New insights into the cellular temporal response to proteostatic stress

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

(2018) Anthony M. Mustoe et al.   CELL

Systematic Characterization of Stress-Induced RNA Granulation

(2018) Sim Namkoong et al.   MOLECULAR CELL

The endoplasmic reticulum–residing chaperone BiP is short-lived and metabolized through N-terminal arginylation

(2018) Sang Mi Shim et al.   Science Signaling

The endoplasmic reticulum–residing chaperone BiP is short-lived and metabolized through N-terminal arginylation

(2018) Sang Mi Shim et al.   Science Signaling

Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals

(2017) Pedro M. Quirós et al.   JOURNAL OF CELL BIOLOGY

Endoplasmic Reticulum Transport of Glutathione by Sec61 Is Regulated by Ero1 and Bip

(2017) Alise J. Ponsero et al.   MOLECULAR CELL

A Unique ISR Program Determines Cellular Responses to Chronic Stress

(2017) Bo-Jhih Guan et al.   MOLECULAR CELL

Serine alleviates oxidative stress via supporting glutathione synthesis and methionine cycle in mice

(2017) Xihong Zhou et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tunicamycin induced endoplasmic reticulum stress promotes apoptosis of prostate cancer cells by activating mTORC1

(2017) Prasun Guha et al.   Oncotarget

Oncogene-Selective Sensitivity to Synchronous Cell Death following Modulation of the Amino Acid Nutrient Cystine

(2017) Ioannis Poursaitidis et al.   Cell Reports

GILZ overexpression attenuates endoplasmic reticulum stress-mediated cell death via the activation of mitochondrial oxidative phosphorylation

(2016) Fanny André et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)

(2016) Nathan D. Berkowitz et al.   BMC BIOINFORMATICS

nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs

(2016) Valentina Gandin et al.   GENOME RESEARCH

The importance of serine metabolism in cancer

(2016) Katherine R. Mattaini et al.   JOURNAL OF CELL BIOLOGY

Comprehensive Identification of RNA-Binding Domains in Human Cells

(2016) Alfredo Castello et al.   MOLECULAR CELL

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress

(2016) Z. Cheng et al.   Molecular Systems Biology

Proteome complexity and the forces that drive proteome imbalance

(2016) J. Wade Harper et al.   NATURE

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Emerging tale of UPR and cancer: an essentiality for malignancy

(2016) Younis Mohammad Hazari et al.   TUMOR BIOLOGY

Identification of a residue crucial for the angiostatic activity of human mini tryptophanyl-tRNA synthetase by focusing on its molecular evolution

(2016) Terumasa Nakamoto et al.   Scientific Reports

Oxidative Homeostasis Regulates the Response to Reductive Endoplasmic Reticulum Stress through Translation Control

(2016) Shuvadeep Maity et al.   Cell Reports

KDM4C and ATF4 Cooperate in Transcriptional Control of Amino Acid Metabolism

(2016) Erhu Zhao et al.   Cell Reports

Global, quantitative and dynamic mapping of protein subcellular localization

(2016) Daniel N Itzhak et al.   eLife

The unfolded protein response in neurodegenerative diseases: a neuropathological perspective

(2015) Wiep Scheper et al.   ACTA NEUROPATHOLOGICA

The Biology of Proteostasis in Aging and Disease

(2015) Johnathan Labbadia et al.   Annual Review of Biochemistry

Priming for Enhanced Defense

(2015) Uwe Conrath et al.   Annual Review of Phytopathology

SHAPE directed RNA folding

(2015) Ronny Lorenz et al.   BIOINFORMATICS

Quantitative visualization of alternative exon expression from RNA-seq data

(2015) Yarden Katz et al.   BIOINFORMATICS

Priming and memory of stress responses in organisms lacking a nervous system

(2015) Monika Hilker et al.   BIOLOGICAL REVIEWS

Translational Tolerance of Mitochondrial Genes to Metabolic Energy Stress Involves TISU and eIF1-eIF4GI Cooperation in Start Codon Selection

(2015) Hadar Sinvani et al.   Cell Metabolism

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Cis-regulatory RNA elements that regulate specialized ribosome activity

(2015) Shifeng Xue et al.   RNA Biology

Localized translation near the mitochondrial outer membrane: An update

(2015) Chen Lesnik et al.   RNA Biology

The Unfolded Protein Response Triggers Selective mRNA Release from the Endoplasmic Reticulum

(2014) David W. Reid et al.   CELL

Molecularly defined unfolded protein response subclasses have distinct correlations with fatty liver disease in zebrafish

(2014) A. M. Vacaru et al.   Disease Models & Mechanisms

Translational Control during Endoplasmic Reticulum Stress beyond Phosphorylation of the Translation Initiation Factor eIF2α

(2014) Bo-Jhih Guan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CHAC1/MGC4504 Is a Novel Proapoptotic Component of the Unfolded Protein Response, Downstream of the ATF4-ATF3-CHOP Cascade

(2014) I. N. Mungrue et al.   JOURNAL OF IMMUNOLOGY

Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKα

(2014) Thomas D. Baird et al.   MOLECULAR BIOLOGY OF THE CELL

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

(2014) Shifeng Xue et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation

(2014) Chase A. Weidmann et al.   RNA

Human tRNA synthetase catalytic nulls with diverse functions

(2014) W.-S. Lo et al.   SCIENCE

Serine and glycine metabolism in cancer

(2014) Ivano Amelio et al.   TRENDS IN BIOCHEMICAL SCIENCES

The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding

(2013) Hong Wang et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Proteostasis: monitoring the health of the proteome in biology, aging and disease

(2013) Richard Morimoto   Alzheimers & Dementia

Down-regulation of PERK enhances resistance to ionizing radiation

(2013) Deepu Oommen et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

When ER stress reaches a dead end

(2013) Hery Urra et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Stress-Regulated Translational Attenuation Adapts Mitochondrial Protein Import through Tim17A Degradation

(2013) T. Kelly Rainbolt et al.   Cell Metabolism

ER stress suppresses DNA double-strand break repair and sensitizes tumor cells to ionizing radiation by stimulating proteasomal degradation of Rad51

(2013) Tohru Yamamori et al.   FEBS LETTERS

Role of HERP and a HERP-related Protein in HRD1-dependent Protein Degradation at the Endoplasmic Reticulum

(2013) Chih-Hsiang Huang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PECA: A Novel Statistical Tool for Deconvoluting Time-Dependent Gene Expression Regulation

(2013) Guoshou Teo et al.   JOURNAL OF PROTEOME RESEARCH

Essential nontranslational functions of tRNA synthetases

(2013) Min Guo et al.   Nature Chemical Biology

Glutathione synthesis

(2012) Shelly C. Lu   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

MITRAC Links Mitochondrial Protein Translocation to Respiratory-Chain Assembly and Translational Regulation

(2012) David U. Mick et al.   CELL

Complexome Profiling Identifies TMEM126B as a Component of the Mitochondrial Complex I Assembly Complex

(2012) Heinrich Heide et al.   Cell Metabolism

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Stress management: How the unfolded protein response impacts fatty liver disease

(2012) Dru Imrie et al.   JOURNAL OF HEPATOLOGY

Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing

(2012) Markus Hafner et al.   METHODS

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

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

Serine starvation induces stress and p53-dependent metabolic remodelling in cancer cells

(2012) Oliver D. K. Maddocks et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Extensive Translatome Remodeling during ER Stress Response in Mammalian Cells

(2012) Iván Ventoso et al.   PLoS One

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

(2012) Kourosh Zarringhalam et al.   PLoS One

New Insights into Translational Regulation in the Endoplasmic Reticulum Unfolded Protein Response

(2012) G. D. Pavitt et al.   Cold Spring Harbor Perspectives in Biology

ER stress modulates cellular metabolism

(2011) Xiaoli Wang et al.   BIOCHEMICAL JOURNAL

htSeqTools: high-throughput sequencing quality control, processing and visualization in R

(2011) Evarist Planet et al.   BIOINFORMATICS

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

(2011) Nicholas T. Ingolia et al.   CELL

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

(2011) B. J. Parker et al.   GENOME RESEARCH

Divergence of Pumilio/fem-3mRNA Binding Factor (PUF) Protein Specificity through Variations in an RNA-binding Pocket

