Computational and Experimental Tools to Monitor the Changes in Translation Efficiency of Plant mRNA on a Genome-Wide Scale: Advantages, Limitations, and Solutions

Arabidopsis thaliana cold-regulated 47 gene 5′-untranslated region enables stable high-level expression of transgenes

(2018) Shotaro Yamasaki et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Accurate design of translational output by a neural network model of ribosome distribution

(2018) Robert Tunney et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential

(2018) Steven T Hill et al.   NUCLEIC ACIDS RESEARCH

The translational landscape of Arabidopsis mitochondria

(2018) Noelya Planchard et al.   NUCLEIC ACIDS RESEARCH

Accurate design of translational output by a neural network model of ribosome distribution

(2018) Robert Tunney et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data

(2018) Travers Ching et al.   PLoS Computational Biology

A Plant Biologist’s Toolbox to Study Translation

(2018) Serina M. Mazzoni-Putman et al.   Frontiers in Plant Science

Following Ribosome Footprints to Understand Translation at a Genome Wide Level

(2018) Guillermo Eastman et al.   Computational and Structural Biotechnology Journal

Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation

(2018) Prakitchai Chotewutmontri et al.   PLoS Genetics

Simple tricks of convolutional neural network architectures improve DNA–protein binding prediction

(2018) Zhen Cao et al.   BIOINFORMATICS

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

uORF-mediated translation allows engineered plant disease resistance without fitness costs

(2017) Guoyong Xu et al.   NATURE

Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest

(2017) Noriya Hayashi et al.   NUCLEIC ACIDS RESEARCH

Translation regulation in plants: an interesting past, an exciting present and a promising future

(2017) Catharina Merchante et al.   PLANT JOURNAL

5′ to 3′ mRNA Decay Contributes to the Regulation of Arabidopsis Seed Germination by Dormancy

(2017) Isabelle Basbouss-Serhal et al.   PLANT PHYSIOLOGY

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

(2017) Polly Yingshan Hsu et al.   PROTEOMICS

Simple and reliable system for transient gene expression for the characteristic signal sequences and the estimation of the localization of target protein in plant cell

(2017) A. A. Tyurin et al.   RUSSIAN JOURNAL OF PLANT PHYSIOLOGY

Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma

(2017) Vivek Sharma et al.   Frontiers in Microbiology

An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene

(2017) Ekaterina V. Sheshukova et al.   Frontiers in Plant Science

Emerging Roles and Landscape of Translating mRNAs in Plants

(2017) Gaurav Sablok et al.   Frontiers in Plant Science

Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq

(2016) Radoslaw Lukoszek et al.   BMC PLANT BIOLOGY

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

(2016) Dmitry E. Andreev et al.   NUCLEIC ACIDS RESEARCH

Ribonuclease selection for ribosome profiling

(2016) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

An Untranslated cis -Element Regulates the Accumulation of Multiple C 4 Enzymes in Gynandropsis gynandra Mesophyll Cells

(2016) Ben P. Williams et al.   PLANT CELL

The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation

(2016) Mayuki Tanaka et al.   PLANT CELL

Carotenogenesis Is Regulated by 5′UTR-Mediated Translation of Phytoene Synthase Splice Variants

(2016) Daniel Álvarez et al.   PLANT PHYSIOLOGY

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

(2016) Polly Yingshan Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient expression of a heterologous gene in plants depends on the nucleotide composition of mRNA’s 5'-region

(2016) A. A. Tyurin et al.   RUSSIAN JOURNAL OF PLANT PHYSIOLOGY

An Easy Method for Plant Polysome Profiling

(2016) Cécile Lecampion et al.   Jove-Journal of Visualized Experiments

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner

(2015) Isao Ebina et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Changes in Polysome Association of mRNA Throughout Growth and Development inArabidopsis thaliana

(2015) Shotaro Yamasaki et al.   PLANT AND CELL PHYSIOLOGY

AtLa1 protein initiates IRES-dependent translation ofWUSCHELmRNA and regulates the stem cell homeostasis ofArabidopsisin response to environmental hazards

(2015) Yuchao Cui et al.   PLANT CELL AND ENVIRONMENT

Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress

(2015) Lei Lei et al.   PLANT JOURNAL

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Profiling of Translatomes of in Vivo-Grown Pollen Tubes Reveals Genes with Roles in Micropylar Guidance during Pollination in Arabidopsis

(2014) S.-Y. Lin et al.   PLANT CELL

Functional and Structural Analysis of Maize Hsp101 IRES

(2014) Augusto Samuel Jiménez-González et al.   PLoS One

Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia inArabidopsis

(2014) Reed Sorenson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Higher plant transformation: principles and molecular tools

(2013) Sylvester Anami et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

A Computational and Experimental Approach Reveals that the 5′-Proximal Region of the 5′-UTR has a Cis-Regulatory Signature Responsible for Heat Stress-Regulated mRNA Translation in Arabidopsis

(2013) Hideyuki Matsuura et al.   PLANT AND CELL PHYSIOLOGY

GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology

(2013) A. Sarrion-Perdigones et al.   PLANT PHYSIOLOGY

Analysis of Genome-Wide Changes in the Translatome of Arabidopsis Seedlings Subjected to Heat Stress

(2013) Emilio Yángüez et al.   PLoS One

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A study on the influence of different promoter and 5′UTR (URM) cassettes from Arabidopsis thaliana on the expression level of the reporter gene β glucuronidase in tobacco and cotton

(2013) Parul Agarwal et al.   TRANSGENIC RESEARCH

BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome

(2012) Hiro Takahashi et al.   BIOINFORMATICS

Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis

(2012) Ming-Jung Liu et al.   Molecular Systems Biology

Expression of heterologous genes in plant systems: New possibilities

(2012) A. O. Vyacheslavova et al.   RUSSIAN JOURNAL OF GENETICS

So you want to know if your message has an IRES?

(2012) Sunnie R. Thompson   Wiley Interdisciplinary Reviews-RNA

Conserved Peptide Upstream Open Reading Frames are Associated with Regulatory Genes in Angiosperms

(2012) Richard A. Jorgensen et al.   Frontiers in Plant Science

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Human–chimpanzee promoter comparisons: Property-conserved evolution?

(2010) Igor V. Deyneko et al.   GENOMICS

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

Genome-Wide Analyses of Early Translational Responses to Elevated Temperature and High Salinity in Arabidopsis thaliana

(2010) Hideyuki Matsuura et al.   PLANT AND CELL PHYSIOLOGY

Dicistronic binary vector system—A versatile tool for gene expression studies in cell cultures and plants

(2009) Zahid Ali et al.   JOURNAL OF BIOTECHNOLOGY

Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

(2009) Carola Engler et al.   PLoS One

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

(2009) N. T. Ingolia et al.   SCIENCE

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE