{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T17:57:38Z","timestamp":1725472658857},"publisher-location":"Berlin, Heidelberg","reference-count":33,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540457794"},{"type":"electronic","value":"9783540462361"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006]]},"DOI":"10.1007\/11880646_7","type":"book-chapter","created":{"date-parts":[[2006,11,17]],"date-time":"2006-11-17T09:13:44Z","timestamp":1163754824000},"page":"150-175","source":"Crossref","is-referenced-by-count":14,"title":["Automated Abstraction Methodology for Genetic Regulatory Networks"],"prefix":"10.1007","author":[{"given":"Hiroyuki","family":"Kuwahara","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris J.","family":"Myers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael S.","family":"Samoilov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan A.","family":"Barker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam P.","family":"Arkin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"1","key":"7_CR1","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1089\/10665270252833208","volume":"9","author":"H.D. Jong","year":"2002","unstructured":"Jong, H.D.: Modeling and simulation of genetic regulatory systems: A literature review. J. Comp. Biol.\u00a09(1), 67\u2013103 (2002)","journal-title":"J. Comp. Biol."},{"key":"7_CR2","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511541773","volume-title":"DNA Microarrays and Gene Expression","author":"P. Baldi","year":"2002","unstructured":"Baldi, P., Hatfield, G.W.: DNA Microarrays and Gene Expression. Cambridge University Press, Cambridge (2002)"},{"key":"7_CR3","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1093\/genetics\/149.4.1633","volume":"149","author":"A. Arkin","year":"1998","unstructured":"Arkin, A., Ross, J., McAdams, H.H.: Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected escherichia coli cells. Genetics\u00a0149, 1633\u20131648 (1998)","journal-title":"Genetics"},{"key":"7_CR4","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1126\/science.1070919","volume":"297","author":"M.B. Elowitz","year":"2002","unstructured":"Elowitz, M.B., Levine, A.J., Siggia, E.D., Swain, P.S.: Stochastic gene expression in a single cell. Science\u00a0297, 1183\u20131186 (2002)","journal-title":"Science"},{"key":"7_CR5","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/nature01258","volume":"420","author":"C.V. Rao","year":"2002","unstructured":"Rao, C.V., Wolf, D.M., Arkin, A.P.: Control, exploitation and tolerance of intracellular noise. Nature\u00a0420, 231\u2013238 (2002)","journal-title":"Nature"},{"issue":"7","key":"7_CR6","doi-asserted-by":"publisher","first-page":"2310","DOI":"10.1073\/pnas.0406841102","volume":"102","author":"M. Samoilov","year":"2005","unstructured":"Samoilov, M., Plyasunov, S., Arkin, A.P.: Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proceedings of the National Academy of Sciences US\u00a0102(7), 2310\u20132315 (2005)","journal-title":"Proceedings of the National Academy of Sciences US"},{"key":"7_CR7","doi-asserted-by":"publisher","first-page":"1811","DOI":"10.1126\/science.1098641","volume":"304","author":"J.M. Raser","year":"2004","unstructured":"Raser, J.M., O\u2019Shea, E.K.: Control of stochasticity in eukaryotic gene expression. Science\u00a0304, 1811\u20131814 (2004)","journal-title":"Science"},{"key":"7_CR8","doi-asserted-by":"publisher","first-page":"8165","DOI":"10.1074\/jbc.M006264200","volume":"276","author":"A.M. Kierzek","year":"2001","unstructured":"Kierzek, A.M., Zaim, J., Zielenkiewicz, P.: The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J. Biol. Chem\u00a0276, 8165 (2001)","journal-title":"J. Biol. Chem"},{"key":"7_CR9","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/0378-4371(92)90283-V","volume":"188","author":"D.T. Gillespie","year":"1992","unstructured":"Gillespie, D.T.: A rigorous derivation of the chemical master equation. Physica A\u00a0188, 404\u2013425 (1992)","journal-title":"Physica A"},{"key":"7_CR10","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/0021-9991(76)90041-3","volume":"22","author":"D.T. Gillespie","year":"1976","unstructured":"Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics\u00a022, 403\u2013434 (1976)","journal-title":"Journal of Computational Physics"},{"key":"7_CR11","doi-asserted-by":"crossref","unstructured":"Turner, T.E., Schnell, S., Burrage, K.: Stochastic approaches for modelling in vivo reactions. Computational Biology\u00a028 (2004)","DOI":"10.1016\/j.compbiolchem.2004.05.001"},{"key":"7_CR12","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1021\/jp993732q","volume":"A 104","author":"M.A. Gibson","year":"2000","unstructured":"Gibson, M.A., Bruck, J.: Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem.\u00a0A 104, 1876\u20131889 (2000)","journal-title":"J. Phys. Chem."},{"key":"7_CR13","unstructured":"Gibson, M., Bruck, J.: An efficient algorithm for generating trajectories of stochastic gene regulation reactions. Technical report, California Institute of Technology (1998)"},{"issue":"4","key":"7_CR14","doi-asserted-by":"publisher","first-page":"1716","DOI":"10.1063\/1.1378322","volume":"115","author":"D.T. Gillespie","year":"2001","unstructured":"Gillespie, D.T.: Approximate accelerated stochastic simulation of chemically reacting systems. Journal of Chemical Physics\u00a0115(4), 1716\u20131733 (2001)","journal-title":"Journal of Chemical Physics"},{"key":"7_CR15","doi-asserted-by":"publisher","first-page":"12784","DOI":"10.1063\/1.1627296","volume":"119","author":"M. Rathinam","year":"2003","unstructured":"Rathinam, M., Cao, Y., Petzold, L., Gillespie, D.: Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method. Journal of Chemical Physics\u00a0119, 12784\u201312794 (2003)","journal-title":"Journal of Chemical Physics"},{"key":"7_CR16","doi-asserted-by":"crossref","unstructured":"Gillespie, D.T., Petzold, L.R.: Improved leap-size selection for accelerated stochastic simulation. Journal of Chemical Physics\u00a0119 (2003)","DOI":"10.1063\/1.1613254"},{"key":"7_CR17","doi-asserted-by":"crossref","unstructured":"Cao, Y., Gillespie, D., Petzold, L.: Avoiding negative populations in explicit tau leaping. Journal of Chemical Physics\u00a0123 (2005)","DOI":"10.1063\/1.1992473"},{"key":"7_CR18","doi-asserted-by":"crossref","unstructured":"Rao, C.V., Arkin, A.P.: Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the gillespie algorithm. J. Phys. Chem.\u00a0118(11) (2003)","DOI":"10.1063\/1.1545446"},{"key":"7_CR19","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1080\/08948550302453","volume":"8","author":"S. Schnell","year":"2003","unstructured":"Schnell, S., Maini, P.K.: A century of enzyme kinetics: Reliability of the k m and v max estimates. Comments on Theoretical Biology\u00a08, 169\u2013187 (2003)","journal-title":"Comments on Theoretical Biology"},{"key":"7_CR20","doi-asserted-by":"crossref","unstructured":"Myers, C.J., Belluomini, W., Killpack, K., Mercer, E., Peskin, E., Zheng, H.: Timed circuits: A new paradigm for high-speed design, pp. 335\u2013340 (2001)","DOI":"10.1145\/370155.370379"},{"key":"7_CR21","volume-title":"Physical Chemistry","author":"R.S. Berry","year":"2000","unstructured":"Berry, R.S., Rice, S.A., Ross, J.: Physical Chemistry, 2nd edn. Oxford University Press, New York (2000)","edition":"2"},{"key":"7_CR22","unstructured":"Systems Biology Workbench\u00a0Development Group, http:\/\/www.sbw-sbml.org\/"},{"key":"7_CR23","unstructured":"BioSPICE, http:\/\/www.biospice.org\/"},{"key":"7_CR24","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1023\/A:1019139423811","volume":"27","author":"S. Schnell","year":"2000","unstructured":"Schnell, S., Mendoza, C.: Enzyme kinetics of multiple alternative substrates. Journal of Mathematical Chemistry\u00a027, 155\u2013170 (2000)","journal-title":"Journal of Mathematical Chemistry"},{"key":"7_CR25","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1073\/pnas.79.4.1129","volume":"79","author":"G.K. Ackers","year":"1982","unstructured":"Ackers, G.K., Johnson, A.D., Shea, M.A.: Quantitative model for gene regulation by \u03bb phage repressor. Proc. Natl. Acad. Sci. USA\u00a079, 1129\u20131133 (1982)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"7_CR26","doi-asserted-by":"crossref","unstructured":"Santill\u00e1n, M., Mackey, M.C.: Why the lysogenic state of phase \u03bb is stable: A mathematical modeling approch. Biophysical Jounal\u00a086 (2004)","DOI":"10.1016\/S0006-3495(04)74085-0"},{"key":"7_CR27","doi-asserted-by":"crossref","unstructured":"Dacol, D.K., Rabitz, H.: Sensitivity analysis of stochastic kinetic models. J. Math. Phys.\u00a025 (1984)","DOI":"10.1063\/1.526478"},{"key":"7_CR28","doi-asserted-by":"publisher","first-page":"2530","DOI":"10.1529\/biophysj.104.053405","volume":"88","author":"R. Gunawan","year":"2005","unstructured":"Gunawan, R., Cao, Y., Petzold, L., Doyle, F.J.: Sensitivity analysis of discrete stochastic systems. Biophysical Journal\u00a088, 2530\u20132540 (2005)","journal-title":"Biophysical Journal"},{"key":"7_CR29","unstructured":"REB2SAC, http:\/\/www.async.ece.utah.edu\/tools\/"},{"key":"7_CR30","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1007\/BF00435190","volume":"122","author":"P. Kourilsky","year":"1973","unstructured":"Kourilsky, P.: Lysogenization by bacteriophage lambda: I. multiple infection and the lysogenic response. Mol. Gen. Genet.\u00a0122, 183\u2013195 (1973)","journal-title":"Mol. Gen. Genet."},{"issue":"25","key":"7_CR31","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"D.T. Gillespie","year":"1977","unstructured":"Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem.\u00a081(25), 2340\u20132361 (1977)","journal-title":"J. Phys. Chem."},{"key":"7_CR32","volume-title":"Markov Processes An Introduction for Physical Scientists","author":"D.T. Gillespie","year":"1992","unstructured":"Gillespie, D.T.: Markov Processes An Introduction for Physical Scientists. Academic Press, London (1992)"},{"key":"7_CR33","volume-title":"Introduction to the Numerical Solution of Markov Chains","author":"W.J. Stewart","year":"1994","unstructured":"Stewart, W.J.: Introduction to the Numerical Solution of Markov Chains. Princeton University Press, Princeton (1994)"}],"container-title":["Lecture Notes in Computer Science","Transactions on Computational Systems Biology VI"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/11880646_7.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,4]],"date-time":"2021-08-04T20:33:40Z","timestamp":1628109220000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/11880646_7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006]]},"ISBN":["9783540457794","9783540462361"],"references-count":33,"URL":"https:\/\/doi.org\/10.1007\/11880646_7","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2006]]}}}