Published in PLoS Comput Biol on November 01, 2012
Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages. Nucleic Acids Res (2014) 1.63
Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. Elife (2014) 1.49
Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO J (2013) 1.25
EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genet (2014) 1.14
The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res (2014) 1.12
Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames. Genome Res (2015) 1.10
Multiple roles of the coding sequence 5' end in gene expression regulation. Nucleic Acids Res (2014) 1.09
Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale. Wiley Interdiscip Rev RNA (2013) 1.02
Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3' untranslated regions. Nucleic Acids Res (2014) 0.96
Ribosome flow model with positive feedback. J R Soc Interface (2013) 0.91
A comparative genomics study on the effect of individual amino acids on ribosome stalling. BMC Genomics (2015) 0.89
A critical analysis of codon optimization in human therapeutics. Trends Mol Med (2014) 0.88
Entrainment to periodic initiation and transition rates in a computational model for gene translation. PLoS One (2014) 0.88
Maximizing protein translation rate in the non-homogeneous ribosome flow model: a convex optimization approach. J R Soc Interface (2014) 0.87
Detecting translational regulation by change point analysis of ribosome profiling data sets. RNA (2014) 0.86
Estimation of ribosome profiling performance and reproducibility at various levels of resolution. Biol Direct (2016) 0.84
Temporally and spatially restricted gene expression profiling. Curr Genomics (2014) 0.83
Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells. BMC Genomics (2016) 0.82
Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data. G3 (Bethesda) (2014) 0.81
Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data. PLoS Comput Biol (2015) 0.80
Properties and determinants of codon decoding time distributions. BMC Genomics (2014) 0.80
Increased functional protein expression using nucleotide sequence features enriched in highly expressed genes in zebrafish. Nucleic Acids Res (2015) 0.80
Ribosome recycling induces optimal translation rate at low ribosomal availability. J R Soc Interface (2014) 0.80
Quantifying the effect of ribosomal density on mRNA stability. PLoS One (2014) 0.79
High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling. PLoS Pathog (2016) 0.78
RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes. Nucleic Acids Res (2015) 0.77
Selection for reduced translation costs at the intronic 5' end in fungi. DNA Res (2016) 0.77
Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing. Proc Natl Acad Sci U S A (2016) 0.77
Protein functional features are reflected in the patterns of mRNA translation speed. BMC Genomics (2015) 0.77
Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP. Cell Rep (2017) 0.76
Role of mRNA structure in the control of protein folding. Nucleic Acids Res (2016) 0.76
Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9. Proc Natl Acad Sci U S A (2016) 0.76
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. Sci Rep (2016) 0.75
Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Res (2016) 0.75
Comparative survey of the relative impact of mRNA features on local ribosome profiling read density. Nat Commun (2016) 0.75
Computational Analysis of Nascent Peptides that Induce Ribosome Stalling and Their Proteomic Distribution in Saccharomyces cerevisiae. RNA (2017) 0.75
Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes. Comput Struct Biotechnol J (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res (1987) 26.51
Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature (2010) 22.04
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (2009) 20.75
A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science (2006) 15.18
The UCSC Known Genes. Bioinformatics (2006) 14.67
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell (2011) 10.56
Human housekeeping genes are compact. Trends Genet (2003) 7.65
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell (2008) 6.91
Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet (2006) 5.97
Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J (1988) 5.61
Codon bias and heterologous protein expression. Trends Biotechnol (2004) 5.20
Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science (2012) 4.61
Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res (2004) 4.51
An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell (2010) 4.45
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature (2012) 4.27
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol (2010) 3.56
High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science (2011) 3.53
Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol (2006) 2.81
Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation. Science (2010) 2.62
Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell (2011) 2.55
Electrostatics in the ribosomal tunnel modulate chain elongation rates. J Mol Biol (2008) 2.32
Genome-wide translational profiling by ribosome footprinting. Methods Enzymol (2010) 1.90
Wobble base-pairing slows in vivo translation elongation in metazoans. RNA (2011) 1.74
Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol (2011) 1.61
Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling. J Biol Chem (2011) 1.56
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. Mol Syst Biol (2009) 1.48
Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 1.37
Ribosome motions modulate electrostatic properties. Biopolymers (2004) 1.27
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc Natl Acad Sci U S A (2011) 1.23
Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Mol Syst Biol (2012) 1.19
Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans. Proc Natl Acad Sci U S A (2006) 1.18
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage. Nucleic Acids Res (2009) 0.89
Both temperature and medium composition regulate RNase E processing efficiency of the rpsO mRNA coding for ribosomal protein S15 of Escherichia coli. J Mol Biol (2002) 0.83
The average common substring approach to phylogenomic reconstruction. J Comput Biol (2006) 1.79
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. Nucleic Acids Res (2010) 1.42
Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Mol Biol Evol (2006) 1.30
Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol (2011) 1.29
Maximum likelihood of phylogenetic networks. Bioinformatics (2006) 1.26
Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics (2007) 1.24
Strong association between mRNA folding strength and protein abundance in S. cerevisiae. EMBO Rep (2012) 1.17
New universal rules of eukaryotic translation initiation fidelity. PLoS Comput Biol (2013) 1.09
Selection for translation efficiency on synonymous polymorphisms in recent human evolution. Genome Biol Evol (2011) 1.05
Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression. Mol Syst Biol (2007) 1.04
Metabolic modeling of endosymbiont genome reduction on a temporal scale. Mol Syst Biol (2011) 0.98
Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics (2005) 0.94
Ribosome flow model with positive feedback. J R Soc Interface (2013) 0.91
Parsimony score of phylogenetic networks: hardness results and a linear-time heuristic. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.90
Stability analysis of the ribosome flow model. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.90
A comparative genomics study on the effect of individual amino acids on ribosome stalling. BMC Genomics (2015) 0.89
Prediction of acute multiple sclerosis relapses by transcription levels of peripheral blood cells. BMC Med Genomics (2009) 0.89
Conservation of the relative tRNA composition in healthy and cancerous tissues. RNA (2012) 0.87
Sequence features of E. coli mRNAs affect their degradation. PLoS One (2011) 0.87
TP53 cancerous mutations exhibit selection for translation efficiency. Cancer Res (2009) 0.86
Efficient manipulations of synonymous mutations for controlling translation rate: an analytical approach. J Comput Biol (2012) 0.86
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinformatics (2010) 0.86
On the steady-state distribution in the homogeneous ribosome flow model. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.86
Reconstruction of ancestral genomic sequences using likelihood. J Comput Biol (2007) 0.83
Ribosome Flow Model on a Ring. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.83
Biological networks: comparison, conservation, and evolution via relative description length. J Comput Biol (2007) 0.81
Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae. BMC Bioinformatics (2013) 0.81
Clone clusters in autoreactive CD4 T-cell lines from probable multiple sclerosis patients form disease-characteristic signatures. Immunology (2009) 0.81
Challenges and obstacles related to solving the codon bias riddles. Biochem Soc Trans (2014) 0.80
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. Bioinformatics (2008) 0.80
Properties and determinants of codon decoding time distributions. BMC Genomics (2014) 0.80
The RNA polymerase flow model of gene transcription. IEEE Trans Biomed Circuits Syst (2014) 0.80
Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes. BMC Genomics (2015) 0.79
Efficient algorithms for reconstructing gene content by co-evolution. BMC Bioinformatics (2011) 0.79
Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae. Front Genet (2012) 0.79
Mapping the translation initiation landscape of an S. cerevisiae gene using fluorescent proteins. Genomics (2013) 0.78
Analysis of coevolving gene families using mutually exclusive orthologous modules. Genome Biol Evol (2011) 0.77
RFMapp: ribosome flow model application. Bioinformatics (2012) 0.77
Maximizing Protein Translation Rate in the Ribosome Flow Model: The Homogeneous Case. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.77
The NET-HMM approach: phylogenetic network inference by combining maximum likelihood and Hidden Markov Models. J Bioinform Comput Biol (2009) 0.76
Ribosomal mutations affecting the translation of genes that use non-optimal codons. FEBS J (2014) 0.75
Most associations between transcript features and gene expression are monotonic. Mol Biosyst (2014) 0.75
Correction: On the Ribosomal Density that Maximizes Protein Translation Rate. PLoS One (2017) 0.75
Controlling mRNA Translation. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75