Department of Biochemistry (ceased 1-10-2018)
1698 publications
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Abrogation of the Brd4-positive transcription elongation factor b complex by Papillomavirus E2 protein contributes to viral oncogene repression
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Leptin modulates innate and adaptive immune cell recruitment after cigarette smoke exposure in mice
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Integrated proteomic analysis reveals a substantial enrichment of protein trafficking processes in hippocampus tissue after hypoxic stress
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Chylomicronemia with low Postheparin Lipoprotein Lipase levels in the setting of GPIHBP1 defects
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Studying in vitro and in vivo protease processing in models of cancer cell death and viral infection by N-terminal COFRADIC
(2010) -
Nlrp3: an immune sensor of cellular stress and infection
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Listeria monocytogenes impairs SUMOylation for efficient infection
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A llama-derived gelsolin single-domain antibody blocks gelsolin-G-actin interaction
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The mitochondrial serine protease HtrA2/Omi cleaves RIP1 during apoptosis of Ba/F3 cells induced by growth factor withdrawal
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Inflammasome-independent role of apoptosis-associated speck-like protein containing a CARD (ASC) in T cell priming is critical for collagen-induced arthritis
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The NLRP3 inflammasome protects against loss of epithelial integrity and mortality during experimental colitis
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NOD-like receptor (NLR) signaling beyond the inflammasome
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- Journal Article
- A1
- open access
Definition of the interacting interfaces of Apobec3G and HIV-1 Vif using MAPPIT mutagenesis analysis
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Increased monomerization of mutant HSPB1 leads to protein hyperactivity in Charcot-Marie-tooth neuropathy
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FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data
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The chaperone-like Protein HYPK acts together with NatA in cotranslational N-terminal acetylation and prevention of Huntingtin aggregation
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Peptide and protein quantification: A map of the minefield
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- Journal Article
- A1
- open access
OLS Dialog : an open-source front end to the Ontology Lookup Service
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Glycosylation signatures in Drosophila : fishing with lectins
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Rover: a tool to visualize and validate quantitative proteomics data from different sources
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ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
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MS-driven protease substrate degradomics
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Caspase-7: a protease involved in apoptosis and inflammation
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Role of NF-κB activation in intestinal immune homeostasis
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Large double copy vectors are functional but show a size-dependent decline in transduction efficiency
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HIV-1 Lentiviral vector immunogenicity is mediated by Toll-Like Receptor 3 (TLR3) and TLR7
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Caspase-1 targets the TLR adaptor Mal at a crucial TIR-domain interaction site
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An alpaca single-domain antibody blocks filopodia formation by obstructing L-plastin-mediated F-actin bundling
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Orally administered L. lactis secreting an anti-TNF Nanobody demonstrate efficacy in chronic colitis
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- Journal Article
- A1
- open access
Identification and expression analysis of splice variants of mouse enabled homologue during development and in adult tissues
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Complementary positional proteomics for screening substrates of endo- and exoproteases
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Manipulation of host cell death pathways during microbial infections
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Strategies towards high-quality binary protein interactome maps
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Cutting edge: proteolytic inactivation of poly(ADP-ribose) polymerase 1 by the Nlrp3 and Nlrc4 inflammasomes
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Inflammasome-dependent release of the alarmin HMGB1 in endotoxemia
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Redundant roles for inflammasome receptors NLRP3 and NLRC4 in host defense against Salmonella
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Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research
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- Conference Paper
- C3
- open access
Definition of the interacting interfaces of Apobec3G and HIV-1 Vif using MAPPIT mutagenesis analysis
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Ena/VASP proteins: focus on interaction partners and Enah splice variants
(2010) -
- Journal Article
- A1
- open access
The miR-17-92 MicroRNA Cluster regulates multiple components of the TGF-beta Pathway in neuroblastoma
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CD248 and its cytoplasmic domain: a therapeutic target for Arthritis
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IL-18 production downstream of the Nlrp3 inflammasome confers protection against colorectal tumor formation
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A quantitative proteomics design for systematic identification of protease cleavage events
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TAZ interacts with zonula occludens-1 and-2 proteins in a PDZ-1 dependent manner
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Astrocytic beta(2)-adrenergic receptors : from physiology to pathology
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- Journal Article
- A1
- open access
Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling
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Who gets cut during cell death?
