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For: Gilchrist MA, Wagner A. A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol 2006;239:417-34. [PMID: 16171830 DOI: 10.1016/j.jtbi.2005.08.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 08/05/2005] [Accepted: 08/08/2005] [Indexed: 11/15/2022]
Number Cited by Other Article(s)
1
Awad S, Valleriani A, Chiarugi D. A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length. NAR Genom Bioinform 2024;6:lqae036. [PMID: 38638702 PMCID: PMC11025885 DOI: 10.1093/nargab/lqae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024]  Open
2
Jain A, Gupta AK. Modeling mRNA Translation With Ribosome Abortions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1600-1605. [PMID: 36044491 DOI: 10.1109/tcbb.2022.3203171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
3
Cope AL, Gilchrist MA. Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach. BMC Genomics 2022;23:408. [PMID: 35637464 PMCID: PMC9153123 DOI: 10.1186/s12864-022-08635-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022]  Open
4
Jain A, Gupta AK. Modeling transport of extended interacting objects with drop-off phenomenon. PLoS One 2022;17:e0267858. [PMID: 35499998 PMCID: PMC9060384 DOI: 10.1371/journal.pone.0267858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/17/2022] [Indexed: 11/19/2022]  Open
5
Introducing Parameter Clustering to the OED Procedure for Model Calibration of a Synthetic Inducible Promoter in S. cerevisiae. Processes (Basel) 2021. [DOI: 10.3390/pr9061053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
6
Specificity of RNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures. GENOMICS PROTEOMICS & BIOINFORMATICS 2021;19:882-900. [PMID: 33607297 PMCID: PMC9403030 DOI: 10.1016/j.gpb.2019.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/03/2019] [Accepted: 11/08/2019] [Indexed: 11/23/2022]
7
Dutta A, Schütz GM, Chowdhury D. Stochastic thermodynamics and modes of operation of a ribosome: A network theoretic perspective. Phys Rev E 2021;101:032402. [PMID: 32289926 DOI: 10.1103/physreve.101.032402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
8
Szavits-Nossan J, Evans MR. Dynamics of ribosomes in mRNA translation under steady- and nonsteady-state conditions. Phys Rev E 2020;101:062404. [PMID: 32688522 DOI: 10.1103/physreve.101.062404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/20/2020] [Indexed: 11/07/2022]
9
McFarland MR, Keller CD, Childers BM, Adeniyi SA, Corrigall H, Raguin A, Romano MC, Stansfield I. The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Nucleic Acids Res 2020;48:3071-3088. [PMID: 32016368 PMCID: PMC7102972 DOI: 10.1093/nar/gkaa055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/13/2022]  Open
10
Dourado H, Lercher MJ. An analytical theory of balanced cellular growth. Nat Commun 2020;11:1226. [PMID: 32144263 PMCID: PMC7060212 DOI: 10.1038/s41467-020-14751-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023]  Open
11
Scott S, Szavits-Nossan J. Power series method for solving TASEP-based models of mRNA translation. Phys Biol 2019;17:015004. [PMID: 31726446 DOI: 10.1088/1478-3975/ab57a0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
12
Beaulieu JM, O’Meara BC, Zaretzki R, Landerer C, Chai J, Gilchrist MA. Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach. Mol Biol Evol 2019;36:834-851. [PMID: 30521036 PMCID: PMC6445302 DOI: 10.1093/molbev/msy222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
13
Cope AL, Hettich RL, Gilchrist MA. Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018;1860:2479-2485. [PMID: 30279149 DOI: 10.1016/j.bbamem.2018.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 10/28/2022]
14
Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources. PLoS Comput Biol 2018;14:e1006055. [PMID: 29614119 PMCID: PMC5898785 DOI: 10.1371/journal.pcbi.1006055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 04/13/2018] [Accepted: 02/15/2018] [Indexed: 11/22/2022]  Open
15
Szavits-Nossan J, Ciandrini L, Romano MC. Deciphering mRNA Sequence Determinants of Protein Production Rate. PHYSICAL REVIEW LETTERS 2018;120:128101. [PMID: 29694095 DOI: 10.1103/physrevlett.120.128101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/18/2018] [Indexed: 06/08/2023]
16
Datta S, Seed B. Influence of multiplicative stochastic variation on translational elongation rates. PLoS One 2018;13:e0191152. [PMID: 29351322 PMCID: PMC5774726 DOI: 10.1371/journal.pone.0191152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 12/30/2017] [Indexed: 11/18/2022]  Open
17
Zarai Y, Margaliot M, Tuller T. A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics. PLoS One 2017;12:e0182178. [PMID: 28832591 PMCID: PMC5568237 DOI: 10.1371/journal.pone.0182178] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2022]  Open
18