(2011) Chen Qiu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phosphorylation of eIF2 Facilitates Ribosomal Bypass of an Inhibitory Upstream ORF to EnhanceCHOPTranslation

(2011) Lakshmi Reddy Palam et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Divalent cations regulate the folding and activation status of integrins during their intracellular trafficking

(2011) S. Tiwari et al.   JOURNAL OF CELL SCIENCE

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Unique translation initiation of mRNAs-containing TISU element

(2011) Rofa Elfakess et al.   NUCLEIC ACIDS RESEARCH

Energy flows, metabolism and translation

(2011) R. Pascal et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Serine Biosynthesis with One Carbon Catabolism and the Glycine Cleavage System Represents a Novel Pathway for ATP Generation

(2011) Alexei Vazquez et al.   PLoS One

Modulating stress responses by the UPRosome: A matter of life and death

(2011) Ute Woehlbier et al.   TRENDS IN BIOCHEMICAL SCIENCES

Glutathione Peroxidase-1 in Health and Disease: From Molecular Mechanisms to Therapeutic Opportunities

(2010) Edith Lubos et al.   ANTIOXIDANTS & REDOX SIGNALING

Reactive oxygen species in cancer

(2010) Geou-Yarh Liou et al.   FREE RADICAL RESEARCH

Assembly factors of human mitochondrial complex I and their defects in disease

(2010) Matthew Mckenzie et al.   IUBMB LIFE

Stress-sensitive Regulation of IFRD1 mRNA Decay Is Mediated by an Upstream Open Reading Frame

(2010) Chenyang Zhao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

HuR Uses AUF1 as a Cofactor To Promote p16INK4 mRNA Decay

(2010) N. Chang et al.   MOLECULAR AND CELLULAR BIOLOGY

Oxidative Protein Folding by an Endoplasmic Reticulum-Localized Peroxiredoxin

(2010) Ester Zito et al.   MOLECULAR CELL

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency

(2010) Sarah E Calvo et al.   NATURE GENETICS

Endoplasmic reticulum stress inducers provide protection against 6-hydroxydopamine-induced cytotoxicity

(2010) Hirokazu Hara et al.   NEUROCHEMISTRY INTERNATIONAL

Mammalian endoplasmic reticulum stress sensor IRE1 signals by dynamic clustering

(2010) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GRP94 in ER quality control and stress responses

(2010) Davide Eletto et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

ER stress protects from retinal degeneration

(2009) César S Mendes et al.   EMBO JOURNAL

An Upstream Open Reading Frame Regulates Translation of GADD34 during Cellular Stresses That Induce eIF2α Phosphorylation

(2009) Yun-Young Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulated Ire1-dependent decay of messenger RNAs in mammalian cells

(2009) Julie Hollien et al.   JOURNAL OF CELL BIOLOGY

Unconventional splicing of XBP1 mRNA occurs in the cytoplasm during the mammalian unfolded protein response

(2009) A. Uemura et al.   JOURNAL OF CELL SCIENCE

Mutation in TACO1, encoding a translational activator of COX I, results in cytochrome c oxidase deficiency and late-onset Leigh syndrome

(2009) Woranontee Weraarpachai et al.   NATURE GENETICS

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

(2009) N. T. Ingolia et al.   SCIENCE

Endoplasmic Reticulum Stress in Disease Pathogenesis

(2008) Jonathan H. Lin et al.   Annual Review of Pathology-Mechanisms of Disease

Phosphorylation of eIF2 DirectsATF5Translational Control in Response to Diverse Stress Conditions

(2008) Donghui Zhou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Preconditioning with Endoplasmic Reticulum Stress Ameliorates Mesangioproliferative Glomerulonephritis

(2008) R. Inagi et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets

(2008) A. R. Morris et al.   MOLECULAR AND CELLULAR BIOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

A Translation Initiation Element Specific to mRNAs with Very Short 5′UTR that Also Regulates Transcription

(2008) Rofa Elfakess et al.   PLoS One

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum

(2008) B. Pyhtila et al.   RNA

Adapting Proteostasis for Disease Intervention

(2008) William E. Balch et al.   SCIENCE

A General Definition and Nomenclature for Alternative Splicing Events

(2008) Michael Sammeth et al.   PLoS Computational Biology