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The metabolism of triglyceride-rich lipoproteins revisited: new players, new insight
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Large-scale protein interactome mapping: strategies and opportunities
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- Journal Article
- A1
- open access
The Ontology Lookup Service : bigger and better
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- Journal Article
- A1
- open access
The Proteomics Identifications database : 2010 update
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Nucleoporin Nup62 in nucleo-cytoplasmic transport and cell migration
(2010) -
Increasing the specificity and the sensitivity in peptide centric proteomics
(2010) -
New insights into the control of cytokine receptor degradation and ectodomain shedding
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Abnormal LPL release leads to chylomicronemia in the presence of GPIHBP1 defects
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Camelid single-domain antibodies as a therapeutic approach for familial amyloidosis of the Finnish type (FAF)
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High-throughput proteomics and bioinformatics : joined at the hip
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PRIDE Converter: making proteomics data-sharing easy
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A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
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Proteomics data collection: 5th ProDaC workshop: 4 March 2009, Kolympari, Crete, Greece
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The PSI semantic validator: a framework to check MIAPE compliance of proteomics data
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Database on Demand: an online tool for the custom generation of FASTA-formatted sequence databases
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Charting online OMICS resources: a navigational chart for clinical researchers
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OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results
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Toward a successful clinical neuroproteomics : the 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, Greece
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- Journal Article
- A1
- open access
The inflammasomes
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Exploring the stability of the villin HeadPiece fold and the interaction of villin HeadPiece and profilin with polyphosphoinositides
(2009) -
- Journal Article
- A1
- open access
Recessive osteogenesis imperfecta caused by LEPRE1 mutations: clinical documentation and identification of the splice form responsible for prolyl 3-hydroxylation
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Application of a Combined Weak Cation-Exchange/Crown Ether Column: First Demonstrations of a Versatile Tool for Proteome Subselection
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MAPPIT (Mammalian Protein-Protein Interaction Trap) analysis of early steps in Toll-like receptor signalling
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- Journal Article
- A2
- open access
Generalized immune activation as a direct result of activated CD4+ T cell killing
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Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
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- Journal Article
- A1
- open access
Differential expression of the interleukin 5 receptor alpha isoforms in blood and tissue eosinophils of nasal polyp patients
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alpha-Skeletal Muscle Actin Mutants Causing Different Congenital Myopathies Induce Similar Cytoskeletal Defects in Cell Line Cultures
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The Mouse Thymosin Beta15 Gene Family Displays Unique Complexity and Encodes A Functional Thymosin Repeat
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Highly efficient peptide separations in proteomics Part 2: Bi- and multidimensional liquid-based separation techniques
(2009) JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES. 877(11-12). p.1019-1039 -
Impaired neural crest migration contributes to midgestation lethality of beta-actin knock-out mouse
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Mammalian two-hybrids come of age
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Analysis of the gamma-secretase interactome and validation of its association with tetraspanin-enriched microdomains
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Improved visualization of protein consensus sequences by iceLogo
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Global Analysis of the Mitochondrial N-Proteome Identifies a Processing Peptidase Critical for Protein Stability
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Identification of Chlamydia trachomatis CT621, a protein delivered through the type III secretion system to the host cell cytoplasm and nucleus
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Caspase-7 deficiency protects from endotoxin-induced lymphocyte apoptosis and improves survival
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A guide to the Proteomics Identifications Database proteomics data repository
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New Activation Modus of STAT3 A TYROSINE-LESS REGION OF THE INTERLEUKIN-22 RECEPTOR RECRUITS STAT3 BY INTERACTING WITH ITS COILED-COIL DOMAIN
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SitePredicting the cleavage of proteinase substrates
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BCL9 is an essential component of canonical Wnt signaling that mediates the differentiation of myogenic progenitors during muscle regeneration
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- Journal Article
- A1
- open access
Down-regulation of myopodin expression reduces invasion and motility of PC-3 prostate cancer cells
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The Interaction of Proline-Rich Ligands with Profilin Probed with an Enzyme-Linked Immunosorbent Assay
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Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans
(2009) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 106(20). p.8157-8162 -
Structure of granzyme C reveals an unusual mechanism of protease autoinhibition
(2009) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 106(14). p.5587-5592 -
- Journal Article
- A1
- open access
Approaching clinical proteomics: current state and future fields of application in fluid proteomics
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- Journal Article
- A1
- open access
Exo70-Mediated Recruitment of Nucleoporin Nup62 at the Leading Edge of Migrating Cells is Required for Cell Migration
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Getting a grip on proteomics data: Proteomics Data Collection (ProDaC)
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Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling
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alpha-Skeletal muscle actin nemaline myopathy mutants cause cell death in cultured muscle cells.
