VIB-UGent Center for Medical Biotechnology

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Title DOI
https://doi.org/10.1038/nbt.2839 ProteomeXchange provides globally coordinated proteomics data submission and dissemination
https://doi.org/10.1038/nature10558 Non-canonical inflammasome activation targets caspase-11
https://doi.org/10.1038/nrm2970 Molecular mechanisms of necroptosis: an ordered cellular explosion
https://doi.org/10.1016/j.cell.2014.10.050 A Proteome-Scale Map of the Human Interactome Network
https://doi.org/10.1007/s00018-008-8281-1 The cell-cell adhesion molecule E-cadherin
https://doi.org/10.1016/j.immuni.2010.03.003 The NLRP3 Inflammasome Protects against Loss of Epithelial Integrity and Mortality during Experimental Colitis
https://doi.org/10.1146/annurev-cellbio-101011-155745 Inflammasomes and Their Roles in Health and Disease
https://doi.org/10.1038/nm.2737 The airway epithelium in asthma
https://doi.org/10.1210/er.2018-00064 Molecular Actions of PPARα in Lipid Metabolism and Inflammation
https://doi.org/10.1038/s41577-022-00792-3 Death by TNF: a road to inflammation
https://doi.org/10.1038/nri2815 The X chromosome in immune functions: when a chromosome makes the difference
https://doi.org/10.1074/mcp.r110.000133 mzML—a Community Standard for Mass Spectrometry Data
https://doi.org/10.1016/j.it.2011.01.005 Emerging role of damage-associated molecular patterns derived from mitochondria in inflammation
https://doi.org/10.1038/cddis.2009.16 Caspase-mediated cleavage of Beclin-1 inactivates Beclin-1-induced autophagy and enhances apoptosis by promoting the release of proapoptotic factors from mitochondria
https://doi.org/10.1016/j.cell.2020.04.031 Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies
https://doi.org/10.1146/annurev-cellbio-101011-155741 Hormonal Interactions in the Regulation of Plant Development
https://doi.org/10.1038/cdd.2009.184 Necroptosis, necrosis and secondary necrosis converge on similar cellular disintegration features
https://doi.org/10.1038/nature17161 Melanoma addiction to the long non-coding RNA SAMMSON
https://doi.org/10.1038/ncomms5767 Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations
https://doi.org/10.1093/nar/gky1031 LNCipedia 5: towards a reference set of human long non-coding RNAs
https://doi.org/10.1016/j.cell.2009.07.045 Global Analysis of the Mitochondrial N-Proteome Identifies a Processing Peptidase Critical for Protein Stability
https://doi.org/10.1016/j.tem.2017.10.010 Therapeutic Mechanisms of Glucocorticoids
https://doi.org/10.12688/f1000research.8460.3 The academic, economic and societal impacts of Open Access: an evidence-based review
https://doi.org/10.1016/j.molcel.2017.02.013 Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics
https://doi.org/10.1016/j.bbamcr.2013.06.010 Cell death by cornification
https://doi.org/10.1038/s41467-020-19015-1 Benchmarking of cell type deconvolution pipelines for transcriptomics data
https://doi.org/10.1016/j.ccell.2019.12.001 An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates
https://doi.org/10.1038/nature10525 A vascular niche and a VEGF–Nrp1 loop regulate the initiation and stemness of skin tumours
https://doi.org/10.1016/j.chom.2010.06.007 Manipulation of Host Cell Death Pathways during Microbial Infections
https://doi.org/10.1038/s41586-020-03046-1 Fat1 deletion promotes hybrid EMT state, tumour stemness and metastasis
https://doi.org/10.1038/nri2936 Emerging inflammasome effector mechanisms
https://doi.org/10.1016/j.ccr.2011.10.022 The NOD-Like Receptor NLRP12 Attenuates Colon Inflammation and Tumorigenesis
https://doi.org/10.1038/nature11250 NLRP6 negatively regulates innate immunity and host defence against bacterial pathogens
https://doi.org/10.1038/cdd.2011.164 Many stimuli pull the necrotic trigger, an overview
https://doi.org/10.1038/ng1764 Mutations in the facilitative glucose transporter GLUT10 alter angiogenesis and cause arterial tortuosity syndrome
https://doi.org/10.1039/d0ee01545h Challenges in the use of hydrogen for maritime applications
https://doi.org/10.1126/science.1249161 PINK1 Loss-of-Function Mutations Affect Mitochondrial Complex I Activity via NdufA10 Ubiquinone Uncoupling
https://doi.org/10.1016/j.neuron.2012.08.022 LRRK2 Controls an EndoA Phosphorylation Cycle in Synaptic Endocytosis
https://doi.org/10.1016/j.tplants.2018.09.004 Protein Language: Post-Translational Modifications Talking to Each Other
https://doi.org/10.1038/cdd.2009.68 Mdm2-mediated ubiquitylation: p53 and beyond
https://doi.org/10.1038/cdd.2008.104 Exosome secretion, including the DNA damage-induced p53-dependent secretory pathway, is severely compromised in TSAP6/Steap3-null mice
https://doi.org/10.1038/s41467-022-31218-2 Cancer cells dying from ferroptosis impede dendritic cell-mediated anti-tumor immunity
https://doi.org/10.1016/j.vaccine.2009.07.007 M2e-based universal influenza A vaccine
https://doi.org/10.1038/nplants.2016.205 Plant cholesterol biosynthetic pathway overlaps with phytosterol metabolism
https://doi.org/10.1016/j.ejcb.2008.04.001 Ins and outs of ADF/cofilin activity and regulation
https://doi.org/10.1038/nature13788 Dietary modulation of the microbiome affects autoinflammatory disease
https://doi.org/10.1038/nature11429 Phosphorylation of NLRC4 is critical for inflammasome activation
https://doi.org/10.1016/j.molcel.2010.11.038 The miR-17-92 MicroRNA Cluster Regulates Multiple Components of the TGF-β Pathway in Neuroblastoma
https://doi.org/10.1016/j.biocel.2009.09.013 Caspase-7: A protease involved in apoptosis and inflammation
https://doi.org/10.1016/j.tibs.2012.02.003 Protein N-terminal acetyltransferases: when the start matters
https://doi.org/10.1038/s41467-020-19684-y STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters
https://doi.org/10.1038/s41586-022-04754-6 Targeting SLC7A11 improves efferocytosis by dendritic cells and wound healing in diabetes
https://doi.org/10.1016/j.cell.2014.01.039 The TPLATE Adaptor Complex Drives Clathrin-Mediated Endocytosis in Plants
https://doi.org/10.1016/j.cmet.2018.07.019 Impairment of Angiogenesis by Fatty Acid Synthase Inhibition Involves mTOR Malonylation
https://doi.org/10.1016/j.it.2011.02.002 The Nlrp3 inflammasome: contributions to intestinal homeostasis
https://doi.org/10.1038/s41477-019-0378-z Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase
https://doi.org/10.1126/science.aar7486 Damage on plants activates Ca 2+ -dependent metacaspases for release of immunomodulatory peptides
https://doi.org/10.1016/j.chom.2015.01.006 Concerted Activation of the AIM2 and NLRP3 Inflammasomes Orchestrates Host Protection against Aspergillus Infection
https://doi.org/10.1016/j.chembiol.2009.04.008 Chemical Inhibition of a Subset of Arabidopsis thaliana GSK3-like Kinases Activates Brassinosteroid Signaling
https://doi.org/10.1038/s41598-017-02599-y Confounding factors of ultrafiltration and protein analysis in extracellular vesicle research
https://doi.org/10.1038/nprot.2008.213 Engineering complex-type N-glycosylation in Pichia pastoris using GlycoSwitch technology
https://doi.org/10.1021/acs.jproteome.9b00328 ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion
https://doi.org/10.1038/mi.2013.14 Division of labor between lung dendritic cells and macrophages in the defense against pulmonary infections
https://doi.org/10.12688/f1000research.12037.3 A multi-disciplinary perspective on emergent and future innovations in peer review
https://doi.org/10.1038/s41573-023-00822-2 Drugging the NLRP3 inflammasome: from signalling mechanisms to therapeutic targets
https://doi.org/10.1093/nar/gkaa1058 MobiDB: intrinsically disordered proteins in 2021
https://doi.org/10.1016/j.chom.2017.07.020 Legionella pneumophila Modulates Mitochondrial Dynamics to Trigger Metabolic Repurposing of Infected Macrophages
https://doi.org/10.1016/j.neuron.2018.01.022 Synaptogyrin-3 Mediates Presynaptic Dysfunction Induced by Tau
https://doi.org/10.1038/onc.2008.140 Snail promotes Wnt target gene expression and interacts with β-catenin
https://doi.org/10.1038/cdd.2008.196 Connexin-related signaling in cell death: to live or let die?
