Mathematical modeling of gene expression: a guide for the perplexed biologist
暂无分享,去创建一个
[1] M. Levine,et al. Computational Models for Neurogenic Gene Expression in the Drosophila Embryo , 2006, Current Biology.
[2] Stanislav Y Shvartsman,et al. Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein. , 2007, Developmental biology.
[3] Johannes Jaeger,et al. Reverse engineering a gene network using an asynchronous parallel evolution strategy , 2010, BMC Systems Biology.
[4] David H. Sharp,et al. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene , 2006, Nature Genetics.
[5] Douglas B. Kell,et al. MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems , 2001, Bioinform..
[6] Michael C Mackey,et al. Influence of catabolite repression and inducer exclusion on the bistable behavior of the lac operon. , 2004, Biophysical journal.
[7] Jason Gertz,et al. Environment-specific combinatorial cis-regulation in synthetic promoters , 2009, Molecular systems biology.
[8] Martin A. Nowak,et al. Inferring Cellular Networks Using Probabilistic Graphical Models , 2004 .
[9] A Babloyantz,et al. Chemical instabilities of “all‐or‐none” type in β ‐ galactosidase induction and active transport , 1972, FEBS letters.
[10] Carmen G. Moles,et al. Parameter estimation in biochemical pathways: a comparison of global optimization methods. , 2003, Genome research.
[11] E. Davidson,et al. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. , 1998, Science.
[12] Nicolas E. Buchler,et al. On schemes of combinatorial transcription logic , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[13] G. Church,et al. Systematic determination of genetic network architecture , 1999, Nature Genetics.
[14] David H. Sharp,et al. Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster , 2004, Genetics.
[15] T. Kornberg,et al. Proteolysis That Is Inhibited by Hedgehog Targets Cubitus interruptus Protein to the Nucleus and Converts It to a Repressor , 1997, Cell.
[16] James B. Brown,et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions , 2009, Genome Biology.
[17] Michal Linial,et al. Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..
[18] George S. Michaels,et al. Sensitivity of Biological Models to Errors in Parameter Estimates , 1999, Pacific Symposium on Biocomputing.
[19] D K Smith,et al. Numerical Optimization , 2001, J. Oper. Res. Soc..
[20] K. Struhl. Fundamentally Different Logic of Gene Regulation in Eukaryotes and Prokaryotes , 1999, Cell.
[21] Vladimir Filkov,et al. Identifying Gene Regulatory Networks from Gene Expression Data , 2005 .
[22] C. Yanofsky,et al. Role of regulatory features of the trp operon of Escherichia coli in mediating a response to a nutritional shift , 1994, Journal of bacteriology.
[23] H. Jäckle,et al. From gradients to stripes in Drosophila embryogenesis: filling in the gaps. , 1996, Trends in genetics : TIG.
[24] Charless C. Fowlkes,et al. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline , 2006, Genome Biology.
[25] T. Ziehn,et al. A global sensitivity study of sulfur chemistry in a premixed methane flame model using HDMR , 2008 .
[26] P. V. von Hippel,et al. Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects. , 1974, Proceedings of the National Academy of Sciences of the United States of America.
[27] Hernan G. Garcia,et al. Transcriptional Regulation by the Numbers 2: Applications , 2004, q-bio/0412011.
[28] M. Santillán,et al. Bistable behavior in a model of the lac operon in Escherichia coli with variable growth rate. , 2008, Biophysical journal.
[29] I. Prigogine,et al. Formative Processes. (Book Reviews: Self-Organization in Nonequilibrium Systems. From Dissipative Structures to Order through Fluctuations) , 1977 .
[30] David H. Sharp,et al. Dynamic control of positional information in the early Drosophila embryo , 2004, Nature.
[31] E. Davidson,et al. Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control. , 2001, Development.
[32] W. Bialek,et al. Stability and Nuclear Dynamics of the Bicoid Morphogen Gradient , 2007, Cell.
[33] E. Siggia,et al. Analysis of Combinatorial cis-Regulation in Synthetic and Genomic Promoters , 2008, Nature.
[34] E. Segal,et al. Predicting expression patterns from regulatory sequence in Drosophila segmentation , 2008, Nature.
[35] N. D. Clarke,et al. Explicit equilibrium modeling of transcription-factor binding and gene regulation , 2005, Genome Biology.
[36] A. McGregor,et al. How to get ahead: the origin, evolution and function of bicoid , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.
[37] D. Tautz,et al. Autonomous concentration-dependent activation and repression of Krüppel by hunchback in the Drosophila embryo. , 1994, Development.
[38] Hidde de Jong,et al. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..
[39] Daniel E. Newburger,et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. , 2009, Genome research.
[40] Justin Crocker,et al. Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts , 2008, PLoS biology.
[41] Xiaozhou Liu,et al. Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects , 2010, BMC Systems Biology.
[42] Esther T. Chan,et al. Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. , 2010, Genomics.
[43] M. Kreitman,et al. Evolutionary dynamics of the enhancer region of even-skipped in Drosophila. , 1995, Molecular biology and evolution.
[44] G. K. Ackers,et al. Quantitative model for gene regulation by lambda phage repressor. , 1982, Proceedings of the National Academy of Sciences of the United States of America.
[45] Daniel St Johnston,et al. Seeing Is Believing The Bicoid Morphogen Gradient Matures , 2004, Cell.
[46] G. Stormo,et al. Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites , 2008, Cell.
[47] Kaj Madsen,et al. Methods for Non-Linear Least Squares Problems , 1999 .
[48] N. Barkai,et al. Robustness of the BMP morphogen gradient in Drosophila embryonic patterning , 2022 .
[49] Claude Desplan,et al. Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila , 1994, Cell.
[50] S. Sinha. Theoretical study of tryptophan operon: Application in microbial technology , 1988, Biotechnology and bioengineering.
[51] Douglas B. Kell,et al. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation , 1998, Bioinform..
[52] M. Laubichler. Review of: Carroll, Sean B., Jennifer K. Grenier and Scott D. Weatherbee: From DNA to diversity : molecular genetics and the evolution of animal design. Malden, Mass [u.a.]: Blackwell Science 2001 , 2003 .
[53] M. Levine,et al. Multiple modes of dorsal‐bHLH transcriptional synergy in the Drosophila embryo. , 1995, The EMBO journal.
[54] W. Bialek,et al. Diffusion and scaling during early embryonic pattern formation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[55] W. Gehring,et al. Localized expression of sloppy paired protein maintains the polarity of Drosophila parasegments. , 1994, Genes & development.
[56] D. Kirschner,et al. A methodology for performing global uncertainty and sensitivity analysis in systems biology. , 2008, Journal of theoretical biology.
[57] Grégoire Nicolis,et al. Self-Organization in nonequilibrium systems , 1977 .
[58] Leon Glass,et al. Reverse Engineering the Gap Gene Network of Drosophila melanogaster , 2006, PLoS Comput. Biol..
[59] Xin He,et al. Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression , 2010, PLoS Comput. Biol..
[60] Michael Hecker,et al. Gene regulatory network inference: Data integration in dynamic models - A review , 2009, Biosyst..
[61] Gregory T. Reeves,et al. Biological Systems from an Engineer's Point of View , 2009, PLoS biology.
[62] J. Keasling,et al. Mathematical Model of the lac Operon: Inducer Exclusion, Catabolite Repression, and Diauxic Growth on Glucose and Lactose , 1997, Biotechnology progress.
[63] M. Levine,et al. The dorsal gradient morphogen regulates stripes of rhomboid expression in the presumptive neuroectoderm of the Drosophila embryo. , 1992, Genes & development.
[64] Madalena Chaves,et al. Robustness and fragility of Boolean models for genetic regulatory networks. , 2005, Journal of theoretical biology.
[65] D. Thieffry,et al. A logical analysis of the Drosophila gap-gene system. , 2001, Journal of theoretical biology.
[66] J. Griffith,et al. Mathematics of cellular control processes. I. Negative feedback to one gene. , 1968, Journal of theoretical biology.
[67] M. A. Shea,et al. The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. , 1985, Journal of molecular biology.
[68] Rainer Spang,et al. Inferring cellular networks – a review , 2007, BMC Bioinformatics.
[69] Xin Zhou,et al. tCal: transcriptional probability calculator using thermodynamic model , 2008, Bioinform..
[70] Terence Hwa,et al. Transcriptional regulation by the numbers: models. , 2005, Current opinion in genetics & development.
[71] J. Mahaffy,et al. Stability analysis for a mathematical model of the lac operon , 1999 .
[72] G. Odell,et al. The segment polarity network is a robust developmental module , 2000, Nature.
[73] P. Reed,et al. Hydrology and Earth System Sciences Discussions Comparing Sensitivity Analysis Methods to Advance Lumped Watershed Model Identification and Evaluation , 2022 .
[74] Christopher R. Myers,et al. Universally Sloppy Parameter Sensitivities in Systems Biology Models , 2007, PLoS Comput. Biol..
[75] Michael C. Mackey,et al. Dynamic behavior in mathematical models of the tryptophan operon. , 2001, Chaos.
[76] A. K. Sen,et al. Dynamic analysis of genetic control and regulation of amino acid synthesis: The tryptophan operon in Escherichia coli , 1990, Biotechnology and bioengineering.
[77] David H. Sharp,et al. Mechanism of eve stripe formation , 1995, Mechanisms of Development.
[78] Brian Ingalls,et al. Sensitivity analysis: from model parameters to system behaviour. , 2008, Essays in biochemistry.
[79] H. Othmer,et al. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.
[80] Necmettin Yildirim,et al. Modeling operon dynamics: the tryptophan and lactose operons as paradigms. , 2004, Comptes rendus biologies.
[81] Ahmet Ay,et al. Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo , 2010, Molecular systems biology.
[82] M. Mackey,et al. Feedback regulation in the lactose operon: a mathematical modeling study and comparison with experimental data. , 2003, Biophysical journal.
[83] Thomas Weise,et al. Global Optimization Algorithms -- Theory and Application , 2009 .
[84] M. Levine,et al. The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo. , 1996, The EMBO journal.
[85] S. Leibler,et al. DNA looping and physical constraints on transcription regulation. , 2003, Journal of molecular biology.
[86] Charless C. Fowlkes,et al. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics , 2006, Genome Biology.
[87] Jose M. G. Vilar,et al. Modeling network dynamics: the lac operon, a case study , 2004 .
[88] Johannes Jaeger,et al. Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation: comparison of spatially discrete and continuous models , 2004 .
[89] B. Goodwin. Oscillatory behavior in enzymatic control processes. , 1965, Advances in enzyme regulation.
[90] Jaap A. Kaandorp,et al. Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster , 2007, Bioinform..
[91] D. Pe’er,et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.
[92] R. D. Bliss,et al. Role of feedback inhibition in stabilizing the classical operon. , 1982, Journal of theoretical biology.
[93] J. Griffith. Mathematics of cellular control processes. II. Positive feedback to one gene. , 1968, Journal of theoretical biology.