Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming

[1]  M. Rodnina,et al.  Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis , 2018, Nucleic acids research.

[2]  M. Rodnina,et al.  Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis , 2018, Nucleic acids research.

[3]  Ayman Habib,et al.  OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement , 2018, PLoS Comput. Biol..

[4]  E. O’Brien,et al.  Non-equilibrium coupling of protein structure and function to translation-elongation kinetics. , 2018, Current opinion in structural biology.

[5]  Alessandra Carbone,et al.  Meet-U: Educating through research immersion , 2018, PLoS Comput. Biol..

[6]  Adam Siepel,et al.  Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. , 2018, Cell systems.

[7]  Fabio Lauria,et al.  riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data , 2017, bioRxiv.

[8]  M. Schatz,et al.  Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution , 2017, bioRxiv.

[9]  R. Green,et al.  eIF5A Functions Globally in Translation Elongation and Termination. , 2017, Molecular cell.

[10]  C. Dieterich,et al.  Bayesian prediction of RNA translation from ribosome profiling , 2017, Nucleic acids research.

[11]  Joshua G. Dunn,et al.  Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data , 2016, BMC Genomics.

[12]  Pascal Barbry,et al.  RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing , 2016, F1000Research.

[13]  T. Tuller,et al.  Estimation of ribosome profiling performance and reproducibility at various levels of resolution , 2016, Biology Direct.

[14]  Carl Kingsford,et al.  Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast , 2016, RECOMB.

[15]  Nicholas T. Ingolia.  Ribosome Footprint Profiling of Translation throughout the Genome , 2016, Cell.

[16]  H. Mori,et al.  Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling , 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

[17]  Bernd Bukau,et al.  Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding , 2016, Nature Communications.

[18]  Rachel Green,et al.  Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling. , 2016, Cell reports.

[19]  M. Bliemer,et al.  Protective Behaviour of Citizens to Transport Accidents Involving Hazardous Materials: A Discrete Choice Experiment Applied to Populated Areas nearby Waterways , 2015, PloS one.

[20]  T. Tuller,et al.  A comparative genomics study on the effect of individual amino acids on ribosome stalling , 2015, BMC Genomics.

[21]  Jeffrey A. Hussmann,et al.  Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast , 2015, bioRxiv.

[22]  R. Lipowsky,et al.  Protein Synthesis in E. coli: Dependence of Codon-Specific Elongation on tRNA Concentration and Codon Usage , 2015, PloS one.

[23]  Fan Zhang,et al.  Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo , 2015, Cell.

[24]  L. Levin,et al.  Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps , 2015, PloS one.

[25]  Jeffrey A. Hussmann,et al.  Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation , 2015, bioRxiv.

[26]  Sebastian A. Leidel,et al.  Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity , 2015, Cell.

[27]  Rachel Green,et al.  High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP. , 2015, Cell reports.

[28]  James Taylor,et al.  Ribosome A and P sites revealed by length analysis of ribosome profiling data , 2015, Nucleic acids research.

[29]  Hunter B. Fraser,et al.  Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation , 2014, Genome research.

[30]  Daphne Koller,et al.  Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation , 2014, Molecular systems biology.

[31]  J. Weissman,et al.  Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling , 2014, Science.

[32]  Jonathan S. Weissman,et al.  Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling , 2014, Science.

[33]  Justin Gardin,et al.  Measurement of average decoding rates of the 61 sense codons in vivo , 2014, eLife.

[34]  Nicholas T Ingolia,et al.  Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. , 2014, Cell reports.

[35]  Vadim N. Gladyshev,et al.  Translation inhibitors cause abnormalities in ribosome profiling experiments , 2014, Nucleic acids research.

[36]  Tamir Tuller,et al.  The effect of tRNA levels on decoding times of mRNA codons , 2014, Nucleic acids research.

[37]  J. Han,et al.  The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways , 2014, eLife.

[38]  Shu-Bing Qian,et al.  Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation , 2014, Cell Research.

[39]  Laura T. Jiménez-Barrón,et al.  Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources , 2014 .

[40]  P. Brown,et al.  Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments , 2014, eLife.

[41]  David H Burkhardt,et al.  Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources , 2014, Cell.

[42]  Rachel Green,et al.  Dom34 Rescues Ribosomes in 3′ Untranslated Regions , 2014, Cell.

[43]  Bernd Bukau,et al.  Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes , 2013, Nature Protocols.

[44]  C. Burge,et al.  Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay , 2013, Genome research.

[45]  Kirsten Jung,et al.  Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P , 2013, Proceedings of the National Academy of Sciences.

[46]  C. J. Woolstenhulme,et al.  eIF5A promotes translation of polyproline motifs. , 2013, Molecular cell.

[47]  Jonathan S. Weissman,et al.  rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments , 2013, Bioinform..

[48]  L. Hurst,et al.  Positively Charged Residues Are the Major Determinants of Ribosomal Velocity , 2013, PLoS biology.

[49]  Kirsten Jung,et al.  Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches , 2013, Science.

[50]  Henning Urlaub,et al.  EF-P Is Essential for Rapid Synthesis of Proteins Containing Consecutive Proline Residues , 2013, Science.

[51]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[52]  Tamir Tuller,et al.  Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells , 2012, PLoS Comput. Biol..

[53]  Anna M. McGeachy,et al.  The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments , 2012, Nature Protocols.

[54]  Gene-Wei Li,et al.  The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria , 2012, Nature.

[55]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[56]  Jianzhi Zhang,et al.  Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency , 2012, PLoS genetics.

[57]  David W. Reid,et al.  Primary Role for Endoplasmic Reticulum-bound Ribosomes in Cellular Translation Identified by Ribosome Profiling* , 2011, The Journal of Biological Chemistry.

[58]  J. Weissman,et al.  Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo , 2011, Cell.

[59]  Nicholas T. Ingolia,et al.  Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.

[60]  Marco Thiel,et al.  The Dynamics of Supply and Demand in mRNA Translation , 2011, PLoS Comput. Biol..

[61]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[62]  N. Malys.  Shine-Dalgarno sequence of bacteriophage T4: GAGG prevails in early genes , 2011, Molecular Biology Reports.

[63]  Bertrand Clarke,et al.  Principles and Theory for Data Mining and Machine Learning , 2009 .

[64]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[65]  A. Hinnebusch,et al.  Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets , 2009, Cell.

[66]  Ed Zintel,et al.  Resources , 1998, IT Prof..

[67]  M. Evans.  Mouse Embryonic Stem Cells , 2007 .

[68]  Achim Leutz,et al.  Translational control of gene expression and disease. , 2002, Trends in molecular medicine.

[69]  Gerard Sierksma,et al.  Linear and Integer Programming: Theory and Practice, Second Edition , 2001 .

[70]  G. Cooper.  Translation of mRNA , 2000 .

[71]  Gerardus Sierksma,et al.  Linear and integer programming - theory and practice , 1999, Pure and applied mathematics.

[72]  P. Good.  Permutation, Parametric, and Bootstrap Tests of Hypotheses , 2005 .

[73]  V. Caron,et al.  United states. , 2018, Nursing standard (Royal College of Nursing (Great Britain) : 1987).

[74]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .