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Review Article

Mathematical modeling of gene expression: a guide for the perplexed biologist

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Pages 137-151 | Received 11 Nov 2010, Accepted 18 Jan 2011, Published online: 21 Mar 2011

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Crossref
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Crossref
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Crossref
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Crossref
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Crossref
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Crossref
Gregory D. McCarthy, Robert A. Drewell & Jacqueline M. Dresch. (2015) Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos . PeerJ 3, pages e1022.
Crossref
Michael D. O’Connell & Gregory T. Reeves. (2015) The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient. PLOS Computational Biology 11:4, pages e1004159.
Crossref
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Crossref
David M. Holloway & Alexander V. Spirov. (2015) Mid-Embryo Patterning and Precision in Drosophila Segmentation: Krüppel Dual Regulation of hunchback. PLOS ONE 10:3, pages e0118450.
Crossref
Konstantin Kozlov, Vitaly Gursky, Ivan Kulakovskiy & Maria Samsonova. (2014) Sequence-based model of gap gene regulatory network. BMC Genomics 15:S12.
Crossref
Yu-Ting Hsiao & Wei-Po Lee. (2014) Reverse engineering gene regulatory networks: Coupling an optimization algorithm with a parameter identification technique. BMC Bioinformatics 15:S15.
Crossref
Manasikan Thammawong, Takahiro Orikasa, Hitomi Umehara, Ilmi Ganga Namali Hewajulige, Tomoko Kaneta, Nobutaka Nakamura, Yasuhiro Ito, Kohei Nakano & Takeo Shiina. (2014) Modeling of the respiration rate and gene expression patterns of cabbage in response to mechanical impact stress using a modified Weibull distribution. Postharvest Biology and Technology 96, pages 118-127.
Crossref
Md. Abul Hassan Samee & Saurabh Sinha. (2014) Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence. PLoS Computational Biology 10:3, pages e1003467.
Crossref
Jelena Erceg, Timothy E. Saunders, Charles Girardot, Damien P. Devos, Lars Hufnagel & Eileen E. M. Furlong. (2014) Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity. PLoS Genetics 10:1, pages e1004060.
Crossref
Wei-Po Lee, Yu-Ting Hsiao & Wei-Che Hwang. (2014) Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment. BMC Systems Biology 8:1, pages 5.
Crossref
Lanay Tierney, Katarzyna Tyc, Edda Klipp & Karl Kuchler. 2014. Human Fungal Pathogens. Human Fungal Pathogens 45 74 .
Liana Amaya Moreno, Ozlem Defterli, Armin Fügenschuh & Gerhard-Wilhelm Weber. 2014. Algorithms for Computational Biology. Algorithms for Computational Biology 35 46 .
Nathanie Trisnadi, Alphan Altinok, Angelike Stathopoulos & Gregory T. Reeves. (2013) Image analysis and empirical modeling of gene and protein expression. Methods 62:1, pages 68-78.
Crossref
Jose M.G. Vilar & Leonor Saiz. (2013) Systems Biophysics of Gene Expression. Biophysical Journal 104:12, pages 2574-2585.
Crossref
A. Pereira, N. Irishina, T. Pérez-Medina, J.F. Magrina, P.M. Magtibay, A. Kovaleva, A. Rodríguez-Tapia & E. Iglesias. (2013) Defining the optimal lymphadenectomy cut-off value in epithelial ovarian cancer staging surgery utilizing a mathematical model of validation. European Journal of Surgical Oncology (EJSO) 39:3, pages 290-296.
Crossref
Jacqueline M. Dresch, Marc A. Thompson, David N. Arnosti & Chichia Chiu. (2013) Two-Layer Mathematical Modeling of Gene Expression: Incorporating DNA-Level Information and System Dynamics. SIAM Journal on Applied Mathematics 73:2, pages 804-826.
Crossref
David Cohen, Inna Kuperstein, Emmanuel Barillot, Andrei Zinovyev & Laurence Calzone. 2013. In Silico Systems Biology. In Silico Systems Biology 107 125 .
David N. Arnosti & Ahmet Ay. (2012) Boolean modeling of gene regulatory networks: Driesch redux. Proceedings of the National Academy of Sciences 109:45, pages 18239-18240.
Crossref
Cecilia Klein, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu & Matteo Brilli. (2012) Structural and dynamical analysis of biological networks. Briefings in Functional Genomics 11:6, pages 420-433.
Crossref
Nicholas K. Priest, Justine K. Rudkin, Edward J. Feil, Jean M. H. van den Elsen, Ambrose Cheung, Sharon J. Peacock, Maisem Laabei, David A. Lucks, Mario Recker & Ruth C. Massey. (2012) From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence?. Nature Reviews Microbiology 10:11, pages 791-797.
Crossref
Eugenio Azpeitia & Elena R. Alvarez-Buylla. (2012) A complex systems approach to Arabidopsis root stem-cell niche developmental mechanisms: from molecules, to networks, to morphogenesis. Plant Molecular Biology 80:4-5, pages 351-363.
Crossref
Juli Atherton, Nathan Boley, Ben Brown, Nobuo Ogawa, Stuart M. Davidson, Michael B. Eisen, Mark D. Biggin & Peter Bickel. (2012) A model for sequential evolution of ligands by exponential enrichment (SELEX) data. The Annals of Applied Statistics 6:3.
Crossref
Till D Frank, Alex Cheong, Mariko Okada-Hatakeyama & Boris N Kholodenko. (2012) Catching transcriptional regulation by thermostatistical modeling. Physical Biology 9:4, pages 045007.
Crossref
Annette Schneider, Ursula Klingmüller & Marcel Schilling. (2012) Short‐term information processing, long‐term responses: Insights by mathematical modeling of signal transduction. BioEssays 34:7, pages 542-550.
Crossref
Till D. Frank, Aimée M. Carmody & Boris N. Kholodenko. (2012) Versatility of Cooperative Transcriptional Activation: A Thermodynamical Modeling Analysis for Greater-Than-Additive and Less-Than-Additive Effects. PLoS ONE 7:4, pages e34439.
Crossref
J. Bachmann, A. Raue, M. Schilling, V. Becker, J. Timmer & U. Klingmüller. (2012) Predictive mathematical models of cancer signalling pathways. Journal of Internal Medicine 271:2, pages 155-165.
Crossref
Gábor Szederkényi, Julio R Banga & Antonio A Alonso. (2011) Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Systems Biology 5:1, pages 177.
Crossref

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