The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1

Engineering ER-stress dependent non-conventional mRNA splicing

(2018) Weihan Li et al.   eLife

Dom34 mediates targeting of exogenous RNA in the antiviral OAS/RNase L pathway

(2018) Takuto Nogimori et al.   NUCLEIC ACIDS RESEARCH

An unfolded protein-induced conformational switch activates mammalian IRE1

(2017) G Elif Karagöz et al.   eLife

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

The integrated stress response

(2016) Karolina Pakos‐Zebrucka et al.   EMBO REPORTS

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress

(2016) Sekyung Oh et al.   Oncotarget

A conformational RNA zipper promotes intron ejection during non-conventional XBP1 mRNA splicing

(2015) J. Peschek et al.   EMBO REPORTS

Ire1-mediated decay in mammalian cells relies on mRNA sequence, structure, and translational status

(2015) Kristin Moore et al.   MOLECULAR BIOLOGY OF THE CELL

A functional link between the co-translational protein translocation pathway and the UPR

(2015) Rachel Plumb et al.   eLife

Structure of the Mammalian Ribosome-Sec61 Complex to 3.4 Å Resolution

(2014) Rebecca M. Voorhees et al.   CELL

The RtcB RNA ligase is an essential component of the metazoan unfolded protein response

(2014) S. G. Kosmaczewski et al.   EMBO REPORTS

A Synthetic Biology Approach Identifies the Mammalian UPR RNA Ligase RtcB

(2014) Yanyan Lu et al.   MOLECULAR CELL

Secondary Structures of rRNAs from All Three Domains of Life

(2014) Anton S. Petrov et al.   PLoS One

The Ribosome as a Hub for Protein Quality Control

(2013) Sebastian Pechmann et al.   MOLECULAR CELL

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Silencing of Lipid Metabolism Genes through IRE1α-Mediated mRNA Decay Lowers Plasma Lipids in Mice

(2012) Jae-Seon So et al.   Cell Metabolism

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule

(2012) B. C. S. Cross et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitsugumin 23 Forms a Massive Bowl-Shaped Assembly and Cation-Conducting Channel

(2011) Elisa Venturi et al.   BIOCHEMISTRY

Structural and functional basis for RNA cleavage by Ire1

(2011) Alexei V Korennykh et al.   BMC BIOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

Angiogenin-Induced tRNA Fragments Inhibit Translation Initiation

(2011) Pavel Ivanov et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Translational Pausing Ensures Membrane Targeting and Cytoplasmic Splicing of XBP1u mRNA

(2011) K. Yanagitani et al.   SCIENCE

The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation

(2011) P. Walter et al.   SCIENCE

Unfolded Proteins Are Ire1-Activating Ligands That Directly Induce the Unfolded Protein Response

(2011) B. M. Gardner et al.   SCIENCE

Molecular Mechanism of Co-translational Protein Targeting by the Signal Recognition Particle

(2011) Ishu Saraogi et al.   TRAFFIC

Mammalian ER stress sensor IRE1β specifically down-regulates the synthesis of secretory pathway proteins

(2010) Daisuke Nakamura et al.   FEBS LETTERS

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

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

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

(2010) Markus Hafner et al.   Jove-Journal of Visualized Experiments

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

IRE1α Kinase Activation Modes Control Alternate Endoribonuclease Outputs to Determine Divergent Cell Fates

(2009) Dan Han et al.   CELL

Angiogenin cleaves tRNA and promotes stress-induced translational repression

(2009) Satoshi Yamasaki et al.   JOURNAL OF CELL BIOLOGY

Regulated Ire1-dependent decay of messenger RNAs in mammalian cells

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

Cotranslational Targeting of XBP1 Protein to the Membrane Promotes Cytoplasmic Splicing of Its Own mRNA

(2009) Kota Yanagitani et al.   MOLECULAR CELL

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Stress induces tRNA cleavage by angiogenin in mammalian cells

(2008) Hanjiang Fu et al.   FEBS LETTERS

The RNA Exosome Component hRrp6 Is a Target for 5-Fluorouracil in Human Cells

(2008) S. Kammler et al.   MOLECULAR CANCER RESEARCH

Messenger RNA targeting to endoplasmic reticulum stress signalling sites

(2008) Tomás Aragón et al.   NATURE

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