Müller, Stefan A new decomposition of the graph Laplacian and the binomial structure of mass-action systems. (English) Zbl 1519.05158 J. Nonlinear Sci. 33, No. 5, Paper No. 91, 29 p. (2023). MSC: 05C50 05C20 05C78 05C92 92E10 92E20 34D20 92C45 PDFBibTeX XMLCite \textit{S. Müller}, J. Nonlinear Sci. 33, No. 5, Paper No. 91, 29 p. (2023; Zbl 1519.05158) Full Text: DOI arXiv
Hernandez, Bryan S.; Mendoza, Eduardo R. Positive equilibria of power law kinetics on networks with independent linkage classes. (English) Zbl 1519.92365 J. Math. Chem. 61, No. 3, 630-651 (2023). Reviewer: Dieter Erle (Dortmund) MSC: 92E20 92C42 05C92 92C40 92C45 PDFBibTeX XMLCite \textit{B. S. Hernandez} and \textit{E. R. Mendoza}, J. Math. Chem. 61, No. 3, 630--651 (2023; Zbl 1519.92365) Full Text: DOI arXiv
Dorogovtsev, Sergey N.; Mendes, José F. F. The nature of complex networks. (English) Zbl 1515.82001 Oxford: Oxford University Press (ISBN 978-0-19-969511-9/hbk). xvi, 449 p. (2022). Reviewer: Norbert Hounkonnou (Cotonou) MSC: 82-01 05-01 82B20 82C20 82C26 82B41 82C43 05C80 05C82 68T05 68R10 60K35 93D30 92C45 PDFBibTeX XMLCite \textit{S. N. Dorogovtsev} and \textit{J. F. F. Mendes}, The nature of complex networks. Oxford: Oxford University Press (2022; Zbl 1515.82001) Full Text: DOI
Anderson, David F.; Nguyen, Tung D. Prevalence of deficiency-zero reaction networks in an Erdős-Rényi framework. (English) Zbl 1492.05142 J. Appl. Probab. 59, No. 2, 384-398 (2022). MSC: 05C80 05C90 92C42 92C45 PDFBibTeX XMLCite \textit{D. F. Anderson} and \textit{T. D. Nguyen}, J. Appl. Probab. 59, No. 2, 384--398 (2022; Zbl 1492.05142) Full Text: DOI arXiv
Yu, Polly Y.; Craciun, Gheorghe; Mincheva, Maya; Pantea, Casian A graph-theoretic condition for delay stability of reaction systems. (English) Zbl 1500.34073 SIAM J. Appl. Dyn. Syst. 21, No. 2, 1092-1118 (2022). Reviewer: Krishnan Balachandran (Coimbatore) MSC: 34K60 34K20 05C92 92C45 92C40 PDFBibTeX XMLCite \textit{P. Y. Yu} et al., SIAM J. Appl. Dyn. Syst. 21, No. 2, 1092--1118 (2022; Zbl 1500.34073) Full Text: DOI arXiv
Feliu, Elisenda; Lax, Christian; Walcher, Sebastian; Wiuf, Carsten Quasi-steady-state and singular perturbation reduction for reaction networks with noninteracting species. (English) Zbl 1496.92029 SIAM J. Appl. Dyn. Syst. 21, No. 2, 782-816 (2022). Reviewer: Dieter Erle (Dortmund) MSC: 92C45 92C42 92D25 34E15 34C20 05C92 05C90 92E10 PDFBibTeX XMLCite \textit{E. Feliu} et al., SIAM J. Appl. Dyn. Syst. 21, No. 2, 782--816 (2022; Zbl 1496.92029) Full Text: DOI arXiv
Conradi Smith, Gregory Douglas Allostery in oligomeric receptor models. (English) Zbl 1453.92121 Math. Med. Biol. 37, No. 3, 313-333 (2020). MSC: 92C45 05C90 PDFBibTeX XMLCite \textit{G. D. Conradi Smith}, Math. Med. Biol. 37, No. 3, 313--333 (2020; Zbl 1453.92121) Full Text: DOI DOI
Manuel, Cassius; von Haeseler, Arndt Structure of the space of taboo-free sequences. (English) Zbl 1451.92240 J. Math. Biol. 81, No. 4-5, 1029-1057 (2020). MSC: 92D20 05C90 PDFBibTeX XMLCite \textit{C. Manuel} and \textit{A. von Haeseler}, J. Math. Biol. 81, No. 4--5, 1029--1057 (2020; Zbl 1451.92240) Full Text: DOI
