Rfmapp: Ribosome flow model application

Bioinformatics

Volumn 28, Issue 12, 2012, Pages 1663-1664

  Zur, Hadas ^a   Tuller, Tamir ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CODON; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETICS; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; PROTEIN SYNTHESIS; RIBOSOME; SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; CODON; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; MODELS, MOLECULAR; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84863523809     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts185     Document Type: Article

References (10)

1. Dos Reis, M., et al. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res., 32, 5036-5044.
2. Gustafsson, C., et al. (2004) Codon bias and heterologous protein expression. Trends Biotechnol., 22, 346-353.
3. Heinrich, R. and Rapoport, T.A. (1980) Mathematical modelling of translation of mRNA in eucaryotes; steady state, time-dependent processes and application to reticulocytes. J. Theor. Biol., 86, 279-313.
4. Ingolia, N.T., et al. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218.
5. Kimchi-Sarfaty, C., et al. (2007) A "Silent" polymorphism in the MDR1 gene changes substrate specificity. Science, 315, 525-528.
6. Plotkin, J.B. and Kudla, G. (2010) Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet., 12, 32-42.
7. Reuveni, S., et al. (2011) Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput. Biol., 7, e1002127.
8. Schwanhausser, B., et al. (2011) Global quantification of mammalian gene expression control. Nature, 473, 337-342.
9. Sharp, P.M. and Li, W.H. (1987). The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res., 15, 1281.
10. Tuller, T., et al. (2011) Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res., 39, 4743-4755.