Rogers DW, Böttcher MA, Traulsen A, Greig D. Ribosome reinitiation can explain length-dependent translation of messenger RNA. PLoS Comput Biol 2017;13:e1005592. [PMID: 28598992 PMCID: PMC5482490 DOI: 10.1371/journal.pcbi.1005592] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/23/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022]  Open
19
Bonnin P, Kern N, Young NT, Stansfield I, Romano MC. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile. PLoS Comput Biol 2017;13:e1005555. [PMID: 28558053 PMCID: PMC5469512 DOI: 10.1371/journal.pcbi.1005555] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 06/13/2017] [Accepted: 05/08/2017] [Indexed: 11/19/2022]  Open
20
Jauhari S, Rizvi SAM. A priori, de novo mathematical exploration of gene expression mechanism via regression viewpoint with briefly cataloged modeling antiquity. INT J BIOMATH 2016. [DOI: 10.1142/s1793524517500061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
21
Zur H, Tuller T. Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution. Nucleic Acids Res 2016;44:9031-9049. [PMID: 27591251 PMCID: PMC5100582 DOI: 10.1093/nar/gkw764] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/19/2016] [Indexed: 12/12/2022]  Open
22
Pantoja-Hernández L, Álvarez-Buylla E, Aguilar-Ibáñez CF, Garay-Arroyo A, Soria-López A, Martínez-García JC. Retroactivity effects dependency on the transcription factors binding mechanisms. J Theor Biol 2016;410:77-106. [PMID: 27524647 DOI: 10.1016/j.jtbi.2016.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 07/29/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022]
23
Hybrid agent-based model for quantitative in-silico cell-free protein synthesis. Biosystems 2016;150:22-34. [PMID: 27501921 DOI: 10.1016/j.biosystems.2016.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 07/05/2016] [Accepted: 07/17/2016] [Indexed: 12/15/2022]
24
Zhao YB, Krishnan J. Probabilistic Boolean Network Modelling and Analysis Framework for mRNA Translation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016;13:754-766. [PMID: 26390498 DOI: 10.1109/tcbb.2015.2478477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
25
Sin C, Chiarugi D, Valleriani A. Quantitative assessment of ribosome drop-off in E. coli. Nucleic Acids Res 2016;44:2528-37. [PMID: 26935582 PMCID: PMC4824120 DOI: 10.1093/nar/gkw137] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/24/2016] [Indexed: 11/14/2022]  Open
26
Heldt FS, Brackley CA, Grebogi C, Thiel M. Community control in cellular protein production: consequences for amino acid starvation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2015;373:rsta.2015.0107. [PMID: 26527812 DOI: 10.1098/rsta.2015.0107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/10/2015] [Indexed: 06/05/2023]
27
Kubatko L, Shah P, Herbei R, Gilchrist MA. A codon model of nucleotide substitution with selection on synonymous codon usage. Mol Phylogenet Evol 2015;94:290-7. [PMID: 26358614 DOI: 10.1016/j.ympev.2015.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 08/22/2015] [Accepted: 08/30/2015] [Indexed: 10/23/2022]
28
Lauria F, Tebaldi T, Lunelli L, Struffi P, Gatto P, Pugliese A, Brigotti M, Montanaro L, Ciribilli Y, Inga A, Quattrone A, Sanguinetti G, Viero G. RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes. Nucleic Acids Res 2015;43:e153. [PMID: 26240374 PMCID: PMC4678843 DOI: 10.1093/nar/gkv781] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/20/2015] [Indexed: 01/14/2023]  Open
29
Gilchrist MA, Chen WC, Shah P, Landerer CL, Zaretzki R. Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone. Genome Biol Evol 2015;7:1559-79. [PMID: 25977456 PMCID: PMC4494061 DOI: 10.1093/gbe/evv087] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
30
Marshall E, Stansfield I, Romano MC. Ribosome recycling induces optimal translation rate at low ribosomal availability. J R Soc Interface 2015;11:20140589. [PMID: 25008084 PMCID: PMC4233708 DOI: 10.1098/rsif.2014.0589] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
31
Fasani RA, Savageau MA. Evolution of a genome-encoded bias in amino acid biosynthetic pathways is a potential indicator of amino acid dynamics in the environment. Mol Biol Evol 2014;31:2865-78. [PMID: 25118252 PMCID: PMC4209129 DOI: 10.1093/molbev/msu225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
32
Edri S, Tuller T. Quantifying the effect of ribosomal density on mRNA stability. PLoS One 2014;9:e102308. [PMID: 25020060 PMCID: PMC4096589 DOI: 10.1371/journal.pone.0102308] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/17/2014] [Indexed: 11/18/2022]  Open
33
Margaliot M, Sontag ED, Tuller T. Entrainment to periodic initiation and transition rates in a computational model for gene translation. PLoS One 2014;9:e96039. [PMID: 24800863 PMCID: PMC4011696 DOI: 10.1371/journal.pone.0096039] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/02/2014] [Indexed: 01/09/2023]  Open
34
Zhao YB, Krishnan J. mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach. BMC SYSTEMS BIOLOGY 2014;8:25. [PMID: 24576337 PMCID: PMC4015640 DOI: 10.1186/1752-0509-8-25] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/08/2014] [Indexed: 01/12/2023]
35
Bailey BL, Visscher K, Watkins J. A stochastic model of translation with -1 programmed ribosomal frameshifting. Phys Biol 2014;11:016009. [PMID: 24501223 DOI: 10.1088/1478-3975/11/1/016009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
36
Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin J. Rate-limiting steps in yeast protein translation. Cell 2013;153:1589-601. [PMID: 23791185 PMCID: PMC3694300 DOI: 10.1016/j.cell.2013.05.049] [Citation(s) in RCA: 334] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 02/11/2013] [Accepted: 05/29/2013] [Indexed: 12/04/2022]
37
Mathematical Modeling of microRNA–Mediated Mechanisms of Translation Repression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013;774:189-224. [DOI: 10.1007/978-94-007-5590-1_11] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
38
Morozova N, Zinovyev A, Nonne N, Pritchard LL, Gorban AN, Harel-Bellan A. Kinetic signatures of microRNA modes of action. RNA (NEW YORK, N.Y.) 2012;18:1635-55. [PMID: 22850425 PMCID: PMC3425779 DOI: 10.1261/rna.032284.112] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
39
Brackley CA, Broomhead DS, Romano MC, Thiel M. A max-plus model of ribosome dynamics during mRNA translation. J Theor Biol 2012;303:128-40. [PMID: 22441134 DOI: 10.1016/j.jtbi.2012.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 02/21/2012] [Accepted: 03/07/2012] [Indexed: 11/16/2022]
40
von der Haar T. Mathematical and Computational Modelling of Ribosomal Movement and Protein Synthesis: an overview. Comput Struct Biotechnol J 2012;1:e201204002. [PMID: 24688632 PMCID: PMC3962216 DOI: 10.5936/csbj.201204002] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 10/31/2011] [Accepted: 11/05/2011] [Indexed: 11/22/2022]  Open
41
Sharma AK, Chowdhury D. Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript. J Theor Biol 2011;289:36-46. [DOI: 10.1016/j.jtbi.2011.08.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 12/31/2022]
42
Gokhale S, Nyayanit D, Gadgil C. A systems view of the protein expression process. SYSTEMS AND SYNTHETIC BIOLOGY 2011. [PMID: 23205157 DOI: 10.1007/s11693-011-9088-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
43
Brackley CA, Romano MC, Thiel M. The dynamics of supply and demand in mRNA translation. PLoS Comput Biol 2011;7:e1002203. [PMID: 22022250 PMCID: PMC3192816 DOI: 10.1371/journal.pcbi.1002203] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 08/04/2011] [Indexed: 11/30/2022]  Open
44
Aoi MC, Rourke BC. Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes. J Mol Evol 2011;73:74-93. [PMID: 21915654 DOI: 10.1007/s00239-011-9457-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 08/19/2011] [Indexed: 01/13/2023]
45
You T, Stansfield I, Romano MC, Brown AJP, Coghill GM. Analysing GCN4 translational control in yeast by stochastic chemical kinetics modelling and simulation. BMC SYSTEMS BIOLOGY 2011;5:131. [PMID: 21851603 PMCID: PMC3201031 DOI: 10.1186/1752-0509-5-131] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 08/18/2011] [Indexed: 12/02/2022]
46
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc Natl Acad Sci U S A 2011;108:10231-6. [PMID: 21646514 DOI: 10.1073/pnas.1016719108] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Huang T, Wan S, Xu Z, Zheng Y, Feng KY, Li HP, Kong X, Cai YD. Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS One 2011;6:e16036. [PMID: 21253596 PMCID: PMC3017080 DOI: 10.1371/journal.pone.0016036] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 12/06/2010] [Indexed: 11/19/2022]  Open
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Shah P, Gilchrist MA. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. PLoS Genet 2010;6:e1001128. [PMID: 20862306 PMCID: PMC2940732 DOI: 10.1371/journal.pgen.1001128] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 08/18/2010] [Indexed: 11/19/2022]  Open
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Ciandrini L, Stansfield I, Romano MC. Role of the particle's stepping cycle in an asymmetric exclusion process: a model of mRNA translation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010;81:051904. [PMID: 20866258 PMCID: PMC3639468 DOI: 10.1103/physreve.81.051904] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Indexed: 05/29/2023]
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Mier-y-Terán-Romero L, Silber M, Hatzimanikatis V. The origins of time-delay in template biopolymerization processes. PLoS Comput Biol 2010;6:e1000726. [PMID: 20369012 PMCID: PMC2848540 DOI: 10.1371/journal.pcbi.1000726] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 02/26/2010] [Indexed: 11/30/2022]  Open
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