https://doi.org/10.1038/s41467-018-04376-5 A20 critically controls microglia activation and inhibits inflammasome-dependent neuroinflammation
https://doi.org/10.1002/mas.21376 Getting intimate with trypsin, the leading protease in proteomics
https://doi.org/10.1146/annurev-arplant-042817-040413 Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants
https://doi.org/10.1038/s41592-021-01301-5 DeepLC can predict retention times for peptides that carry as-yet unseen modifications
https://doi.org/10.1002/adfm.200700416 In vivo Cellular Uptake, Degradation, and Biocompatibility of Polyelectrolyte Microcapsules
https://doi.org/10.1038/s41590-020-00849-2 Does tissue imprinting restrict macrophage plasticity?
https://doi.org/10.1016/s0039-6109(05)70549-1 THE MESENTERIC CIRCULATION
https://doi.org/10.1016/j.molcel.2017.01.020 The ER Stress Sensor PERK Coordinates ER-Plasma Membrane Contact Site Formation through Interaction with Filamin-A and F-Actin Remodeling
https://doi.org/10.1105/tpc.113.115907 ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development
https://doi.org/10.1038/nature08963 Listeria monocytogenes impairs SUMOylation for efficient infection
https://doi.org/10.1038/emboj.2011.85 T‐cell receptor‐induced JNK activation requires proteolytic inactivation of CYLD by MALT1
https://doi.org/10.1126/science.aap7607 Mutations in LZTR1 drive human disease by dysregulating RAS ubiquitination
https://doi.org/10.1038/ncomms14153 The ancient CYP716 family is a major contributor to the diversification of eudicot triterpenoid biosynthesis
https://doi.org/10.1016/j.tplants.2014.10.002 Plant innate immunity – sunny side up?
https://doi.org/10.1021/pr501246w The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation
https://doi.org/10.3389/fimmu.2020.621931 Interleukin-1 as Innate Mediator of T Cell Immunity
https://doi.org/10.1016/j.cytogfr.2011.09.003 NOD-like receptors and the innate immune system: Coping with danger, damage and death
https://doi.org/10.1038/s41574-020-0349-5 Nuclear receptor crosstalk — defining the mechanisms for therapeutic innovation
https://doi.org/10.1128/mmbr.00064-15 The Interactome of the Glucocorticoid Receptor and Its Influence on the Actions of Glucocorticoids in Combatting Inflammatory and Infectious Diseases
https://doi.org/10.1038/cdd.2017.58 When PERK inhibitors turn out to be new potent RIPK1 inhibitors: critical issues on the specificity and use of GSK2606414 and GSK2656157
https://doi.org/10.1186/s12967-019-1804-8 How mRNA therapeutics are entering the monoclonal antibody field
https://doi.org/10.1007/s00018-011-0757-8 Cyclic AMP: a selective modulator of NF-κB action
https://doi.org/10.1074/jbc.m112.377465 The Neural Cell Adhesion Molecules L1 and CHL1 Are Cleaved by BACE1 Protease in Vivo
https://doi.org/10.1118/1.2241992 Accuracy of patient dose calculation for lung IMRT: A comparison of Monte Carlo, convolution/superposition, and pencil beam computations
https://doi.org/10.1016/j.immuni.2015.11.006 Toll-like Receptor 4 Engagement on Dendritic Cells Restrains Phago-Lysosome Fusion and Promotes Cross-Presentation of Antigens
https://doi.org/10.1038/ncomms14937 Structure and antagonism of the receptor complex mediated by human TSLP in allergy and asthma
https://doi.org/10.1105/tpc.15.00269 Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf
https://doi.org/10.1021/acs.jproteome.8b00716 Unipept 4.0: Functional Analysis of Metaproteome Data
https://doi.org/10.12688/f1000research.8460.1 The academic, economic and societal impacts of Open Access: an evidence-based review
https://doi.org/10.1038/s41586-023-05838-7 RHOJ controls EMT-associated resistance to chemotherapy