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Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli.

Tuan-Anh T, Ly LT, Viet NQ, Bao PT.

BMC Bioinformatics. 2017 Feb 10;18(1):100. doi: 10.1186/s12859-017-1517-z.


Tissue Specific Expression Levels of Apoptosis Involved Genes Have Correlations with Codon and Amino Acid Usage.

Hajjari M, Sadeghi I, Salavaty A, Nasiri H, Birgani MT.

Genomics Inform. 2016 Dec;14(4):234-240. doi: 10.5808/GI.2016.14.4.234. Epub 2016 Dec 31.


Operon mRNAs are organized into ORF-centric structures that predict translation efficiency.

Burkhardt DH, Rouskin S, Zhang Y, Li GW, Weissman JS, Gross CA.

Elife. 2017 Jan 31;6. pii: e22037. doi: 10.7554/eLife.22037.


Comparison of aldehyde-producing activities of cyanobacterial acyl-(acyl carrier protein) reductases.

Kudo H, Nawa R, Hayashi Y, Arai M.

Biotechnol Biofuels. 2016 Nov 1;9:234. eCollection 2016 Nov 1.


Triple Isotope Effects Support Concerted Hydride and Proton Transfer and Promoting Vibrations in Human Heart Lactate Dehydrogenase.

Wang Z, Chang EP, Schramm VL.

J Am Chem Soc. 2016 Nov 16;138(45):15004-15010. Epub 2016 Nov 4.


Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution.

Zur H, Tuller T.

Nucleic Acids Res. 2016 Nov 2;44(19):9031-9049. Epub 2016 Sep 2.


Side effects of extra tRNA supplied in a typical bacterial protein production scenario.

Søgaard KM, Nørholm MH.

Protein Sci. 2016 Nov;25(11):2102-2108. doi: 10.1002/pro.3011. Epub 2016 Oct 15.


Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast.

Gamble CE, Brule CE, Dean KM, Fields S, Grayhack EJ.

Cell. 2016 Jul 28;166(3):679-90. doi: 10.1016/j.cell.2016.05.070. Epub 2016 Jun 30.


Quality over quantity: optimizing co-translational protein folding with non-'optimal' synonymous codons.

Jacobson GN, Clark PL.

Curr Opin Struct Biol. 2016 Jun;38:102-10. doi: 10.1016/ Epub 2016 Jun 16. Review.


Putative virulence factors of Corynebacterium pseudotuberculosis FRC41: vaccine potential and protein expression.

Santana-Jorge KT, Santos TM, Tartaglia NR, Aguiar EL, Souza RF, Mariutti RB, Eberle RJ, Arni RK, Portela RW, Meyer R, Azevedo V.

Microb Cell Fact. 2016 May 16;15:83. doi: 10.1186/s12934-016-0479-6.


Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.

Jeschek M, Gerngross D, Panke S.

Nat Commun. 2016 Mar 31;7:11163. doi: 10.1038/ncomms11163.


The Selective Advantage of Synonymous Codon Usage Bias in Salmonella.

Brandis G, Hughes D.

PLoS Genet. 2016 Mar 10;12(3):e1005926. doi: 10.1371/journal.pgen.1005926. eCollection 2016 Mar 10.


A model for competition for ribosomes in the cell.

Raveh A, Margaliot M, Sontag ED, Tuller T.

J R Soc Interface. 2016 Mar;13(116). pii: 20151062. doi: 10.1098/rsif.2015.1062.


Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging.

Fernandes A, Vinga S.

PLoS One. 2016 Mar 2;11(3):e0150369. doi: 10.1371/journal.pone.0150369. eCollection 2016 Mar 2.


Compensating the Fitness Costs of Synonymous Mutations.

Knöppel A, Näsvall J, Andersson DI.

Mol Biol Evol. 2016 Jun;33(6):1461-77. doi: 10.1093/molbev/msw028. Epub 2016 Feb 16.


Biochemical characterization of two haloalkane dehalogenases: DccA from Caulobacter crescentus and DsaA from Saccharomonospora azurea.

Carlucci L, Zhou E, Malashkevich VN, Almo SC, Mundorff EC.

Protein Sci. 2016 Apr;25(4):877-86. doi: 10.1002/pro.2895. Epub 2016 Feb 21.


A Cyan Fluorescent Reporter Expressed from the Chloroplast Genome of Marchantia polymorpha.

Boehm CR, Ueda M, Nishimura Y, Shikanai T, Haseloff J.

Plant Cell Physiol. 2016 Feb;57(2):291-9. doi: 10.1093/pcp/pcv160. Epub 2015 Dec 3.


Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.

Gritsenko AA, Hulsman M, Reinders MJ, de Ridder D.

PLoS Comput Biol. 2015 Aug 14;11(8):e1004336. doi: 10.1371/journal.pcbi.1004336. eCollection 2015 Aug 14.

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