Exploring autophagy with Gene Ontology

Phosphatidylinositol-3-phosphate in the regulation of autophagy membrane dynamics

(2017) Anna Chiara Nascimbeni et al.   FEBS Journal

Autophagy and Microglia: Novel Partners in Neurodegeneration and Aging

(2017) Ainhoa Plaza-Zabala et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Autophagy and Neurodegeneration: Pathogenic Mechanisms and Therapeutic Opportunities

(2017) Fiona M. Menzies et al.   NEURON

Emerging Mechanisms in Initiating and Terminating Autophagy

(2017) Manuela Antonioli et al.   TRENDS IN BIOCHEMICAL SCIENCES

Neuronal Mitophagy in Neurodegenerative Diseases

(2017) Marta Martinez-Vicente   Frontiers in Molecular Neuroscience

iLIR database: A web resource for LIR motif-containing proteins in eukaryotes

(2016) Anne-Claire Jacomin et al.   Autophagy

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

(2016) Daniel J Klionsky et al.   Autophagy

Pexophagy in yeasts

(2016) Masahide Oku et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Stress granules at the intersection of autophagy and ALS

(2016) Zachary Monahan et al.   BRAIN RESEARCH

An overview of macroautophagy in yeast

(2016) Xin Wen et al.   JOURNAL OF MOLECULAR BIOLOGY

Using the Gene Ontology to Annotate Key Players in Parkinson’s Disease

(2016) R. E. Foulger et al.   NEUROINFORMATICS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Autophagy in cancer metastasis

(2016) E E Mowers et al.   ONCOGENE

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

(2016) Marc Feuermann et al.   Database-The Journal of Biological Databases and Curation

Modeling biochemical pathways in the gene ontology

(2016) David P. Hill et al.   Database-The Journal of Biological Databases and Curation

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

Integrative transcriptomic meta-analysis of Parkinson’s disease and depression identifies NAMPT as a potential blood biomarker for de novo Parkinson’s disease

(2016) Jose A. Santiago et al.   Scientific Reports

Subcellular Clearance and Accumulation of Huntington Disease Protein: A Mini-Review

(2016) Ting Zhao et al.   Frontiers in Molecular Neuroscience

Dysregulation of autophagy and mitochondrial function in Parkinson’s disease

(2016) Bao Wang et al.   Translational Neurodegeneration

Autophagy Constitutes a Protective Mechanism against Ethanol Toxicity in Mouse Astrocytes and Neurons

(2016) Antoni Pla et al.   PLoS One

Defective Autophagy, Mitochondrial Clearance and Lipophagy in Niemann-Pick Type B Lymphocytes

(2016) Barbara Canonico et al.   PLoS One

Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes

(2015) Adva Shemi et al.   Autophagy

Autophagy Regulatory Network — A systems-level bioinformatics resource for studying the mechanism and regulation of autophagy

(2015) Dénes Türei et al.   Autophagy

Thyroid hormone induction of mitochondrial activity is coupled to mitophagy via ROS-AMPK-ULK1 signaling

(2015) Rohit A Sinha et al.   Autophagy

An essential role for chaperone-mediated autophagy in cell cycle progression

(2015) Maimon E Hubbi et al.   Autophagy

Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism

(2015) Sejal Patel et al.   BMC BIOINFORMATICS

Blood transcriptomics of drug-naïve sporadic Parkinson’s disease patients

(2015) Raffaella Calligaris et al.   BMC GENOMICS

Representing virus-host interactions and other multi-organism processes in the Gene Ontology

(2015) R. E. Foulger et al.   BMC MICROBIOLOGY

Autophagy Receptor NDP52 Regulates Pathogen-Containing Autophagosome Maturation

(2015) Pauline Verlhac et al.   Cell Host & Microbe

Association of TLR9 polymorphisms with sporadic Parkinson's disease in Chinese Han population

(2015) Konghua Zhu et al.   INTERNATIONAL JOURNAL OF NEUROSCIENCE

Molecular mechanisms mediating mitochondrial dynamics and mitophagy and their functional roles in the cardiovascular system