Rus, Jernej Parallelism of stable traces. (English) Zbl 1421.05060 Art Discrete Appl. Math. 2, No. 1, Paper No. P1.07, 13 p. (2019). MSC: 05C45 05C85 94C15 05C90 92C45 PDFBibTeX XMLCite \textit{J. Rus}, Art Discrete Appl. Math. 2, No. 1, Paper No. P1.07, 13 p. (2019; Zbl 1421.05060) Full Text: DOI arXiv
Feinberg, Martin Foundations of chemical reaction network theory. (English) Zbl 1420.92001 Applied Mathematical Sciences 202. Cham: Springer (ISBN 978-3-030-03857-1/hbk; 978-3-030-03858-8/ebook). xxix, 454 p. (2019). Reviewer: Dieter Erle (Dortmund) MSC: 92-02 92E20 92C40 92C42 92C45 76V05 93D05 05C90 PDFBibTeX XMLCite \textit{M. Feinberg}, Foundations of chemical reaction network theory. Cham: Springer (2019; Zbl 1420.92001) Full Text: DOI
Wong, Felix; Dutta, Annwesha; Chowdhury, Debashish; Gunawardena, Jeremy Structural conditions on complex networks for the Michaelis-Menten input-output response. (English) Zbl 1416.92085 Proc. Natl. Acad. Sci. USA 115, No. 39, 9738-9743 (2018). MSC: 92C45 05C82 PDFBibTeX XMLCite \textit{F. Wong} et al., Proc. Natl. Acad. Sci. USA 115, No. 39, 9738--9743 (2018; Zbl 1416.92085) Full Text: DOI
Pérez Millán, Mercedes; Dickenstein, Alicia The structure of MESSI biological systems. (English) Zbl 1395.92071 SIAM J. Appl. Dyn. Syst. 17, No. 2, 1650-1682 (2018). MSC: 92C42 92C45 05B35 52C40 PDFBibTeX XMLCite \textit{M. Pérez Millán} and \textit{A. Dickenstein}, SIAM J. Appl. Dyn. Syst. 17, No. 2, 1650--1682 (2018; Zbl 1395.92071) Full Text: DOI arXiv
Conradi, Carsten; Mincheva, Maya Graph-theoretic analysis of multistationarity using degree theory. (English) Zbl 1519.92082 Math. Comput. Simul. 133, 76-90 (2017). MSC: 92C45 92C42 05C90 PDFBibTeX XMLCite \textit{C. Conradi} and \textit{M. Mincheva}, Math. Comput. Simul. 133, 76--90 (2017; Zbl 1519.92082) Full Text: DOI arXiv
Tomellini, M.; Fanfoni, M. Interplay between Kolmogorov-Johnson-Mehl-Avrami kinetics and Poisson-Voronoi tessellation. (English) Zbl 1360.82031 Phys. Lett., A 380, No. 24, 2031-2037 (2016). MSC: 82B26 82C26 80A30 92C45 05B45 PDFBibTeX XMLCite \textit{M. Tomellini} and \textit{M. Fanfoni}, Phys. Lett., A 380, No. 24, 2031--2037 (2016; Zbl 1360.82031) Full Text: DOI
Kan, Xingye; Lee, Chang Hyeong; Othmer, Hans G. A multi-time-scale analysis of chemical reaction networks. II: Stochastic systems. (English) Zbl 1353.92049 J. Math. Biol. 73, No. 5, 1081-1129 (2016). MSC: 92C45 80A30 34E13 05C90 PDFBibTeX XMLCite \textit{X. Kan} et al., J. Math. Biol. 73, No. 5, 1081--1129 (2016; Zbl 1353.92049) Full Text: DOI arXiv Link
Gábor, Attila; Hangos, Katalin M.; Szederkényi, Gábor Linear conjugacy in biochemical reaction networks with rational reaction rates. (English) Zbl 1349.92067 J. Math. Chem. 54, No. 8, 1658-1676 (2016). MSC: 92C45 92E20 05C90 PDFBibTeX XMLCite \textit{A. Gábor} et al., J. Math. Chem. 54, No. 8, 1658--1676 (2016; Zbl 1349.92067) Full Text: DOI Link
Mirzaev, Inom; Bortz, David M. Laplacian dynamics with synthesis and degradation. (English) Zbl 1335.92036 Bull. Math. Biol. 77, No. 6, 1013-1045 (2015). MSC: 92C45 05C90 PDFBibTeX XMLCite \textit{I. Mirzaev} and \textit{D. M. Bortz}, Bull. Math. Biol. 77, No. 6, 1013--1045 (2015; Zbl 1335.92036) Full Text: DOI arXiv Link
Gábor, Attila; Hangos, Katalin M.; Banga, Julio R.; Szederkényi, Gábor Reaction network realizations of rational biochemical systems and their structural properties. (English) Zbl 1331.92057 J. Math. Chem. 53, No. 8, 1657-1686 (2015). MSC: 92C45 05C90 92C40 PDFBibTeX XMLCite \textit{A. Gábor} et al., J. Math. Chem. 53, No. 8, 1657--1686 (2015; Zbl 1331.92057) Full Text: DOI
Palsson, Bernhard Ø. Systems biology. Constraint-based reconstruction and analysis. (English) Zbl 1321.92013 Cambridge: Cambridge University Press (ISBN 978-1-107-03885-1/hbk; 978-1-139-85461-0/ebook). xviii, 431 p. (2015). MSC: 92-01 92C42 92C40 92C45 05C90 92D10 PDFBibTeX XMLCite \textit{B. Ø. Palsson}, Systems biology. Constraint-based reconstruction and analysis. Cambridge: Cambridge University Press (2015; Zbl 1321.92013) Full Text: DOI
Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F. 50 shades of rule composition. From chemical reactions to higher levels of abstraction. (English) Zbl 1402.92166 Fages, François (ed.) et al., Formal methods in macro-biology. First international conference, FMMB 2014, Nouméa, New Caledonia, September 22–24, 2014. Proceedings. Berlin: Springer (ISBN 978-3-319-10397-6/pbk). Lecture Notes in Computer Science 8738. Lecture Notes in Bioinformatics, 117-135 (2014). MSC: 92C40 05C90 PDFBibTeX XMLCite \textit{J. L. Andersen} et al., Lect. Notes Comput. Sci. 8738, 117--135 (2014; Zbl 1402.92166) Full Text: DOI
Feliu, Elisenda; Wiuf, Carsten Variable elimination in post-translational modification reaction networks with mass-action kinetics. (English) Zbl 1256.92019 J. Math. Biol. 66, No. 1-2, 281-310 (2013). MSC: 92C42 92C45 05C90 80A30 PDFBibTeX XMLCite \textit{E. Feliu} and \textit{C. Wiuf}, J. Math. Biol. 66, No. 1--2, 281--310 (2013; Zbl 1256.92019) Full Text: DOI arXiv
Mincheva, Maya Oscillations in biochemical reaction networks arising from pairs of subnetworks. (English) Zbl 1334.92179 Bull. Math. Biol. 73, No. 10, 2277-2304 (2011). MSC: 92C45 05C90 PDFBibTeX XMLCite \textit{M. Mincheva}, Bull. Math. Biol. 73, No. 10, 2277--2304 (2011; Zbl 1334.92179) Full Text: DOI
Demaine, Erik D.; Patitz, Matthew J.; Schweller, Robert T.; Summers, Scott M. Self-assembly of arbitrary shapes using RNAse enzymes: meeting the Kolmogorov bound with small scale factor (extended abstract). (English) Zbl 1230.68069 Schwentick, Thomas (ed.) et al., STACS 2011. 28th international symposium on theoretical aspects of computer science, Dortmund, Germany, March 10–12, 2011. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik (ISBN 978-3-939897-25-5). LIPIcs – Leibniz International Proceedings in Informatics 9, 201-212, electronic only (2011). MSC: 68Q05 05B45 68Q30 52C20 PDFBibTeX XMLCite \textit{E. D. Demaine} et al., LIPIcs -- Leibniz Int. Proc. Inform. 9, 201--212 (2011; Zbl 1230.68069) Full Text: DOI Link
Angeli, David; De Leenheer, Patrick; Sontag, Eduardo Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates. (English) Zbl 1204.92038 J. Math. Biol. 61, No. 4, 581-616 (2010). MSC: 92C45 05C90 37N25 PDFBibTeX XMLCite \textit{D. Angeli} et al., J. Math. Biol. 61, No. 4, 581--616 (2010; Zbl 1204.92038) Full Text: DOI
