Zhang, Manyu; Zhao, Alice; Guo, Chun; Guo, Lingzhong A combined modelling and experimental study of heat shock factor SUMOylation in response to heat shock. (English) Zbl 1472.92110 J. Theor. Biol. 530, Article ID 110877, 10 p. (2021). MSC: 92C40 PDFBibTeX XMLCite \textit{M. Zhang} et al., J. Theor. Biol. 530, Article ID 110877, 10 p. (2021; Zbl 1472.92110) Full Text: DOI
Avello, Paula; Davis, Seth J.; Pitchford, Jonathan W. Temperature robustness in Arabidopsis circadian clock models is facilitated by repressive interactions, autoregulation, and three-node feedbacks. (English) Zbl 1457.92017 J. Theor. Biol. 509, Article ID 110495, 10 p. (2021). MSC: 92B25 PDFBibTeX XMLCite \textit{P. Avello} et al., J. Theor. Biol. 509, Article ID 110495, 10 p. (2021; Zbl 1457.92017) Full Text: DOI
Parra-Rojas, César; Fürtig, Boris; Schwalbe, Harald; Hernandez-Vargas, Esteban A. Quantitative modeling of the function of kinetically driven transcriptional riboswitches. (English) Zbl 1455.92049 J. Theor. Biol. 506, Article ID 110406, 9 p. (2020). MSC: 92C40 92-10 PDFBibTeX XMLCite \textit{C. Parra-Rojas} et al., J. Theor. Biol. 506, Article ID 110406, 9 p. (2020; Zbl 1455.92049) Full Text: DOI DOI
Nakajima, Rafael Takahiro; Costa, Pedro Rafael; Lemke, Ney Cooperative and sequence-dependent model for RNAP dynamics: application to ribosomal gene transcription. (English) Zbl 1430.92049 J. Theor. Biol. 488, Article ID 110134, 7 p. (2020). MSC: 92D10 PDFBibTeX XMLCite \textit{R. T. Nakajima} et al., J. Theor. Biol. 488, Article ID 110134, 7 p. (2020; Zbl 1430.92049) Full Text: DOI
Réda, Clémence; Wilczyński, Bartek Automated inference of gene regulatory networks using explicit regulatory modules. (English) Zbl 1429.92075 J. Theor. Biol. 486, Article ID 110091, 16 p. (2020). MSC: 92C42 92C40 PDFBibTeX XMLCite \textit{C. Réda} and \textit{B. Wilczyński}, J. Theor. Biol. 486, Article ID 110091, 16 p. (2020; Zbl 1429.92075) Full Text: DOI
Belitsky, V.; Schütz, G. M. RNA polymerase interactions and elongation rate. (English) Zbl 1406.92170 J. Theor. Biol. 462, 370-380 (2019). MSC: 92C40 PDFBibTeX XMLCite \textit{V. Belitsky} and \textit{G. M. Schütz}, J. Theor. Biol. 462, 370--380 (2019; Zbl 1406.92170) Full Text: DOI arXiv
Grinevich, Andrey A.; Yakushevich, Ludmila V. The influence of the DNA torque on the dynamics of transcription bubbles in plasmid PTTQ18. (English) Zbl 1400.92394 J. Theor. Biol. 453, 68-77 (2018). MSC: 92D20 92C40 35Q92 PDFBibTeX XMLCite \textit{A. A. Grinevich} and \textit{L. V. Yakushevich}, J. Theor. Biol. 453, 68--77 (2018; Zbl 1400.92394) Full Text: DOI
Fiorentino, Jonathan; De Martino, Andrea Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis. (English) Zbl 1382.92126 J. Theor. Biol. 430, 53-63 (2017). MSC: 92C40 92C45 PDFBibTeX XMLCite \textit{J. Fiorentino} and \textit{A. De Martino}, J. Theor. Biol. 430, 53--63 (2017; Zbl 1382.92126) Full Text: DOI arXiv
Almeira, N.; Risau-Gusman, S. Role of transcriptional bursts in cellular oscillations. (English) Zbl 1381.92021 J. Theor. Biol. 426, 49-56 (2017). MSC: 92C40 92C45 92B25 PDFBibTeX XMLCite \textit{N. Almeira} and \textit{S. Risau-Gusman}, J. Theor. Biol. 426, 49--56 (2017; Zbl 1381.92021) Full Text: DOI arXiv Link
Kuetche, Victor K. Ab initio bubble-driven denaturation of double-stranded DNA: self-mechanical theory. (English) Zbl 1343.92381 J. Theor. Biol. 401, 15-29 (2016). MSC: 92D20 92E10 PDFBibTeX XMLCite \textit{V. K. Kuetche}, J. Theor. Biol. 401, 15--29 (2016; Zbl 1343.92381) Full Text: DOI
Shreif, Zeina; Striegel, Deborah A.; Periwal, Vipul The jigsaw puzzle of sequence phenotype inference: piecing together Shannon entropy, importance sampling, and empirical Bayes. (English) Zbl 1343.92322 J. Theor. Biol. 380, 399-413 (2015). MSC: 92D10 94A17 62P10 PDFBibTeX XMLCite \textit{Z. Shreif} et al., J. Theor. Biol. 380, 399--413 (2015; Zbl 1343.92322) Full Text: DOI arXiv Link
Li, Rui; Xu, Liufang; Shi, Hualin Strategy of tuning gene expression ratio in prokaryotic cell from perspective of noise and correlation. (English) Zbl 1314.92101 J. Theor. Biol. 365, 377-389 (2015). MSC: 92D10 92C40 62P10 PDFBibTeX XMLCite \textit{R. Li} et al., J. Theor. Biol. 365, 377--389 (2015; Zbl 1314.92101) Full Text: DOI
Bhattacharya, Bonhi S.; Sweby, Peter K.; Minihane, Anne-Marie; Jackson, Kim G.; Tindall, Marcus J. A mathematical model of the sterol regulatory element binding protein 2 cholesterol biosynthesis pathway. (English) Zbl 1412.92079 J. Theor. Biol. 349, 150-162 (2014). MSC: 92C40 PDFBibTeX XMLCite \textit{B. S. Bhattacharya} et al., J. Theor. Biol. 349, 150--162 (2014; Zbl 1412.92079) Full Text: DOI
Zambrano, Samuel; Bianchi, Marco E.; Agresti, Alessandra A simple model of NF-\(\kappa\)B dynamics reproduces experimental observations. (English) Zbl 1412.92141 J. Theor. Biol. 347, 44-53 (2014). MSC: 92C45 92C40 PDFBibTeX XMLCite \textit{S. Zambrano} et al., J. Theor. Biol. 347, 44--53 (2014; Zbl 1412.92141) Full Text: DOI
Yu, Jianshe; Sun, Qiwen; Tang, Moxun The nonlinear dynamics and fluctuations of mRNA levels in cross-talking pathway activated transcription. (English) Zbl 1310.92025 J. Theor. Biol. 363, 223-234 (2014). Reviewer: Irina Ioana Mohorianu (Norwich) MSC: 92C40 60J20 PDFBibTeX XMLCite \textit{J. Yu} et al., J. Theor. Biol. 363, 223--234 (2014; Zbl 1310.92025) Full Text: DOI
Dasmahapatra, Srinandan Model of haplotype and phenotype in the evolution of a duplicated autoregulatory activator. (English) Zbl 1314.92097 J. Theor. Biol. 325, 83-102 (2013). MSC: 92D10 92D15 PDFBibTeX XMLCite \textit{S. Dasmahapatra}, J. Theor. Biol. 325, 83--102 (2013; Zbl 1314.92097) Full Text: DOI arXiv Link
Martins, Leonardo; Mäkelä, Jarno; Häkkinen, Antti; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Fonseca, José M.; Ribeiro, Andre S. Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time. (English) Zbl 1397.92213 J. Theor. Biol. 301, 83-94 (2012). MSC: 92C40 PDFBibTeX XMLCite \textit{L. Martins} et al., J. Theor. Biol. 301, 83--94 (2012; Zbl 1397.92213) Full Text: DOI
Larsson, Jan-Åke; Wadströmer, Niclas; Hermanson, Ola; Lendahl, Urban; Forchheimer, Robert Modelling cell lineage using a meta-Boolean tree model with a relation to gene regulatory networks. (English) Zbl 1411.92026 J. Theor. Biol. 268, 62-76 (2011). MSC: 92C15 92C42 PDFBibTeX XMLCite \textit{J.-Å. Larsson} et al., J. Theor. Biol. 268, 62--76 (2011; Zbl 1411.92026) Full Text: DOI Link
Li, Wentian On parameters of the human genome. (English) Zbl 1397.92458 J. Theor. Biol. 288, 92-104 (2011). MSC: 92D10 92C40 PDFBibTeX XMLCite \textit{W. Li}, J. Theor. Biol. 288, 92--104 (2011; Zbl 1397.92458) Full Text: DOI
Michel, Denis Hierarchical cooperativity mediated by chromatin remodeling; the model of the MMTV transcription regulation. (English) Zbl 1397.92214 J. Theor. Biol. 287, 74-81 (2011). MSC: 92C40 92C45 PDFBibTeX XMLCite \textit{D. Michel}, J. Theor. Biol. 287, 74--81 (2011; Zbl 1397.92214) Full Text: DOI arXiv
Häkkinen, Antti; Healy, Shannon; Jacobs, Howard T.; Ribeiro, Andre S. Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse. (English) Zbl 1397.92527 J. Theor. Biol. 281, 74-83 (2011). MSC: 92D20 68P20 PDFBibTeX XMLCite \textit{A. Häkkinen} et al., J. Theor. Biol. 281, 74--83 (2011; Zbl 1397.92527) Full Text: DOI HAL
Mackey, Michael C.; Tyran-Kamińska, Marta; Yvinec, Romain Molecular distributions in gene regulatory dynamics. (English) Zbl 1331.92046 J. Theor. Biol. 274, 84-96 (2011). MSC: 92C40 92C45 PDFBibTeX XMLCite \textit{M. C. Mackey} et al., J. Theor. Biol. 274, 84--96 (2011; Zbl 1331.92046) Full Text: DOI arXiv
Markert, Elke K.; Baas, Nils; Levine, Arnold J.; Vazquez, Alexei Higher order Boolean networks as models of cell state dynamics. (English) Zbl 1406.92153 J. Theor. Biol. 264, No. 3, 945-951 (2010). MSC: 92C37 92C42 PDFBibTeX XMLCite \textit{E. K. Markert} et al., J. Theor. Biol. 264, No. 3, 945--951 (2010; Zbl 1406.92153) Full Text: DOI arXiv
Polynikis, A.; Hogan, S. J.; di Bernardo, M. Comparing different ODE modelling approaches for gene regulatory networks. (English) Zbl 1403.92095 J. Theor. Biol. 261, No. 4, 511-530 (2009). MSC: 92C42 92C40 PDFBibTeX XMLCite \textit{A. Polynikis} et al., J. Theor. Biol. 261, No. 4, 511--530 (2009; Zbl 1403.92095) Full Text: DOI HAL
Ababneh, Anas M. The role of polarization interactions in the wrapping/unwrapping of nucleosomal DNA around the histone octamer: implications to gene regulation. (English) Zbl 1402.92164 J. Theor. Biol. 258, No. 2, 229-239 (2009). MSC: 92C40 PDFBibTeX XMLCite \textit{A. M. Ababneh}, J. Theor. Biol. 258, No. 2, 229--239 (2009; Zbl 1402.92164) 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
Pienaar, Elsje; Viljoen, Hendrik J. The tri-frame model. (English) Zbl 1398.92081 J. Theor. Biol. 251, No. 4, 616-627 (2008). MSC: 92C40 PDFBibTeX XMLCite \textit{E. Pienaar} and \textit{H. J. Viljoen}, J. Theor. Biol. 251, No. 4, 616--627 (2008; Zbl 1398.92081) Full Text: DOI Link
Wagner, Günter P.; Otto, Wolfgang; Lynch, Vincent; Stadler, Peter F. A stochastic model for the evolution of transcription factor binding site abundance. (English) Zbl 1455.92055 J. Theor. Biol. 247, No. 3, 544-553 (2007). MSC: 92C40 92D15 PDFBibTeX XMLCite \textit{G. P. Wagner} et al., J. Theor. Biol. 247, No. 3, 544--553 (2007; Zbl 1455.92055) Full Text: DOI
Widder, Stefanie; Schicho, Josef; Schuster, Peter Dynamic patterns of gene regulation. I: Simple two-gene systems. (English) Zbl 1451.92140 J. Theor. Biol. 246, No. 3, 395-419 (2007). MSC: 92C40 92C45 34C23 PDFBibTeX XMLCite \textit{S. Widder} et al., J. Theor. Biol. 246, No. 3, 395--419 (2007; Zbl 1451.92140) Full Text: DOI
Mitrophanov, Alexander Y.; Churchward, Gordon; Borodovsky, Mark Control of Streptococcus pyogenes virulence: modeling of the CovR/S signal transduction system. (English) Zbl 1451.92203 J. Theor. Biol. 246, No. 1, 113-128 (2007). MSC: 92C70 92C42 34K60 PDFBibTeX XMLCite \textit{A. Y. Mitrophanov} et al., J. Theor. Biol. 246, No. 1, 113--128 (2007; Zbl 1451.92203) Full Text: DOI
Peercy, Bradford E.; Cox, Steven J.; Shalel-Levanon, Sagit; San, Ka-Yiu; Bennett, George A kinetic model of oxygen regulation of cytochrome production in Escherichia coli. (English) Zbl 1447.92186 J. Theor. Biol. 242, No. 3, 547-563 (2006). MSC: 92C45 PDFBibTeX XMLCite \textit{B. E. Peercy} et al., J. Theor. Biol. 242, No. 3, 547--563 (2006; Zbl 1447.92186) Full Text: DOI
Voronin, Yegor A.; Sidorov, Igor A.; Pathak, Vinay K. A probability model predicting initiation efficiency of retroviral vectors with two primer-binding sites. (English) Zbl 1447.92159 J. Theor. Biol. 242, No. 2, 347-355 (2006). MSC: 92C40 PDFBibTeX XMLCite \textit{Y. A. Voronin} et al., J. Theor. Biol. 242, No. 2, 347--355 (2006; Zbl 1447.92159) Full Text: DOI
Rempala, Grzegorz A.; Ramos, Kenneth S.; Kalbfleisch, Ted A stochastic model of gene transcription: an application to L1 retrotransposition events. (English) Zbl 1447.92150 J. Theor. Biol. 242, No. 1, 101-116 (2006). MSC: 92C40 92C45 62P10 PDFBibTeX XMLCite \textit{G. A. Rempala} et al., J. Theor. Biol. 242, No. 1, 101--116 (2006; Zbl 1447.92150) Full Text: DOI
Roeder, Ingo; Glauche, Ingmar Towards an understanding of lineage specification in hematopoietic stem cells: a mathematical model for the interaction of transcription factors GATA-1 and PU.1. (English) Zbl 1447.92050 J. Theor. Biol. 241, No. 4, 852-865 (2006). MSC: 92C15 PDFBibTeX XMLCite \textit{I. Roeder} and \textit{I. Glauche}, J. Theor. Biol. 241, No. 4, 852--865 (2006; Zbl 1447.92050) Full Text: DOI arXiv
Lipniacki, Tomasz; Paszek, Pawel; Marciniak-Czochra, Anna; Brasier, Allan R.; Kimmel, Marek Transcriptional stochasticity in gene expression. (English) Zbl 1445.92113 J. Theor. Biol. 238, No. 2, 348-367 (2006). MSC: 92C40 35Q92 PDFBibTeX XMLCite \textit{T. Lipniacki} et al., J. Theor. Biol. 238, No. 2, 348--367 (2006; Zbl 1445.92113) Full Text: DOI
Bahramian, M. Bahman; Zarbl, Helmut GENE impedance: a natural process for control of gene expression and the origin of RNA interference. (English) Zbl 1442.92047 J. Theor. Biol. 233, No. 3, 301-314 (2005); erratum ibid. 236, No. 1, 1 (2005). MSC: 92C40 PDFBibTeX XMLCite \textit{M. B. Bahramian} and \textit{H. Zarbl}, J. Theor. Biol. 233, No. 3, 301--314 (2005; Zbl 1442.92047) Full Text: DOI
Yates, Andrew; Callard, Robin; Stark, Jaroslav Combining cytokine signalling with T-bet and GATA-3 regulation in Th1 and Th2 differentiation: a model for cellular decision-making. (English) Zbl 1447.92130 J. Theor. Biol. 231, No. 2, 181-196 (2004). MSC: 92C37 92C15 PDFBibTeX XMLCite \textit{A. Yates} et al., J. Theor. Biol. 231, No. 2, 181--196 (2004; Zbl 1447.92130) Full Text: DOI
Forger, Daniel B.; Peskin, Charles S. Model based conjectures on mammalian clock controversies. (English) Zbl 1447.92008 J. Theor. Biol. 230, No. 4, 533-539 (2004). MSC: 92B25 PDFBibTeX XMLCite \textit{D. B. Forger} and \textit{C. S. Peskin}, J. Theor. Biol. 230, No. 4, 533--539 (2004; Zbl 1447.92008) Full Text: DOI
Lamboy, Warren F.; Moreno-Hagelsieb, Gabriel A new method of solution for the occupancy problem and its application to operon size prediction. (English) Zbl 1439.92126 J. Theor. Biol. 227, No. 3, 315-322 (2004). MSC: 92D10 PDFBibTeX XMLCite \textit{W. F. Lamboy} and \textit{G. Moreno-Hagelsieb}, J. Theor. Biol. 227, No. 3, 315--322 (2004; Zbl 1439.92126) Full Text: DOI