Quantitative Proteomics Reveals the Induction of Mitophagy in Tumor Necrosis Factor-α-activated (TNFα) Macrophages

Making autophagosomes: Localized synthesis of phosphatidylinositol 3-phosphate holds the clue

(2014) Simon Walker et al.   Autophagy

Posttranslational regulation of self-renewal capacity: insights from proteome and phosphoproteome analyses of stem cell leukemia

(2012) M. Trost et al.   BLOOD

Defining TNF-α and IL-1β induced nascent proteins: Combining bio‐orthogonal non‐canonical amino acid tagging and proteomics

(2012) Ka-Yee (Grace) Choi et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Autophagy, mitochondria and oxidative stress: cross-talk and redox signalling

(2011) Jisun Lee et al.   BIOCHEMICAL JOURNAL

Historical perspectives on tumor necrosis factor and its superfamily: 25 years later, a golden journey

(2011) B. B. Aggarwal et al.   BLOOD

Broad activation of the ubiquitin–proteasome system by Parkin is critical for mitophagy

(2011) Nickie C. Chan et al.   HUMAN MOLECULAR GENETICS

Autophagy in immunity and cell-autonomous defense against intracellular microbes

(2011) Vojo Deretic   IMMUNOLOGICAL REVIEWS

Autophagy in immunity and inflammation

(2011) Beth Levine et al.   NATURE

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

ProteoConnections: A bioinformatics platform to facilitate proteome and phosphoproteome analyses

(2011) Mathieu Courcelles et al.   PROTEOMICS

BisoGenet: a new tool for gene network building, visualization and analysis

(2010) Alexander Martin et al.   BMC BIOINFORMATICS

Activated macrophages utilize glycolytic ATP to maintain mitochondrial membrane potential and prevent apoptotic cell death

(2010) A Garedew et al.   CELL DEATH AND DIFFERENTIATION

Antigen processing via autophagy—not only for MHC class II presentation anymore?

(2010) Christian Münz   CURRENT OPINION IN IMMUNOLOGY

p62/SQSTM1 cooperates with Parkin for perinuclear clustering of depolarized mitochondria

(2010) Kei Okatsu et al.   GENES TO CELLS

TNF-α Induces Macroautophagy and Regulates MHC Class II Expression in Human Skeletal Muscle Cells

(2010) Christian W. Keller et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Activation and induction of cytosolic phospholipase A2 by TNF-α mediated through Nox2, MAPKs, NF-κB, and p300 in human tracheal smooth muscle cells

(2010) Chiang-Wen Lee et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Proteomic Analysis of Tumor Necrosis Factor-α-Induced Secretome of Human Adipose Tissue-Derived Mesenchymal Stem Cells

(2010) Mi Jeong Lee et al.   JOURNAL OF PROTEOME RESEARCH

Molecular characterization of the evolution of phagosomes

(2010) Jonathan Boulais et al.   Molecular Systems Biology

A role for mitochondria in NLRP3 inflammasome activation

(2010) Rongbin Zhou et al.   NATURE

PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1

(2010) Sven Geisler et al.   NATURE CELL BIOLOGY

Tumor Necrosis Factor-α and Apoptosis Signal-Regulating Kinase 1 Control Reactive Oxygen Species Release, Mitochondrial Autophagy and C-Jun N-Terminal Kinase/P38 Phosphorylation During Necrotizing Enterocolitis

(2010) Naira Baregamian et al.   Oxidative Medicine and Cellular Longevity

Temporal and spatial profiling of nuclei-associated proteins upon TNF-α/NF-κB signaling

(2009) Dan-jun Ma et al.   CELL RESEARCH

The Phagosomal Proteome in Interferon-γ-Activated Macrophages

(2009) Matthias Trost et al.   IMMUNITY

Autophagy enhances the presentation of endogenous viral antigens on MHC class I molecules during HSV-1 infection

(2009) Luc English et al.   NATURE IMMUNOLOGY

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

(2009) Da Wei Huang et al.   Nature Protocols

Dynamics and diversity in autophagy mechanisms: lessons from yeast

(2009) Hitoshi Nakatogawa et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Atg16L Complex Specifies the Site of LC3 Lipidation for Membrane Biogenesis in Autophagy

(2008) Naonobu Fujita et al.   MOLECULAR BIOLOGY OF THE CELL

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH