Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit

MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments

(2020) Klemens Wild et al.   Nature Communications

Chaperone Interactions at the Ribosome

(2019) Elke Deuerling et al.   Cold Spring Harbor Perspectives in Biology

Functional Modules of the Proteostasis Network

(2019) Gopal G. Jayaraj et al.   Cold Spring Harbor Perspectives in Biology

Dual Role of Ribosome-Binding Domain of NAC as a Potent Suppressor of Protein Aggregation and Aging-Related Proteinopathies

(2019) Koning Shen et al.   MOLECULAR CELL

Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex

(2019) L. Telley et al.   SCIENCE

Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments

(2019) Anne-Sophie Hafner et al.   SCIENCE

Selective ribosome profiling to study interactions of translating ribosomes in yeast

(2019) Carla V. Galmozzi et al.   Nature Protocols

Local translation in neurons: visualization and function

(2019) Christine E. Holt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Development and Arealization of the Cerebral Cortex

(2019) Cathryn R. Cadwell et al.   NEURON

TTC5 mediates autoregulation of tubulin via mRNA degradation

(2019) Zhewang Lin et al.   SCIENCE

mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding

(2018) M. Delarue et al.   CELL

Differential Dependence of GABAergic and Glutamatergic Neurons on Glia for the Establishment of Synaptic Transmission

(2018) Paul Turko et al.   CEREBRAL CORTEX

Structure of a prehandover mammalian ribosomal SRP·SRP receptor targeting complex

(2018) Kan Kobayashi et al.   SCIENCE

ER Proteostasis Control of Neuronal Physiology and Synaptic Function

(2018) Gabriela Martínez et al.   TRENDS IN NEUROSCIENCES

Downregulation of ribosome biogenesis during early forebrain development

(2018) Kevin F Chau et al.   eLife

cisTEM, user-friendly software for single-particle image processing

(2018) Timothy Grant et al.   eLife

The role of ErbB3 binding protein 1 in cancer: Friend or foe?

(2018) Dang Quan Nguyen et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis

(2018) Koshi Imami et al.   MOLECULAR CELL

Translational Control during Developmental Transitions

(2018) Felipe Karam Teixeira et al.   Cold Spring Harbor Perspectives in Biology

Translational Control in the Brain in Health and Disease

(2018) Wayne S. Sossin et al.   Cold Spring Harbor Perspectives in Biology

Mechanisms of Cotranslational Maturation of Newly Synthesized Proteins

(2018) Günter Kramer et al.   Annual Review of Biochemistry

Ribosome–NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation

(2018) Alexandra G. Knorr et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polarity Acquisition in Cortical Neurons Is Driven by Synergistic Action of Sox9-Regulated Wwp1 and Wwp2 E3 Ubiquitin Ligases and Intronic miR-140

(2018) Mateusz C. Ambrozkiewicz et al.   NEURON

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification

(2018) Cheng Zhang et al.   ULTRAMICROSCOPY

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis

(2018) Julia Flis et al.   Cell Reports

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Regulation of mRNA Translation in Neurons—A Matter of Life and Death

(2017) Mridu Kapur et al.   NEURON

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Ribosomopathies: There’s strength in numbers

(2017) Eric W. Mills et al.   SCIENCE

RNA localization is a key determinant of neurite-enriched proteome

(2017) Alessandra Zappulo et al.   Nature Communications

Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling

(2017) Scott A. Yuzwa et al.   Cell Reports

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

(2016) Joshua G. Dunn et al.   BMC GENOMICS

Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation

(2016) Basil Johannes Greber et al.   CELL

The frontier of RNA metamorphosis and ribosome signature in neocortical development

(2016) Matthew L. Kraushar et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL NEUROSCIENCE

Cotranslational signal-independent SRP preloading during membrane targeting

(2016) Justin W. Chartron et al.   NATURE

Global profiling of SRP interaction with nascent polypeptides

(2016) Daniela Schibich et al.   NATURE

Dynamics of ribosome scanning and recycling revealed by translation complex profiling

(2016) Stuart K. Archer et al.   NATURE

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

(2016) John C. Silbereis et al.   NEURON

Ribonuclease selection for ribosome profiling

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

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association

(2016) T. Sprink et al.   Science Advances

Translating the Genome in Time and Space: Specialized Ribosomes, RNA Regulons, and RNA-Binding Proteins

(2015) Zhen Shi et al.   Annual Review of Cell and Developmental Biology

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

(2015) Vicent Pelechano et al.   CELL

Structural Snapshots of Actively Translating Human Ribosomes

(2015) Elmar Behrmann et al.   CELL

Thalamic WNT3 Secretion Spatiotemporally Regulates the Neocortical Ribosome Signature and mRNA Translation to Specify Neocortical Cell Subtypes

(2015) M. L. Kraushar et al.   JOURNAL OF NEUROSCIENCE

Structure and Assembly Pathway of the Ribosome Quality Control Complex

(2015) Sichen Shao et al.   MOLECULAR CELL

Structural basis for stop codon recognition in eukaryotes

(2015) Alan Brown et al.   NATURE

Specification of synaptic connectivity by cell surface interactions

(2015) Joris de Wit et al.   NATURE REVIEWS NEUROSCIENCE

The principle of antagonism ensures protein targeting specificity at the endoplasmic reticulum

(2015) M. Gamerdinger et al.   SCIENCE

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

(2014) Rebecca M. Voorhees et al.   CELL

Remote Control of Gene Function by Local Translation

(2014) Hosung Jung et al.   CELL

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

The complete structure of the large subunit of the mammalian mitochondrial ribosome

(2014) Basil J. Greber et al.   NATURE

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Neuronal morphometry directly from bitmap images

(2014) Tiago A Ferreira et al.   NATURE METHODS

Structural basis for interaction of a cotranslational chaperone with the eukaryotic ribosome

(2014) Yixiao Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3′ untranslated regions

(2014) Teemu P. Miettinen et al.   NUCLEIC ACIDS RESEARCH

Temporally defined neocortical translation and polysome assembly are determined by the RNA-binding protein Hu antigen R

(2014) M. L. Kraushar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling

(2014) C. H. Jan et al.   SCIENCE

QuaNCAT: quantitating proteome dynamics in primary cells

(2013) Andrew J M Howden et al.   NATURE METHODS

Post-transcriptional regulatory elements and spatiotemporal specification of neocortical stem cells and projection neurons

(2013) E.M. DeBoer et al.   NEUROSCIENCE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Selective enrichment of newly synthesized proteins for quantitative secretome analysis

(2012) Katrin Eichelbaum et al.   NATURE BIOTECHNOLOGY

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

(2012) Fang-Chieh Chou et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

(2011) M. H. Longair et al.   BIOINFORMATICS

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Proteostasis and Movement Disorders: Parkinson's Disease and Amyotrophic Lateral Sclerosis

(2011) D. A. Bosco et al.   Cold Spring Harbor Perspectives in Biology

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

P48 Ebp1 acts as a downstream mediator of Trk signaling in neurons, contributing neuronal differentiation

(2010) Il-Sun Kwon et al.   NEUROCHEMISTRY INTERNATIONAL

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

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

(2009) Da Wei Huang et al.   Nature Protocols

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

(2009) N. T. Ingolia et al.   SCIENCE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach 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

Global analysis of cellular protein translation by pulsed SILAC

(2008) Björn Schwanhäusser et al.   PROTEOMICS