The landscape of eukaryotic mRNPs

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

(2019) Rayner M. L. Queiroz et al.   NATURE BIOTECHNOLOGY

Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration

(2019) Ze’ev Melamed et al.   NATURE NEUROSCIENCE

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

(2019) Erika C. Urdaneta et al.   Nature Communications

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

(2019) Haopeng Yu et al.   RNA Biology

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

(2019) Andrea Riba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNase L Reprograms Translation by Widespread mRNA Turnover Escaped by Antiviral mRNAs

(2019) James M. Burke et al.   MOLECULAR CELL

RNA secondary structure profiling in zebrafish reveals unique regulatory features

(2018) Kriti Kaushik et al.   BMC GENOMICS

Capturing the interactome of newly transcribed RNA

(2018) Xichen Bao et al.   NATURE METHODS

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

(2018) Briana Van Treeck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

COMRADES determines in vivo RNA structures and interactions

(2018) Omer Ziv et al.   NATURE METHODS

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

(2018) Jakob Trendel et al.   CELL

mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction

(2018) Anthony Khong et al.   JOURNAL OF CELL BIOLOGY

Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway

(2018) Srivathsan Adivarahan et al.   MOLECULAR CELL

The Story of RNA Folding, as Told in Epochs

(2018) Daniel Herschlag et al.   Cold Spring Harbor Perspectives in Biology

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

(2018) Wan-Jung C. Lai et al.   Nature Communications

Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription

(2018) Sarah Gilbertson et al.   eLife

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

(2017) Anthony Khong et al.   MOLECULAR CELL

Yeast eIF4A enhances recruitment of mRNAs regardless of their structural complexity

(2017) Paul Yourik et al.   eLife

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

(2016) Alexander Borodavka et al.   BIOPHYSICAL JOURNAL

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

(2016) Chong Wang et al.   CELL

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

(2016) Xavier Pichon et al.   JOURNAL OF CELL BIOLOGY

Comprehensive Identification of RNA-Binding Domains in Human Cells

(2016) Alfredo Castello et al.   MOLECULAR CELL

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Readthrough transcription: How are DoGs made and what do they do?

(2016) Anna Vilborg et al.   RNA Biology

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

(2016) Allison Piovesan et al.   Database-The Journal of Biological Databases and Curation

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion

(2015) Guramrit Singh et al.   Annual Review of Biochemistry

The Nuclear Proteome of a Vertebrate

(2015) Martin Wühr et al.   CURRENT BIOLOGY

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus

(2015) Sager J. Gosai et al.   MOLECULAR CELL

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

The separation between the 5′-3′ ends in long RNA molecules is short and nearly constant

(2014) Nehemías Leija-Martínez et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Yuanhui Mao et al.   NUCLEIC ACIDS RESEARCH

A stem-loop structure directs oskar mRNA to microtubule minus ends

(2014) H. Jambor et al.   RNA

Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding

(2014) Jian-Rong Yang et al.   PLOS BIOLOGY

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

(2014) Ian M Silverman et al.   GENOME BIOLOGY

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

(2013) Silvi Rouskin et al.   NATURE

Dynamics of translation by single ribosomes through mRNA secondary structures

(2013) Chunlai Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

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

(2012) Hadas Zur et al.   EMBO REPORTS

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Global analysis of yeast mRNPs

(2012) Sarah F Mitchell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

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

(2011) Nicholas T. Ingolia et al.   CELL

The size of RNA as an ideal branched polymer

(2011) Li Tai Fang et al.   JOURNAL OF CHEMICAL PHYSICS

Expected distance between terminal nucleotides of RNA secondary structures

(2011) Peter Clote et al.   JOURNAL OF MATHEMATICAL BIOLOGY

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

The ribosome uses two active mechanisms to unwind messenger RNA during translation

(2011) Xiaohui Qu et al.   NATURE

mRNA pseudoknot structures can act as ribosomal roadblocks

(2011) Jesper Tholstrup et al.   NUCLEIC ACIDS RESEARCH

Visualizing large RNA molecules in solution

(2011) A. Gopal et al.   RNA

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The ends of a large RNA molecule are necessarily close

(2010) Aron M. Yoffe et al.   NUCLEIC ACIDS RESEARCH

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

Purification of Nuclear Poly(A)-binding Protein Nab2 Reveals Association with the Yeast Transcriptome and a Messenger Ribonucleoprotein Core Structure

(2009) Julien Batisse et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

(2009) David G. Hendrickson et al.   PLOS BIOLOGY

Following translation by single ribosomes one codon at a time

(2008) Jin-Der Wen et al.   NATURE

Predicting the sizes of large RNA molecules

(2008) A. M. Yoffe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA