Spatial proteomics: a powerful discovery tool for cell biology

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

Neuronal functions of adaptor complexes involved in protein sorting

(2018) Carlos M Guardia et al.   CURRENT OPINION IN NEUROBIOLOGY

Proximity labeling: spatially resolved proteomic mapping for neurobiology

(2018) Shuo Han et al.   CURRENT OPINION IN NEUROBIOLOGY

A quantitative map of human Condensins provides new insights into mitotic chromosome architecture

(2018) Nike Walther et al.   JOURNAL OF CELL BIOLOGY

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

(2018) Ji-Young Youn et al.   MOLECULAR CELL

How many human proteoforms are there?

(2018) Ruedi Aebersold et al.   Nature Chemical Biology

Genome-wide SWAp-Tag yeast libraries for proteome exploration

(2018) Uri Weill et al.   NATURE METHODS

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

Quanti.us: a tool for rapid, flexible, crowd-based annotation of images

(2018) Alex J. Hughes et al.   NATURE METHODS

Genome-wide C-SWAT library for high-throughput yeast genome tagging

(2018) Matthias Meurer et al.   NATURE METHODS

Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging

(2018) Antonio Z Politi et al.   Nature Protocols

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Controlling compartmentalization by non-membrane-bound organelles

(2018) Richard J. Wheeler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

NUFIP1 is a ribosome receptor for starvation-induced ribophagy

(2018) Gregory A. Wyant et al.   SCIENCE

Toolbox: Creating a systematic database of secretory pathway proteins uncovers new cargo for COPI

(2018) Uri Weill et al.   TRAFFIC

Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast

(2018) Silvia G. Chuartzman et al.   YEAST

An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations

(2018) Xiaonan Liu et al.   Nature Communications

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

(2018) Ying Zhu et al.   Nature Communications

CEP128 Localizes to the Subdistal Appendages of the Mother Centriole and Regulates TGF-β/BMP Signaling at the Primary Cilium

(2018) Maren Mönnich et al.   Cell Reports

Role of the AP-5 adaptor protein complex in late endosome-to-Golgi retrieval

(2018) Jennifer Hirst et al.   PLOS BIOLOGY

Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins

(2018) Alex X Lu et al.   eLife

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

(2018) Katrina Meyer et al.   CELL

Experimental and computational framework for a dynamic protein atlas of human cell division

(2018) Yin Cai et al.   NATURE

Deep learning is combined with massive-scale citizen science to improve large-scale image classification

(2018) Devin P Sullivan et al.   NATURE BIOTECHNOLOGY

Efficient proximity labeling in living cells and organisms with TurboID

(2018) Tess C Branon et al.   NATURE BIOTECHNOLOGY

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

(2018) Chawin Ounkomol et al.   NATURE METHODS

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A

(2018) Alexandra K. Davies et al.   Nature Communications

An expanded toolkit for gene tagging based on MiMIC and scarless CRISPR tagging in Drosophila

(2018) David Li-Kroeger et al.   eLife

Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis

(2018) Natalie Krahmer et al.   DEVELOPMENTAL CELL

YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries

(2018) Benjamin Dubreuil et al.   NUCLEIC ACIDS RESEARCH

Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization

(2017) Brock Roberts et al.   MOLECULAR BIOLOGY OF THE CELL

Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)

(2017) Faraz K. Mardakheh et al.   Molecular BioSystems

Automated analysis of high‐content microscopy data with deep learning

(2017) Oren Z Kraus et al.   Molecular Systems Biology

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Top-down characterization of endogenous protein complexes with native proteomics

(2017) Owen S Skinner et al.   Nature Chemical Biology

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

Fluorescence nanoscopy in cell biology

(2017) Steffen J. Sahl et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Primer on Concepts and Applications of Proteomics in Neuroscience

(2017) Fabian Hosp et al.   NEURON

MoonProt 2.0: an expansion and update of the moonlighting proteins database

(2017) Chang Chen et al.   NUCLEIC ACIDS RESEARCH

MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins

(2017) Luís Franco-Serrano et al.   NUCLEIC ACIDS RESEARCH

Organellar Omics-A Reviving Strategy to Untangle the Biomolecular Complexity of the Cell

(2017) Arun Kumar Tharkeshwar et al.   PROTEOMICS

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

Close Encounters – Probing Proximal Proteins in Live or Fixed Cells

(2017) Peter Lönn et al.   TRENDS IN BIOCHEMICAL SCIENCES

Charting organellar importomes by quantitative mass spectrometry

(2017) Christian D. Peikert et al.   Nature Communications

Improved split fluorescent proteins for endogenous protein labeling

(2017) Siyu Feng et al.   Nature Communications

Region and cell-type resolved quantitative proteomic map of the human heart

(2017) Sophia Doll et al.   Nature Communications

Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale

(2017) Marcel Morgenstern et al.   Cell Reports

A Mass Spectrometry-Based Approach for Mapping Protein Subcellular Localization Reveals the Spatial Proteome of Mouse Primary Neurons

(2017) Daniel N. Itzhak et al.   Cell Reports

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning

(2017) Tanel Pärnamaa et al.   G3-Genes Genomes Genetics

In vitro-engineered non-antibody protein therapeutics

(2017) Rudo Simeon et al.   Protein & Cell

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

(2017) Pornchai Kaewsapsak et al.   eLife

Classifying and segmenting microscopy images with deep multiple instance learning

(2016) Oren Z. Kraus et al.   BIOINFORMATICS

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

(2016) Xinping Yang et al.   CELL

Phase separation in biology; functional organization of a higher order

(2016) Diana M. Mitrea et al.   Cell Communication and Signaling

High-throughput fluorescence microscopic analysis of protein abundance and localization in budding yeast

(2016) Nikko P. Torres et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins

(2016) Marie Skogs et al.   JOURNAL OF PROTEOME RESEARCH

Protein species and moonlighting proteins: Very small changes in a protein's covalent structure can change its biochemical function

(2016) Constance J. Jeffery   Journal of Proteomics

Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome

(2016) Michel Jadot et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Tracking the proteome

(2016) Stéphane Larochelle   NATURE METHODS

MetaMass, a tool for meta-analysis of subcellular proteomics data

(2016) Fridtjof Lund-Johansen et al.   NATURE METHODS

A proposal for validation of antibodies

(2016) Mathias Uhlen et al.   NATURE METHODS

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

(2016) Stefka Tyanova et al.   NATURE METHODS

A scalable strategy for high-throughput GFP tagging of endogenous human proteins

(2016) Manuel D. Leonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Filling the Void: Proximity-Based Labeling of Proteins in Living Cells

(2016) Dae In Kim et al.   TRENDS IN CELL BIOLOGY

High-Content Screening for Quantitative Cell Biology

(2016) Mojca Mattiazzi Usaj et al.   TRENDS IN CELL BIOLOGY

Versatile protein tagging in cells with split fluorescent protein

(2016) Daichi Kamiyama et al.   Nature Communications

A draft map of the mouse pluripotent stem cell spatial proteome

(2016) Andy Christoforou et al.   Nature Communications

Global, quantitative and dynamic mapping of protein subcellular localization

(2016) Daniel N Itzhak et al.   eLife

The Size of the Human Proteome: The Width and Depth

(2016) Elena A. Ponomarenko et al.   International Journal of Analytical Chemistry

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection

(2016) Pierre M. Jean Beltran et al.   Cell Systems

An Unsupervised kNN Method to Systematically Detect Changes in Protein Localization in High-Throughput Microscopy Images

(2016) Alex Xijie Lu et al.   PLoS One

Super-resolution imaging of fluorescently labeled, endogenous RNA Polymerase II in living cells with CRISPR/Cas9-mediated gene editing

(2016) Won-Ki Cho et al.   Scientific Reports

A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface

(2015) Gagan D. Gupta et al.   CELL

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

The Nuclear Proteome of a Vertebrate

(2015) Martin Wühr et al.   CURRENT BIOLOGY

Reproducibility crisis: Blame it on the antibodies

(2015) Monya Baker   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

Multidimensional proteomics for cell biology

(2015) Mark Larance et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Mechanisms Regulating Protein Localization

(2015) Nicholas C. Bauer et al.   TRAFFIC

Extreme multifunctional proteins identified from a human protein interaction network

(2015) Charles E. Chapple et al.   Nature Communications

CRISPR/Cas9-mediated endogenous protein tagging for RESOLFT super-resolution microscopy of living human cells

(2015) Michael Ratz et al.   Scientific Reports

Efficient CRISPR-Cas9-Mediated Generation of Knockin Human Pluripotent Stem Cells Lacking Undesired Mutations at the Targeted Locus

(2015) Florian T. Merkle et al.   Cell Reports

CYCLoPs: A Comprehensive Database Constructed from Automated Analysis of Protein Abundance and Subcellular Localization Patterns in Saccharomyces cerevisiae

(2015) J. L. Y. Koh et al.   G3-Genes Genomes Genetics

Why study moonlighting proteins?

(2015) Constance J. Jeffery   Frontiers in Genetics

Antibody performance in western blot applications is context-dependent

(2014) Cajsa Älgenäs et al.   Biotechnology Journal

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction

(2014) Michael P. Weekes et al.   CELL

A Foundation for Reliable Spatial Proteomics Data Analysis

(2014) Laurent Gatto et al.   MOLECULAR & CELLULAR PROTEOMICS

Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein–protein interactions

(2014) Georg H. H. Borner et al.   MOLECULAR BIOLOGY OF THE CELL

Proteomic Mapping of the Human Mitochondrial Intermembrane Space in Live Cells via Ratiometric APEX Tagging

(2014) Victoria Hung et al.   MOLECULAR CELL

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

The emergence of proteome-wide technologies: systematic analysis of proteins comes of age

(2014) Michal Breker et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Determining the subcellular location of new proteins from microscope images using local features

(2013) Luis Pedro Coelho et al.   BIOINFORMATICS

A novel single-cell screening platform reveals proteome plasticity during yeast stress responses

(2013) Michal Breker et al.   JOURNAL OF CELL BIOLOGY

The effect of organelle discovery upon sub-cellular protein localisation

(2013) L.M. Breckels et al.   Journal of Proteomics

Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence

(2013) Natalie Krahmer et al.   MOLECULAR & CELLULAR PROTEOMICS

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells

(2013) Charlotte Stadler et al.   NATURE METHODS

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

LoQAtE—Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast

(2013) Michal Breker et al.   NUCLEIC ACIDS RESEARCH

Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae

(2013) Aprotim Mazumder et al.   NUCLEIC ACIDS RESEARCH

A chemostat array enables the spatio-temporal analysis of the yeast proteome

(2013) N. Denervaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

(2013) H.-W. Rhee et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

Protein subcellular location pattern classification in cellular images using latent discriminative models

(2012) J. Li et al.   BIOINFORMATICS

Progress toward single cell metabolomics

(2012) Stanislav S Rubakhin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles

(2012) Georg H.H. Borner et al.   JOURNAL OF CELL BIOLOGY

Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy

(2012) Charlotte Stadler et al.   Journal of Proteomics

Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress

(2012) Johnny M. Tkach et al.   NATURE CELL BIOLOGY

Immunolabeling artifacts and the need for live-cell imaging

(2012) Ulrike Schnell et al.   NATURE METHODS

Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas

(2012) Jieyue Li et al.   PLoS One

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

The mitochondrial contact site complex, a determinant of mitochondrial architecture

(2011) Max Harner et al.   EMBO JOURNAL

Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods

(2011) Lis Jakobsen et al.   EMBO JOURNAL

Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells

(2011) Jeffrey B. Doyon et al.   NATURE CELL BIOLOGY

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images

(2010) Michael Riffle et al.   BMC BIOINFORMATICS

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

A single fixation protocol for proteome-wide immunofluorescence localization studies

(2009) Charlotte Stadler et al.   Journal of Proteomics

Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells

(2009) Milana Frenkel-Morgenstern et al.   NUCLEIC ACIDS RESEARCH

Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation

(2009) R. Narayanaswamy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE