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

Discovering and linking public omics data sets using the Omics Discovery Index

(2017) Yasset Perez-Riverol et al.   NATURE BIOTECHNOLOGY

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency

(2017) Arun Kumar Tharkeshwar et al.   Scientific Reports

Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein–Protein Interaction Analysis, and Protein Function Exploration

(2017) Els Beghein et al.   Frontiers in Immunology

In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons

(2017) Chee Yeun Chung et al.   Cell Systems

In Situ Detection of Protein Complexes and Modifications by Chemical Ligation Proximity Assay

(2016) Rui Hong et al.   BIOCONJUGATE CHEMISTRY

Restricted Location of PSEN2/γ-Secretase Determines Substrate Specificity and Generates an Intracellular Aβ Pool

(2016) Ragna Sannerud et al.   CELL

The awesome lysosome

(2016) A. Ballabio   EMBO Molecular Medicine

Current investigations into magnetic nanoparticles for biomedical applications

(2016) Xiaoming Li et al.   JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A

Lysosome acidification by photoactivated nanoparticles restores autophagy under lipotoxicity

(2016) Kyle M. Trudeau et al.   JOURNAL OF CELL BIOLOGY

DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction

(2016) S. Ohta et al.   SCIENCE

A draft map of the mouse pluripotent stem cell spatial proteome

(2016) Andy Christoforou et al.   Nature Communications

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues

(2016) Idit Kosti et al.   Scientific Reports

Early etiology of Alzheimer’s disease: tipping the balance toward autophagy or endosomal dysfunction?

(2015) Aleksandar Peric et al.   ACTA NEUROPATHOLOGICA

Proximity-Induced Covalent Labeling of Proteins with a Reactive Fluorophore-Binding Peptide Tag

(2015) Murat Sunbul et al.   BIOCONJUGATE CHEMISTRY

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

(2015) Gagan D. Gupta et al.   CELL

Magnetic nanoparticles: In vivo cancer diagnosis and therapy

(2015) Michele K. Lima-Tenório et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

Protein Neighbors and Proximity Proteomics

(2015) Johanna S. Rees et al.   MOLECULAR & CELLULAR PROTEOMICS

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

The systematic analysis of protein–lipid interactions comes of age

(2015) Antoine-Emmanuel Saliba et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Presenilin 1 Maintains Lysosomal Ca2+ Homeostasis via TRPML1 by Regulating vATPase-Mediated Lysosome Acidification

(2015) Ju-Hyun Lee et al.   Cell Reports

Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

(2015) Tino Pleiner et al.   eLife

The endosomal-lysosomal system: from acidification and cargo sorting to neurodegeneration

(2015) Yong-Bo Hu et al.   Translational Neurodegeneration

Synthetic Antiferromagnetic Nanoparticles as Potential Contrast Agents in MRI

(2014) Ruben Van Roosbroeck et al.   ACS Nano

Lipidomics: Analysis of the Lipid Composition of Cells and Subcellular Organelles by Electrospray Ionization Mass Spectrometry

(2014) Britta Brügger   Annual Review of Biochemistry

New Insights into the DT40 B Cell Receptor Cluster Using a Proteomic Proximity Labeling Assay

(2014) Xue-Wen Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2014) Victoria Hung et al.   MOLECULAR CELL

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Lipid landscapes and pipelines in membrane homeostasis

(2014) Joost C.M. Holthuis et al.   NATURE

Directed evolution of APEX2 for electron microscopy and proximity labeling

(2014) Stephanie S Lam et al.   NATURE METHODS

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Sensitive in vivo cell detection using size-optimized superparamagnetic nanoparticles

(2013) Jesse Trekker et al.   BIOMATERIALS

Marked by association: techniques for proximity-dependent labeling of proteins in eukaryotic cells

(2013) Kyle J. Roux   CELLULAR AND MOLECULAR LIFE SCIENCES

Organellar lipidomics—background and perspectives

(2013) Christian Klose et al.   CURRENT OPINION IN CELL BIOLOGY

The role of autophagy in neurodegenerative disease

(2013) Ralph A Nixon   NATURE MEDICINE

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

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

(2013) H.-W. Rhee et al.   SCIENCE

Lysosomal storage disorders: The cellular impact of lysosomal dysfunction

(2012) Frances M. Platt et al.   JOURNAL OF CELL BIOLOGY

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

A simple guide to biochemical approaches for analyzing protein–lipid interactions

(2012) Hongxia Zhao et al.   MOLECULAR BIOLOGY OF THE CELL

Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy

(2012) Jeffrey D Martell et al.   NATURE BIOTECHNOLOGY

Acidic Nanoparticles Are Trafficked to Lysosomes and Restore an Acidic Lysosomal pH and Degradative Function to Compromised ARPE-19 Cells

(2012) Gabriel C. Baltazar et al.   PLoS One

Protein localization in disease and therapy

(2011) M.-C. Hung et al.   JOURNAL OF CELL SCIENCE

Magnetic nanoparticles: recent advances in synthesis, self-assembly and applications

(2011) Srikanth Singamaneni et al.   JOURNAL OF MATERIALS CHEMISTRY

A novel strategy for the comprehensive analysis of the biomolecular composition of isolated plasma membranes

(2011) D. B. Thimiri Govinda Raj et al.   Molecular Systems Biology

A proteomics approach to the cell-surface interactome using the enzyme-mediated activation of radical sources reaction

(2011) Songlin Jiang et al.   PROTEOMICS

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

Lipidomics reveals a remarkable diversity of lipids in human plasma,

(2010) Oswald Quehenberger et al.   JOURNAL OF LIPID RESEARCH

pH-Responsive Nanoparticles for Drug Delivery

(2010) Weiwei Gao et al.   MOLECULAR PHARMACEUTICS

Computational solutions to large-scale data management and analysis

(2010) Eric E. Schadt et al.   NATURE REVIEWS GENETICS

From iron oxide nanoparticles towards advanced iron-based inorganic materials designed for biomedical applications

(2010) Albert Figuerola et al.   PHARMACOLOGICAL RESEARCH

Organelle proteomics experimental designs and analysis

(2010) Laurent Gatto et al.   PROTEOMICS

Between a chicken and a grape: estimating the number of human genes

(2010) Mihaela Pertea et al.   GENOME BIOLOGY

Magnetic nanoparticles for theragnostics

(2009) Veronica I. Shubayev et al.   ADVANCED DRUG DELIVERY REVIEWS

Mapping Organelle Proteins and Protein Complexes inDrosophila melanogaster

(2009) Denise J. L. Tan et al.   JOURNAL OF PROTEOME RESEARCH

The Lipidomes of Vesicular Stomatitis Virus, Semliki Forest Virus, and the Host Plasma Membrane Analyzed by Quantitative Shotgun Mass Spectrometry

(2009) L. Kalvodova et al.   JOURNAL OF VIROLOGY

The Organelle Proteome of the DT40 Lymphocyte Cell Line

(2009) Stephanie L. Hall et al.   MOLECULAR & CELLULAR PROTEOMICS

Lysosomal disorders: From storage to cellular damage

(2008) Andrea Ballabio et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Miniaturizing free-flow electrophoresis – a critical review

(2008) Dietrich Kohlheyer et al.   ELECTROPHORESIS

Evolution of organelle-associated protein profiling

(2008) Wei Yan et al.   Journal of Proteomics

Flow cytometry-assisted purification and proteomic analysis of the corticotropes dense-core secretory granules

(2008) Daniel J. Gauthier et al.   PROTEOMICS

Proteomic profiling of exosomes: Current perspectives

(2008) Richard J. Simpson et al.   PROTEOMICS