(2015) Yoshiyuki Ikeda et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Selective autophagy: Xenophagy

(2015) Kyle A. Bauckman et al.   METHODS

PI(5)P Regulates Autophagosome Biogenesis

(2015) Mariella Vicinanza et al.   MOLECULAR CELL

Mouse genome database 2016

(2015) Carol J. Bult et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Regulation of autophagy by amino acids and MTOR-dependent signal transduction

(2014) Alfred J. Meijer et al.   AMINO ACIDS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

An Integrated Ontology Resource to Explore and Study Host-Virus Relationships

(2014) Patrick Masson et al.   PLoS One

TermGenie – a web-application for pattern-based ontology class generation

(2014) Heiko Dietze et al.   Journal of Biomedical Semantics

The Atg8 family: multifunctional ubiquitin-like key regulators of autophagy

(2013) Moran Rawet Slobodkin et al.   Essays in Biochemistry

The Mechanism and Physiological Function of Macroautophagy

(2013) Daniel J. Klionsky et al.   Journal of Innate Immunity

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map

(2013) Kazuhiro A. Fujita et al.   MOLECULAR NEUROBIOLOGY

Receptor interacting protein kinase 2–mediated mitophagy regulates inflammasome activation during virus infection

(2013) Christopher Lupfer et al.   NATURE IMMUNOLOGY

Impaired autophagy and APP processing in Alzheimer's disease: The potential role of Beclin 1 interactome

(2013) Antero Salminen et al.   PROGRESS IN NEUROBIOLOGY

A guide to best practices for Gene Ontology (GO) manual annotation

(2013) R. Balakrishnan et al.   Database-The Journal of Biological Databases and Curation

Interaction between FIP200 and ATG16L1 distinguishes ULK1 complex–dependent and –independent autophagy

(2012) Noor Gammoh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Role of Atg Proteins in Autophagosome Formation

(2011) Noboru Mizushima et al.   Annual Review of Cell and Developmental Biology

A comprehensive glossary of autophagy-related molecules and processes (2ndedition)

(2011) Daniel J Klionsky et al.   Autophagy

The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray

(2011) Etienne Moussay et al.   Autophagy

Microautophagy in mammalian cells: Revisiting a 40-year-old conundrum

(2011) Dalibor Mijaljica et al.   Autophagy

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

Autophagy Regulates Cholesterol Efflux from Macrophage Foam Cells via Lysosomal Acid Lipase

(2011) Mireille Ouimet et al.   Cell Metabolism

Autophagy: for better or for worse

(2011) Ellen Wirawan et al.   CELL RESEARCH

Microautophagy of Cytosolic Proteins by Late Endosomes

(2011) Ranjit Sahu et al.   DEVELOPMENTAL CELL

Atg8: an autophagy-related ubiquitin-like protein family

(2011) Tomer Shpilka et al.   GENOME BIOLOGY

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Cross-product extensions of the Gene Ontology

(2010) Christopher J. Mungall et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Network organization of the human autophagy system

(2010) Christian Behrends et al.   NATURE

The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research

(2010) K. Homma et al.   NUCLEIC ACIDS RESEARCH

ViralZone: a knowledge resource to understand virus diversity

(2010) Chantal Hulo et al.   NUCLEIC ACIDS RESEARCH

Chaperone-mediated autophagy: Molecular mechanisms and physiological relevance

(2010) Samantha J. Orenstein et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The late stage of autophagy: cellular events and molecular regulation

(2010) Jingjing Tong et al.   Protein & Cell

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

PpAtg30 Tags Peroxisomes for Turnover by Selective Autophagy

(2008) Jean-Claude Farré et al.   DEVELOPMENTAL CELL

Toll-like receptors control autophagy

(2008) Mónica A Delgado et al.   EMBO JOURNAL

MyD88 and Trif Target Beclin 1 to Trigger Autophagy in Macrophages

(2008) Chong-Shan Shi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum

(2008) Elizabeth L. Axe et al.   JOURNAL OF CELL BIOLOGY