Bowsher, Clive G. Stochastic kinetic models: dynamic independence, modularity and graphs. (English) Zbl 1203.92033 Ann. Stat. 38, No. 4, 2242-2281 (2010). MSC: 92C45 60G55 92C37 05C20 92C42 37N25 05C90 PDFBibTeX XMLCite \textit{C. G. Bowsher}, Ann. Stat. 38, No. 4, 2242--2281 (2010; Zbl 1203.92033) Full Text: DOI arXiv
Baeumer, Boris; Chatterjee, Lipika; Hinow, Peter; Rades, Thomas; Radunskaya, Ami; Tucker, Ian Predicting the drug release kinetics of matrix tablets. (English) Zbl 1169.92022 Discrete Contin. Dyn. Syst., Ser. B 12, No. 2, 261-277 (2009). MSC: 92C50 92C45 05C90 35Q92 60G50 PDFBibTeX XMLCite \textit{B. Baeumer} et al., Discrete Contin. Dyn. Syst., Ser. B 12, No. 2, 261--277 (2009; Zbl 1169.92022) Full Text: DOI arXiv
Planes, F. J.; Beasley, J. E. Path finding approaches and metabolic pathways. (English) Zbl 1182.92038 Discrete Appl. Math. 157, No. 10, 2244-2256 (2009). MSC: 92C45 92C42 05C90 90C10 05C38 PDFBibTeX XMLCite \textit{F. J. Planes} and \textit{J. E. Beasley}, Discrete Appl. Math. 157, No. 10, 2244--2256 (2009; Zbl 1182.92038) Full Text: DOI
Blazewicz, Jacek; Formanowicz, Dorota; Formanowicz, Piotr; Sackmann, Andrea; Sajkowski, Michał Modeling the process of human body iron homeostasis using a variant of timed Petri nets. (English) Zbl 1194.92018 Discrete Appl. Math. 157, No. 10, 2221-2231 (2009). MSC: 92C30 05C90 92C45 92C40 PDFBibTeX XMLCite \textit{J. Blazewicz} et al., Discrete Appl. Math. 157, No. 10, 2221--2231 (2009; Zbl 1194.92018) Full Text: DOI
Macula, Anthony J.; Gal, Susannah; Andam, Cheryl; Bishop, Morgan A.; Renz, Thomas E. PCR nonadaptive group testing of DNA libraries for biomolecular computing and taggant applications. (English) Zbl 1171.92323 Discrete Math. Algorithms Appl. 1, No. 1, 59-69 (2009). MSC: 92C45 92C40 05B99 62P10 05C90 PDFBibTeX XMLCite \textit{A. J. Macula} et al., Discrete Math. Algorithms Appl. 1, No. 1, 59--69 (2009; Zbl 1171.92323) Full Text: DOI
Domijan, Mirela; Kirkilionis, Markus Graph theory and qualitative analysis of reaction networks. (English) Zbl 1141.92021 Netw. Heterog. Media 3, No. 2, 295-322 (2008). MSC: 92C45 37N25 05C90 92E20 PDFBibTeX XMLCite \textit{M. Domijan} and \textit{M. Kirkilionis}, Netw. Heterog. Media 3, No. 2, 295--322 (2008; Zbl 1141.92021) Full Text: DOI
Fages, François; Soliman, Sylvain From reaction models to influence graphs and back: a theorem. (English) Zbl 1375.92021 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, 90-102 (2008). MSC: 92C40 92C45 05C90 PDFBibTeX XMLCite \textit{F. Fages} and \textit{S. Soliman}, Lect. Notes Comput. Sci. 5054, 90--102 (2008; Zbl 1375.92021) Full Text: DOI
Angeli, David; De Leenheer, Patrick; Sontag, Eduardo D. A Petri net approach to the study of persistence in chemical reaction networks. (English) Zbl 1133.92322 Math. Biosci. 210, No. 2, 598-618 (2007). MSC: 92C45 68Q85 05C90 37N25 92E20 05C20 PDFBibTeX XMLCite \textit{D. Angeli} et al., Math. Biosci. 210, No. 2, 598--618 (2007; Zbl 1133.92322) Full Text: DOI arXiv
Ehrenfeucht, A.; Rozenberg, G. Events and modules in reaction systems. (English) Zbl 1119.93011 Theor. Comput. Sci. 376, No. 1-2, 3-16 (2007). MSC: 93A30 92C45 05C90 PDFBibTeX XMLCite \textit{A. Ehrenfeucht} and \textit{G. Rozenberg}, Theor. Comput. Sci. 376, No. 1--2, 3--16 (2007; Zbl 1119.93011) Full Text: DOI
Sardana, S.; Madan, A. K. Application of graph theory: Relationship of molecular connectivity index, Wiener’s index and eccentric connectivity index with diuretic activity. (English) Zbl 1018.92018 Match 43, 85-98 (2001). MSC: 92C50 05C90 92E10 92C45 PDFBibTeX XMLCite \textit{S. Sardana} and \textit{A. K. Madan}, Match 43, 85--98 (2001; Zbl 1018.92018)
Goldman, Deborah; Istrail, Sorin; Lancia, Giuseppe; Piccolboni, Antonio; Walenz, Brian Algorithmic strategies in combinatorial chemistry. (English) Zbl 0963.92015 Proceedings of the 11th annual ACM-SIAM symposium on Discrete algorithms. San Francisco, CA, USA, January 9-11, 2000. Philadelphia, PA: SIAM. 275-284 (2000). MSC: 92C40 92-08 05C90 92C45 65Y20 PDFBibTeX XMLCite \textit{D. Goldman} et al., in: Proceedings of the 11th annual ACM-SIAM symposium on discrete algorithms, SODA 2000, San Francisco, CA, USA, January 9--11, 2000. Philadelphia, PA: SIAM. 275--284 (2000; Zbl 0963.92015)
Wieland, Thomas Combinatorics of combinatorial chemistry. (English) Zbl 0890.92014 J. Math. Chem. 21, No. 2, 141-157 (1997). MSC: 92C45 05C90 92E20 PDFBibTeX XMLCite \textit{T. Wieland}, J. Math. Chem. 21, No. 2, 141--157 (1997; Zbl 0890.92014) Full Text: DOI
Pevzner, P. A. DNA physical mapping and alternating Eulerian cycles in colored graphs. (English) Zbl 0840.92011 Algorithmica 13, No. 1-2, 77-105 (1995). MSC: 92C40 68R10 05C90 68R15 05C15 PDFBibTeX XMLCite \textit{P. A. Pevzner}, Algorithmica 13, No. 1--2, 77--105 (1995; Zbl 0840.92011) Full Text: DOI
Siegel, D.; Chen, Y. F. Global stability of deficiency zero chemical networks. (English) Zbl 0823.92011 Can. Appl. Math. Q. 2, No. 3, 413-434 (1994). MSC: 92C45 05C90 92E20 34A99 34D99 PDFBibTeX XMLCite \textit{D. Siegel} and \textit{Y. F. Chen}, Can. Appl. Math. Q. 2, No. 3, 413--434 (1994; Zbl 0823.92011)
Skiena, Steven S.; Sundaram, Gopalakrishnan A partial digest approach to restriction site mapping. (English) Zbl 0790.92014 Bull. Math. Biol. 56, No. 2, 275-294 (1994). MSC: 92C40 92-08 68R99 92D20 68U99 68R05 05A99 PDFBibTeX XMLCite \textit{S. S. Skiena} and \textit{G. Sundaram}, Bull. Math. Biol. 56, No. 2, 275--294 (1994; Zbl 0790.92014) Full Text: DOI
Sellers, Peter H. Combinatorial aspects of enzyme kinetics. (English) Zbl 0719.92012 Applications of combinatorics and graph theory to biological and social sciences, Proc. Workshop 1987-88, IMA Vol. Math. Appl. 17, 295-314 (1989). Reviewer: D.Dorninger (Wien) MSC: 92C45 92E10 55U15 80A30 05C65 PDFBibTeX XML
Chou, Kuo-Chen; Jiang, Shou-Ping; Liu, Wei-Min; Chih-Hao, Fee Graph theory of enzyme kinetics. I: Steady-state reaction systems. (English) Zbl 0399.92007 Sci. Sin. 22, 341-358 (1979). MSC: 92Cxx 92Exx 05C99 PDFBibTeX XMLCite \textit{K.-C. Chou} et al., Sci. Sin. 22, 341--358 (1979; Zbl 0399.92007)