Controlling mRNA Translation
暂无分享,去创建一个
Michael Margaliot | Eduardo D. Sontag | Tamir Tuller | Yoram Zarai | Eduardo Sontag | M. Margaliot | Y. Zarai | T. Tuller
[1] Michael Margaliot,et al. Entrainment to Periodic Initiation and Transition Rates in a Computational Model for Gene Translation , 2014, PloS one.
[2] Fred Brauer,et al. Compartmental Models in Epidemiology , 2008, Mathematical Epidemiology.
[3] M. Margaliot,et al. Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach , 2014, Journal of The Royal Society Interface.
[4] T. Tuller,et al. A comparative genomics study on the effect of individual amino acids on ribosome stalling , 2015, BMC Genomics.
[5] A Fahr,et al. Compartment modeling. , 2001, Advanced drug delivery reviews.
[6] Eytan Ruppin,et al. Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae , 2007, PLoS Comput. Biol..
[7] Isaac Meilijson,et al. Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model , 2011, PLoS Comput. Biol..
[8] L. E. Becker,et al. On self-propulsion of micro-machines at low Reynolds number: Purcell's three-link swimmer , 2003, Journal of Fluid Mechanics.
[9] Michael Margaliot,et al. On the Ribosomal Density that Maximizes Protein Translation Rate , 2016, PloS one.
[10] Nicolae Radu Zabet,et al. A novel and versatile computational tool to model translation , 2012, Bioinform..
[11] E. O’Shea,et al. An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation , 2014, Cell.
[12] Roded Sharan,et al. TP53 cancerous mutations exhibit selection for translation efficiency. , 2009, Cancer research.
[13] Eduardo D. Sontag,et al. Mathematical Control Theory: Deterministic Finite Dimensional Systems , 1990 .
[14] Alexander Olshevsky,et al. Minimal Controllability Problems , 2013, IEEE Transactions on Control of Network Systems.
[15] John A. Jacquez,et al. Qualitative Theory of Compartmental Systems , 1993, SIAM Rev..
[16] Tamir Tuller,et al. Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: An Analytical Approach , 2012, J. Comput. Biol..
[17] Zoya Ignatova,et al. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding , 2009, Nature Structural &Molecular Biology.
[18] B. F. Doolin,et al. Large scale dynamic systems , 1975 .
[19] Chen Yanover,et al. Building better drugs: developing and regulating engineered therapeutic proteins. , 2013, Trends in pharmacological sciences.
[20] Debashish Chowdhury,et al. Stochastic Transport in Complex Systems: From Molecules to Vehicles , 2010 .
[21] Reinhard Lipowsky,et al. Effect of ribosome shielding on mRNA stability , 2013, Physical biology.
[22] Michael Margaliot,et al. A model for competition for ribosomes in the cell , 2015, Journal of The Royal Society Interface.
[23] G Pohl,et al. Expression of human insulin-like growth factor I in bacteria: use of optimized gene fusion vectors to facilitate protein purification. , 1987, Biochemistry.
[24] Michael Margaliot,et al. Ribosome Flow Model on a Ring , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[25] Lippincott-Schwartz,et al. Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .
[26] M. Margaliot,et al. Sensitivity of mRNA Translation , 2014, Scientific Reports.
[27] Ching-tai Lin. Structural controllability , 1974 .
[28] Kim Sneppen,et al. The functional half-life of an mRNA depends on the ribosome spacing in an early coding region. , 2011, Journal of molecular biology.
[29] Vassily Hatzimanikatis,et al. A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data , 2013, PLoS Comput. Biol..
[30] Ran Elkon,et al. p53 induces transcriptional and translational programs to suppress cell proliferation and growth , 2013, Genome Biology.
[31] Naomi R Wray,et al. Translation elongation factor eEF1A2 is a potential oncoprotein that is overexpressed in two-thirds of breast tumours , 2005, BMC Cancer.
[32] L. E. Johnson,et al. Control and controllability in compartmental systems , 1976 .
[33] Hal L. Smith,et al. Monotone Dynamical Systems: An Introduction To The Theory Of Competitive And Cooperative Systems (Mathematical Surveys And Monographs) By Hal L. Smith , 1995 .
[34] R. Jackson,et al. The mechanism of eukaryotic translation initiation and principles of its regulation , 2010, Nature Reviews Molecular Cell Biology.
[35] John D. Storey,et al. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[36] Albert-László Barabási,et al. Controllability of complex networks , 2011, Nature.
[37] Claus O. Wilke,et al. Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution , 2008, Cell.
[38] Izhak Bucher,et al. On the slow dynamics of near-field acoustically levitated objects under High excitation frequencies , 2015 .
[39] C. Scorer,et al. Foreign gene expression in yeast: a review , 1992, Yeast.
[40] J. Jacquez. Compartmental analysis in biology and medicine , 1985 .
[41] C. Kurland,et al. Translational accuracy and the fitness of bacteria. , 1992, Annual review of genetics.
[42] Nicholas T. Ingolia,et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis , 2012, Nature.
[43] Tamir Tuller,et al. Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution , 2016, Nucleic acids research.
[44] Kelvin H. Lee,et al. Totally asymmetric exclusion process with extended objects: a model for protein synthesis. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[45] Michael Margaliot,et al. Ribosome flow model with positive feedback , 2013, Journal of The Royal Society Interface.
[46] Tamir Tuller,et al. Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells , 2012, PLoS Comput. Biol..
[47] Eduardo D. Sontag,et al. Mathematical control theory: deterministic finite dimensional systems (2nd ed.) , 1998 .
[48] J. Plotkin,et al. Synonymous but not the same: the causes and consequences of codon bias , 2011, Nature Reviews Genetics.
[49] D. I. Stewart,et al. Heterologous biopharmaceutical protein expression in Streptomyces. , 1997, Trends in biotechnology.
[50] J. Belasco,et al. Lost in translation: the influence of ribosomes on bacterial mRNA decay. , 2005, Genes & development.
[51] Masami Ito,et al. On the structural controllability of compartmental systems , 1984 .
[52] R. A. Blythe,et al. Nonequilibrium steady states of matrix-product form: a solver's guide , 2007, 0706.1678.
[53] E. Purcell. Life at Low Reynolds Number , 2008 .
[54] Tamir Tuller,et al. Quantifying the Effect of Ribosomal Density on mRNA Stability , 2014, PloS one.
[55] Tamir Tuller,et al. New Universal Rules of Eukaryotic Translation Initiation Fidelity , 2013, PLoS Comput. Biol..
[56] Judith Frydman,et al. Evolutionary conservation of codon optimality reveals hidden signatures of co-translational folding , 2012, Nature Structural &Molecular Biology.
[57] J. Plotkin,et al. Rate-Limiting Steps in Yeast Protein Translation , 2013, Cell.
[58] Michael Margaliot,et al. Stability Analysis of the Ribosome Flow Model , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[59] B. Schmittmann,et al. Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments , 2011, 1108.3312.
[60] Bernd Bukau,et al. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding , 2016, Nature Communications.
[61] Michael Margaliot,et al. Controlling the ribosomal density profile in mRNA translation , 2016, 2016 IEEE 55th Conference on Decision and Control (CDC).
[62] Michael Margaliot,et al. Explicit Expression for the Steady-State Translation Rate in the Infinite-Dimensional Homogeneous Ribosome Flow Model , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[63] T. Elston,et al. Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.
[64] H. Mayeda,et al. Strong Structural Controllability , 1979 .
[65] Guy-Bart Stan,et al. Modelling essential interactions between synthetic genes and their chassis cell , 2014, 53rd IEEE Conference on Decision and Control.
[66] T. Tuller,et al. Multiple roles of the coding sequence 5′ end in gene expression regulation , 2014, Nucleic acids research.
[67] G. Dougan,et al. Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation , 2010, Science.
[68] Christopher A. Voigt,et al. Automated Design of Synthetic Ribosome Binding Sites to Precisely Control Protein Expression , 2009, Nature Biotechnology.
[69] Tamar Unger,et al. A Recombinant Collagen–mRNA Platform for Controllable Protein Synthesis , 2015, Chembiochem : a European journal of chemical biology.