Deciphering the rules of mRNA structure differentiation in Saccharomyces cerevisiae in vivo and in vitro with deep neural networks

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences

(2017) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning

(2017) Sai Zhang et al.   Cell Systems

Ribosome Elongation Stall Directs Gene-specific Translation in the Integrated Stress Response

(2016) Sara K. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

(2016) Daniel A. Nissley et al.   Nature Communications

A comparative genomics study on the effect of individual amino acids on ribosome stalling

(2015) Renana Sabi et al.   BMC GENOMICS

The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function

(2015) Fran Supek   JOURNAL OF MOLECULAR EVOLUTION

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

(2015) Thomas E. Gorochowski et al.   NUCLEIC ACIDS RESEARCH

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae

(2014) Yuanhui Mao et al.   NUCLEIC ACIDS RESEARCH

Genetic Influences on Translation in Yeast

(2014) Frank W. Albert et al.   PLoS Genetics

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

Number Variation of High Stability Regions Is Correlated with Gene Functions

(2013) Yuanhui Mao et al.   Genome Biology and Evolution

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Genome-Wide Analysis of Selective Constraints on High Stability Regions of mRNA Reveals Multiple Compensatory Mutations in Escherichia coli

(2013) Yuanhui Mao et al.   PLoS One

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling

(2013) Boris Zinshteyn et al.   PLoS Genetics

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

(2012) Hadas Zur et al.   EMBO REPORTS

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

(2012) Z. Ouyang et al.   GENOME RESEARCH

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

GC content around splice sites affects splicing through pre-mRNA secondary structures

(2011) Jing Zhang et al.   BMC GENOMICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Translation efficiency is determined by both codon bias and folding energy

(2010) Tamir Tuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA Localization: Gene Expression in the Spatial Dimension

(2009) Kelsey C. Martin et al.   CELL

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Eukaryotic initiation factor 6 is rate-limiting in translation, growth and transformation

(2008) Valentina Gandin et al.   NATURE