 68Q87 92C42 PDFBibTeX XMLCite \textit{S. van Bakel} et al., Electron. Notes Theor. Comput. Sci. 220, No. 3, 181--197 (2008; Zbl 1286.68360) Full Text: DOI
Gaffney, E. A.; Heath, J. K.; Kwiatkowska, M. Z. A mass action model of a fibroblast growth factor signaling pathway and its simplification. (English) Zbl 1169.92012 Bull. Math. Biol. 70, No. 8, 2229-2263 (2008). MSC: 92C30 37N25 PDFBibTeX XMLCite \textit{E. A. Gaffney} et al., Bull. Math. Biol. 70, No. 8, 2229--2263 (2008; Zbl 1169.92012) Full Text: DOI Link
Tymchyshyn, Oksana; Kwiatkowska, Marta Combining intra- and inter-cellular dynamics to investigate intestinal homeostasis. (English) Zbl 1375.92015 Fisher, Jasmin (ed.), Formal methods in systems biology. First international workshop, FMSB 2008, Cambridge, UK, June 4–5, 2008. Proceedings. Berlin: Springer (ISBN 978-3-540-68410-7/pbk). Lecture Notes in Computer Science 5054. Lecture Notes in Bioinformatics, 63-76 (2008). MSC: 92C30 92C42 68Q85 PDFBibTeX XMLCite \textit{O. Tymchyshyn} and \textit{M. Kwiatkowska}, Lect. Notes Comput. Sci. 5054, 63--76 (2008; Zbl 1375.92015) Full Text: DOI
Fisher, Jasmin; Henzinger, Thomas A.; Mateescu, Maria; Piterman, Nir Bounded asynchrony: concurrency for modeling cell-cell interactions. (English) Zbl 1375.92018 Fisher, Jasmin (ed.), Formal methods in systems biology. First international workshop, FMSB 2008, Cambridge, UK, June 4–5, 2008. Proceedings. Berlin: Springer (ISBN 978-3-540-68410-7/pbk). Lecture Notes in Computer Science 5054. Lecture Notes in Bioinformatics, 17-32 (2008). MSC: 92C37 68Q60 68Q85 PDFBibTeX XMLCite \textit{J. Fisher} et al., Lect. Notes Comput. Sci. 5054, 17--32 (2008; Zbl 1375.92018) Full Text: DOI
Heath, John; Kwiatkowska, Marta; Norman, Gethin; Parker, David; Tymchyshyn, Oksana Probabilistic model checking of complex biological pathways. (English) Zbl 1133.68043 Theor. Comput. Sci. 391, No. 3, 239-257 (2008). MSC: 68Q60 92C40 92E20 PDFBibTeX XMLCite \textit{J. Heath} et al., Theor. Comput. Sci. 391, No. 3, 239--257 (2008; Zbl 1133.68043) Full Text: DOI Link
Cardelli, Luca On process rate semantics. (English) Zbl 1133.68054 Theor. Comput. Sci. 391, No. 3, 190-215 (2008). MSC: 68Q85 92E20 PDFBibTeX XMLCite \textit{L. Cardelli}, Theor. Comput. Sci. 391, No. 3, 190--215 (2008; Zbl 1133.68054) Full Text: DOI