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- Conference Paper
- C1
- open access
A review of COFRADIC techniques targeting protein N-terminal acetylation
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- Journal Article
- A2
- open access
Phenotypes induced by NM causing α-skeletal muscle actin mutants in fibroblasts, Sol 8 myoblasts and myotubes
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Actin isoform expression patterns during mammalian development and in pathology: insights from mouse models
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Analysis of the translationally controlled tumour protein in the nematodes Ostertagia ostertagi and Caenorhabditis elegans suggests a pivotal role in egg production
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The actin-capping protein CapG localizes to microtubule-dependent organelles during the cell cycle
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Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs
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An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments
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Analysis of proteins in Chlamydia trachomatis L2 outer membrane complex, COMC
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Hybrid N-glycans on the host protective activation-associated secreted proteins of Ostertagia ostertagi and their importance in immunogenicity (vol 161, pg 67, 2008)
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The atypical kinase Cdk5 is activated by insulin, regulates the association between GLUT4 and E-Syt1, and modulates glucose transport in 3T3-L1 adipocytes
(2009) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 106(11). p.4249-4253 -
An empirical framework for binary interactome mapping
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Array MAPPIT: High-Throughput Interactome Analysis in Mammalian Cells
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An experimentally derived confidence score for binary protein-protein interactions
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The PDZ2 domain of zonula occludens-1 and-2 is a phosphoinositide binding domain
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In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography
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- Journal Article
- A1
- open access
Identification and Functional Characterization of N-Terminally Acetylated Proteins in Drosophila melanogaster
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- Journal Article
- A1
- open access
Glyburide inhibits the Cryopyrin/Nalp3 inflammasome
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Fungal Zymosan and Mannan Activate the Cryopyrin Inflammasome
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IL-33 Raises Alarm
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Association of C-Terminal Ubiquitin Hydrolase BRCA1-Associated Protein 1 with Cell Cycle Regulator Host Cell Factor 1
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Inflammasomes: guardians of cytosolic sanctity
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The Intracellular Sensor NLRP3 Mediates Key Innate and Healing Responses to Influenza A Virus via the Regulation of Caspase-1
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Caspase substrates: easily caught in deep waters?
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Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity
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Unbalancing the phosphatidylinositol-4,5-bisphosphate-cofilin interaction impairs cell steering
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Approaching Clinical Proteomics: Current State and Future Fields of Application in Cellular Proteomics
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New insights into the beta-thymosin family via characterization and classification of different thymosin beta 15 isoforms
(2009) -
Alpha-actin mutations in congenital myopathies: identification of cell death as a new cellular Nemaline Myopathy phenotype and induction of similar cytoskeletal defects by mutants associated with different myopathies
(2009) -
- Journal Article
- A1
- open access
The Ontology Lookup Service : more data and better tools for controlled vocabulary queries
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Proteomics data collection: 3rd ProDaC workshop April 22nd 2008, Toledo, Spain
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The HUPO Brain Proteome project wish list : summary of the 9th HUPO BPP Workshop 9-10 January 2008, Barbados
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- Journal Article
- A1
- open access
PRIDE : new developments and new datasets
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Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
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OMSSAGUI: an open-source user interface component to configure and run the OMSSA search engine
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Functional characterization of naturally occurring pathogenic mutations in the human leptin receptor
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6th HUPO Annual World Congress : Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea
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Proteomics data collection : 2nd ProDaC workshop : 5 October 2007, Seoul, Korea
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Identification and characterization of a novel specific secreted protein family for selected members of the subfamily Ostertagiinae (Nematoda)
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The mitochondrial serine protease HtrA2/Omi: an overview
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Ins and outs of ADF/cofilin activity and regulation
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A protein domain-based interactome network for C. elegans early embryogenesis
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MAPPIT analysis of early Toll-like receptor signalling events
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- Journal Article
- A1
- open access
HyperISGylation of old world monkey ISG15 in human cells
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- Journal Article
- A1
- open access
Atypical Mowat-Wilson patient confirms the importance of the novel association between ZFHX1B/SIP1 and NuRD corepressor complex
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Highly efficient peptide separations in proteomics - Part 1. Unidimensional high performance liquid chromatography
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Peptizer: a tool for assessing false positive peptide identifications and manually validating selected results
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SOCS proteins and cytokine signalling: the many faces of the SOCS box
(2008) -
The many faces of the SOCS box
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- Journal Article
- A1
- open access
MAPPIT: a versatile tool to study cytokine receptor signalling
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The Tandem PDZ Protein Syntenin Interacts with the Aminoacyl tRNA Synthetase Complex in a Lysyl-tRNA Synthetase-Dependent Manner
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- Journal Article
- A1
- open access
Stable isotopic labeling in proteomics
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- Journal Article
- A1
- open access
The F-actin filament capping protein CapG is a bona fide nucleolar protein
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- Book Chapter
- open access
Protein processing characterized by a gel-free proteomics approach
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S100B Expression in forensic brain trauma fatalities: a valuable tool?
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The proteome of the human neuroblastoma cell line SH-SY5Y: an enlarged proteome
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Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)
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Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death
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Human Proteinpedia enables sharing of human protein data
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Increased Inflammatory Gene Expression in ABC Transporter-Deficient Macrophages Free Cholesterol Accumulation, Increased Signaling via Toll-Like Receptors, and Neutrophil Infiltration of Atherosclerotic Lesions
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Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes
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Hybrid N-glycans on the host protective activation-associated secreted proteins of Ostertagia ostertagi and their importance in immunogenicity
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Analyzing large-scale proteomics projects with latent semantic indexing
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IMMUNOMODULATION OF CANCER CELL MIGRATION AND INVASION USING RECOMBINANT CAMELID NANOBODIES AGAINST CYTOSKELETAL PROTEINS
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TLR-4, IL-1R and TNF-R signaling to NF-kappa B: variations on a common theme
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High-quality binary protein interaction map of the yeast interactome network
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An influenza A vaccine based on tetrameric ectodomain of matrix protein 2
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Insulin receptor substrate 4 couples the leptin receptor to multiple signaling pathways
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Mechanistic insight into taxol-induced cell death
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Multiple isoforms of the tumor suppressor myopodin are simultaneously transcribed in cancer cells
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Listeria comet tails: the actin-based motility machinery at work
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Disentanglement of protease substrate repertoires
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Evaluation of Digitally Encoded Layer-by-layer Coated Microparticles as Cell Carriers
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Unravelling the RIP4 signaling pathway to NF-kappa B
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MAPPIT (MAmmalian Protein-Protein Interaction Trap) as a tool to study HIV reverse transcriptase dimerization in intact human cells
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Elongin B/C recruitment regulates substrate binding by CIS
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Caspase-14 is a crucial protease in proper stratum corneum formation
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Analysis of the transthyretin-like (TTL) gene family in Ostertagia ostertagi - Comparison with other strongylid nematodes and Caenorhabditis elegans
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Evaluation of encoded layer-by-layer coated microparticles as protease sensors
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The actin propulsive machinery: The proteome of Listeria monocytogenes tails
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A new role for nuclear transport factor 2 and Ran: Nuclear import of CapG
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Predicting the effect of a point mutation on a protein fold: The villin and advillin headpieces and their Pro62Ala mutants
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- Journal Article
- A1
- open access
Gender-enriched transcription of activation associated secreted proteins in Ostertagia ostertagi
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- Journal Article
- A1
- open access
Characterization of a Listeria monocytogenes protein interfering with Rab5a
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- Conference Paper
- C3
- open access
Multiple roles for the SOCS box
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- PhD Thesis
- open access
Linking TNF-induced dysfunction and formation of methylglyoxal derived AGEs in endothelial cells
(2008) -
- PhD Thesis
- open access
SOCS proteins and cytokine signalling: the many faces of the SOCS box
(2008) -
- Journal Article
- A1
- open access
The Protein Identifier Cross-Referencing (PICR) service : reconciling protein identifiers across multiple source databases
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High performance proteomics : 7th HUPO Brain Proteome project workshop, March 7-9, 2007, Wellcome Trust Conference Centre, Hinxton, UK
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Annotating the human proteome: beyond establishing a parts list
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The PSI formal document process and its implementation on the PSI website
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On the origin and evolution of vertebrate and viral profilins
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Proteomics for everyday use : activities of the HUPO Brain Proteome project during the 5th HUPO world congress
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Proteomics data collection : the 1st ProDaC workshop: 26 April 2007, Ecole Normale Supérieur, Lyon, France
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Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis
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A la carte proteomics with an emphasis on gel-free techniques
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Implementation and application of a versatile clustering tool for tandem mass spectrometry data
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Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses
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The minimum information about a proteomics experiment (MIAPE)
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Structural and Functional Implications of the PXWK-motif in HeadPiece Domains
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Structural and Functional Implicationof the PXWK-motif in HeadPiece Domains
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Structure-function relationship of actin binding modules studied by NMR
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Atomistic Prediction of the structure of the Advillin headpiece and its Pro62Ala mutant
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MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results
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The C-terminus of CIS defines its interaction pattern
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Tumor necrosis factor modulates glycolysis, the glyoxalase system and induces the formation of specific methylglyoxal-modified proteins in aortic endothelial cells
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The MAPPIT toolbox: novel strategies to analyze molecular interactions in intact cells
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- Journal Article
- A1
- open access
Caspase-1 inflammasomes in infection and inflammation
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Intracellular NOD-like receptors in host defense and disease
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Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy
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Proteomics data validation: why all must provide data
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Caspase-14 protects against epidermal UVB photo-damage and water loss.
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Combination of COFRADIC and high temperature - extended column length conventional liquid chromatography: A very efficient way to tackle complex protein samples, such as serum
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Tumour necrosis factor induces phosphorylation primarily of the nitric-oxide-responsive form of glyoxalase I
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Paper of the year 2006: Award to Pamela Hamill
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Proteome-wide identification of HtrA2/Omi substrates
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Expression of chemokines and gelatinase B in sympathetic ophthalmia
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Proteolytic cleavage of the Chlamydia pneumoniae major outer membrane protein in the absence of Pmp10
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Identification and evaluation of protein-protein interactions involved in NF-kB signaling using MAPPIT technology
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Assessing a novel microfluidic interface for shotgun proteome analyses
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A new approach for mapping sialylated N-glycosites in serum proteomes
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The MAGUK protein MPP7 binds to the polarity protein hDlg1 and facilitates epithelial tight junction formation
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The transcriptional repressor Glis2 is a novel binding partner for p120 catenin
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The tandem PDZ domains of syntenin promote cell invasion
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Functional and profiling studies prove that prostate cancer upregulated neuroblastoma thymosin beta is the true human homologue of rat thymosin beta 15
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Mammalian protein-protein interaction trap (MAPPIT) analysis of STAT5, CIS, and SOCS2 interactions with the growth hormone receptor
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Novel role of WD40 and SOCS box protein-2 in steady-state distribution of granulocyte colony-stimulating factor receptor and G-CSF-controlled proliferation and differentiation signaling
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Methylglyoxal suppresses TNF-alpha-induced NF-kappa B activation by inhibiting NF-kappa B DNA-binding
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Caspase-14 protects against epidermal UVB photodamage and water loss
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Caspase-14 protects against epidermal UVB photo-damage and water loss
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Identification and characterization of filaggrin as a caspase-14 substrate
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Downregulation of gelsolin family proteins counteracts cancer cell invasion in vitro
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MAPPIT analysis of TLR adaptor complexes
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The LIM domains of WLIM1 define a new class of actin bundling modules
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Leptin induces inflammation-related genes in RINm5F insulinoma cells
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- Journal Article
- A1
- open access
Vaccination against Ostertagia ostertagi with subfractions of the protective ES-thiol fraction
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Role of the glyoxalase system and its substrate methylglyoxal in tumour necrosis factor induced necrotic cell death
(2007) -
- PhD Thesis
- open access
MAPPIT analysis of the early events in Toll-Like receptor signalling
(2007) -
Ligand interactions of profilins from invertebrates and vertebrates, in search of their cellular roles
(2007) -
HUPO Brain Proteome Project : summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
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HUPO Brain Proteome Project : summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
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The HUPO Brain Proteome project jamboree: centralised summary of the pilot studies
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Functional annotation of proteins identified in human brain during the HUPO Brain Proteome project pilot study
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The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome project pilot study results
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Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome project pilot phase
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- Journal Article
- A1
- open access
Cell_motility : a cross-platform, open source application for the study of cell motion paths
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Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells
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- Journal Article
- A1
- open access
PRIDE : a public repository of protein and peptide identifications for the proteomics community
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A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes
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A comparison of the HUPO Brain Proteome project pilot with other proteomics studies
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Proteome-wide characterization of N-glycosylation events by diagonal chromatography
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Multirepeat beta-thymosins
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Nasal IL-5 levels determine the response to anti-IL-5 treatment in patients with nasal polyps
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- Journal Article
- A1
- open access
Tobacco WLIM1 is a novel F-actin binding protein involved in actin cytoskeleton remodeling
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Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering