Group Publications


Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. Scientific Reports 2017
Tuning Metabolome Coverage in Reversed Phase LC-MS Metabolomics of MeOH Extracted Samples Using the Reconstitution Solvent Composition. Analytical Chemistry 2017
Discrimination of pancreatic cancer and pancreatitis by LC-MS metabolomics. Metabolomics : Official journal of the Metabolomic Society 2017
Comparative proteomics reveals signature metabolisms of exponentially growingand stationary phase marine bacteria. Environmental microbiology 2017
Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics. IEEE/ACM transactions on computational biology and bioinformatics 2017
Proteogenomics produces comprehensive and highly accurate protein-coding geneannotation in a complete genome assembly of Malassezia sympodialis. Nucleic acids research 2017
A multi-step peptidolytic cascade for amino acid recovery in chloroplasts. Nature chemical biology 2017
Immunohistochemical Typing of Adenocarcinomas of the Pancreatobiliary SystemImproves Diagnosis and Prognostic Stratification. PloS one 2016
Validation and development of MTH1 inhibitors for treatment of cancer. Annals of oncology : official journal of the European Society for Medical Oncology 2016
Mesenchymal state of intimal cells may explain higher propensity to ascendingaortic aneurysm in bicuspid aortic valves. Scientific reports 2016
Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is AssociatedWith Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM. Arteriosclerosis, thrombosis, and vascular biology 2016
Proteomics Suggests a Role for APC-Survivin in Response to Somatostatin AnalogTreatment of Neuroendocrine Tumors. The Journal of clinical endocrinology and metabolism 2016
In Vivo Effects of Mesenchymal Stromal Cells in Two Patients With Severe AcuteRespiratory Distress Syndrome. Stem cells translational medicine 2016
Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes:implications for hepatic gene expression. Nucleic acids research 2016
Alterations in the membrane-associated proteome fraction of alveolarmacrophages in sarcoidosis. Sarcoidosis, vasculitis, and diffuse lung diseases : official journal of WASOG 2016
Cells release subpopulations of exosomes with distinct molecular andbiological properties. Scientific reports 2016
Genetic and epigenetic background and protein expression profiles in relationto telomerase activation in medullary thyroid carcinoma. Oncotarget 2016
Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes RevealsModulation of Angiogenesis via Nuclear Factor-KappaB Signaling. Stem cells (Dayton, Ohio) 2016
Proteomics Analysis Reveals Distinct Corona Composition on MagneticNanoparticles with Different Surface Coatings: Implications for Interactionswith Primary Human Macrophages. PloS one 2015
Multi-level omics analysis in a murine model of dystrophin loss andtherapeutic restoration. Human molecular genetics 2015
Identifying and Assessing Interesting Subgroups in a Heterogeneous Population. BioMed research international 2015
Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/IronCofactor. The Journal of biological chemistry 2015
PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatinat the Lamina Promote Oscillating Transcription. Molecular cell 2015
In Vivo Effects of Mesenchymal Stromal Cells in Two Patients With Severe AcuteRespiratory Distress Syndrome. Stem cells translational medicine 2015
Serum-free culture alters the quantity and protein composition ofneuroblastoma-derived extracellular vesicles. Journal of extracellular vesicles 2015
Secretome protein signature of human gastrointestinal stromal tumor cells. Experimental cell research 2015
Differential protein expression profiles of cyst fluid from papillary thyroidcarcinoma and benign thyroid lesions. PloS one 2015
Molecular stratification of metastatic melanoma using gene expressionprofiling: Prediction of survival outcome and benefit from molecular targetedtherapy. Oncotarget 2015
Frequency and distribution of Notch mutations in tumor cell lines. BMC cancer 2015
Proteomics profiling identify CAPS as a potential predictive marker oftamoxifen resistance in estrogen receptor positive breast cancer. Clinical proteomics 2015
RIFINs are adhesins implicated in severe Plasmodium falciparum malaria. Nature medicine 2015
Rewired metabolism in drug-resistant leukemia cells: a metabolic switchhallmarked by reduced dependence on exogenous glutamine. The Journal of biological chemistry 2015
Ultrafiltration with size-exclusion liquid chromatography for high yieldisolation of extracellular vesicles preserving intact biophysical andfunctional properties. Nanomedicine : nanotechnology, biology, and medicine 2015
Multi-omic data analysis using Galaxy. Nature biotechnology 2015
An overview of polyurethane foams in higher specification foam mattresses. Ostomy/wound management 2015
The mutational landscapes of genetic and chemical models of Kras-driven lungcancer. Nature 2015
Investigating the applicability of antibodies generated within the humanprotein atlas as capture agents in immunoenrichment coupled to massspectrometry. Journal of proteome research 2014
Immunoproteomics using polyclonal antibodies and stable isotope-labeledaffinity-purified recombinant proteins. Molecular & cellular proteomics : MCP 2014
Proteomics analysis of melanoma metastases: association between S100A13expression and chemotherapy resistance. British journal of cancer 2014
SpliceVista, a tool for splice variant identification and visualization inshotgun proteomics data. Molecular & cellular proteomics : MCP 2014
Mass spectrometry-based plasma proteomics: state of the art and futureoutlook. Expert review of proteomics 2014
Differentially expressed proteins in malignant and benign adrenocorticaltumors. PloS one 2014
Proteome screening of pleural effusions identifies galectin 1 as a diagnosticbiomarker and highlights several prognostic biomarkers for malignantmesothelioma. Molecular & cellular proteomics : MCP 2014
Integrated molecular portrait of non-small cell lung cancers. BMC medical genomics 2013
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nature methods 2014
Quantitative accuracy in mass spectrometry based proteomics of complexsamples: the impact of labeling and precursor interference. Journal of proteomics 2014
Selectivity analysis of single binder assays used in plasma protein profiling. Proteomics 2013
Direct observation of structurally encoded metal discrimination and ether bondformation in a heterodinuclear metalloprotein. Proceedings of the National Academy of Sciences of the United States of America 2013
Organellar oligopeptidase (OOP) provides a complementary pathway for targetingpeptide degradation in mitochondria and chloroplasts. Proceedings of the National Academy of Sciences of the United States of America 2013
Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in humanliver function. Genome biology 2013
Quantitative proteomics profiling of primary lung adenocarcinoma tumorsreveals functional perturbations in tumor metabolism. Journal of proteome research 2013
Retinoic acid receptor alpha is associated with tamoxifen resistance in breastcancer. Nature communications 2013
Protein quantification by peptide quality control (PQPQ) of shotgun proteomicsdata. Methods in molecular biology (Clifton, N.J.) 2013
Stable isotope labeling methods in protein profiling. Methods in molecular biology (Clifton, N.J.) 2013
Narrow-range peptide isoelectric focusing as peptide prefractionation methodprior to tandem mass spectrometry analysis. Methods in molecular biology (Clifton, N.J.) 2013
S100A4 interacts with p53 in the nucleus and promotes p53 degradation. Oncogene 2013
MYC inhibition induces metabolic changes leading to accumulation of lipiddroplets in tumor cells. Proceedings of the National Academy of Sciences of the United States of America 2013
Mammalian target of rapamycin (mTor) mediates tau protein dyshomeostasis:implication for Alzheimer disease. The Journal of biological chemistry 2013
Defining, comparing, and improving iTRAQ quantification in mass spectrometryproteomics data. Molecular & cellular proteomics : MCP 2013
Genomic insights into the atopic eczema-associated skin commensal yeastMalassezia sympodialis. mBio 2013
A novel prefractionation method combining protein and peptide isoelectricfocusing in immobilized pH gradient strips. Journal of proteome research 2013
A combined proteomic and transcriptomic approach shows diverging molecularmechanisms in thoracic aortic aneurysm development in patients with tricuspid-and bicuspid aortic valve. Molecular & cellular proteomics : MCP 2013
Quantitative intact proteomics investigations of alveolar macrophages insarcoidosis. The European respiratory journal 2013
In vitro oxidative inactivation of human presequence protease (hPreP). Free radical biology & medicine 2012
Network enrichment analysis: extension of gene-set enrichment analysis to genenetworks. BMC bioinformatics 2012
Tumour suppressor p16(INK4a) - anoikis-favouring decrease in N/O-glycan/cellsurface sialylation by down-regulation of enzymes in sialic acid biosynthesisin tandem in a pancreatic carcinoma model. The FEBS journal 2012
Proteomic screen reveals Fbw7 as a modulator of the NF-B pathway. Nature communications 2012
Tumor proteomics by multivariate analysis on individual pathway data forcharacterization of vulvar cancer phenotypes. Molecular & cellular proteomics : MCP 2012
Proteomic profiling of follicular and papillary thyroid tumors. European journal of endocrinology 2012
Thapsigargin down-regulates protein levels of GRP78/BiP in INS-1E cells. Journal of cellular biochemistry 2012
Enhanced information output from shotgun proteomics data by proteinquantification and peptide quality control (PQPQ). Molecular & cellular proteomics : MCP 2011
Penicillin-binding protein 5 can form a homo-oligomeric complex in the innermembrane of Escherichia coli. Protein science : a publication of the Protein Society 2011
Identification of chromatophore membrane protein complexes formed underdifferent nitrogen availability conditions in Rhodospirillum rubrum. Journal of proteome research 2011
Phosphoproteomic profiling of NSCLC cells reveals that ephrin B3 regulatespro-survival signaling through Akt1-mediated phosphorylation of the EphA2receptor. Journal of proteome research 2011
Design of a peptide-based vector, PepFect6, for efficient delivery of siRNA incell culture and systemically in vivo. Nucleic acids research 2011
Systematic analysis of native membrane protein complexes in Escherichia coli. Journal of proteome research 2011
Proteomics in clinical prostate research. Proteomics. Clinical applications 2007
Vascular endothelial growth factor receptor 2 and downstream p38 mitogen-activated protein kinase are possible candidate markers of intrinsicresistance to adjuvant endocrine treatment in steroid receptor positive breastcancer. Breast cancer research and treatment 2011
Multivariate meta-analysis of proteomics data from human prostate and colontumours. BMC bioinformatics 2010
Diagnostic and prognostic role of plasma levels of two forms of cytokeratin 18in patients with non-small-cell lung cancer. European journal of cancer (Oxford, England : 1990) 2011
Observed peptide pI and retention time shifts as a result of post-translational modifications in multidimensional separations using narrow-rangeIPG-IEF. Amino acids 2011
Lung cancer proteomics, clinical and technological considerations. Journal of proteomics 2010
Proteomic study of thyroid tumors reveals frequent up-regulation of the Ca2+-binding protein S100A6 in papillary thyroid carcinoma. Thyroid : official journal of the American Thyroid Association 2010
A novel method for sample preparation of fresh lung cancer tissue forproteomics analysis by tumor cell enrichment and removal of bloodcontaminants. Proteome science 2010
A comparison between protein profiles of B cell subpopulations and mantle celllymphoma cells. Proteome science 2009
Correlating gene and protein expression data using Correlated Factor Analysis. BMC bioinformatics 2009
N(alpha)-tosyl-L-phenylalanine chloromethyl ketone induces caspase-dependentapoptosis in transformed human B cell lines with transcriptional down-regulation of anti-apoptotic HS1-associated protein X-1. The Journal of biological chemistry 2009
Use of narrow-range peptide IEF to improve detection of lung adenocarcinomamarkers in plasma and pleural effusion. Proteomics 2009
Significantly higher levels of vascular endothelial growth factor (VEGF) andshorter survival times for patients with primary operable triple-negativebreast cancer. Annals of oncology : official journal of the European Society for Medical Oncology 2009
Robustness and accuracy of high speed LC-MS separations for global peptidequantitation and biomarker discovery. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences 2009
Affinity prefractionation for MS-based plasma proteomics. Proteomics 2009
Proteomics and pathway analysis identifies JNK signaling as critical for highlinear energy transfer radiation-induced apoptosis in non-small lung cancercells. Molecular & cellular proteomics : MCP 2009
Quantitative membrane proteomics applying narrow range peptide isoelectricfocusing for studies of small cell lung cancer resistance mechanisms. Proteomics 2008
Tumor expression of S100A6 correlates with survival of patients with stage Inon-small-cell lung cancer. Lung cancer (Amsterdam, Netherlands) 2009
Evaluation of three principally different intact protein prefractionationmethods for plasma biomarker discovery. Journal of proteome research 2008
Proteomic data analysis workflow for discovery of candidate biomarker peakspredictive of clinical outcome for patients with acute myeloid leukemia. Journal of proteome research 2008
Multiple ionization mass spectrometry strategy used to reveal the complexityof metabolomics. Analytical chemistry 2008
Up-regulation, modification, and translocation of S100A6 induced by exposureto ionizing radiation revealed by proteomics profiling. Molecular & cellular proteomics : MCP 2007
iTRAQ compatibility of peptide immobilized pH gradient isoelectric focusing. Proteomics 2007
Annotated regions of significance of SELDI-TOF-MS spectra for detectingprotein biomarkers. Proteomics 2006
Pre-fractionation of archival frozen tumours for proteomics applications. Journal of biotechnology 2006
Finding regions of significance in SELDI measurements for identifying proteinbiomarkers. Bioinformatics (Oxford, England) 2006
p53 is involved in clearance of ionizing radiation-induced RAD51 foci in ahuman colon cancer cell line. Biochemical and biophysical research communications 2006
The binding specificity and affinity determinants of family 1 and family 3cellulose binding modules. Proceedings of the National Academy of Sciences of the United States of America 2003
Engineering of staphylococcal surfaces for biotechnological applications. Journal of biotechnology 2002
Stable linker peptides for a cellulose-binding domain-lipase fusion proteinexpressed in Pichia pastoris. Protein engineering 2001
Generation of metal-binding staphylococci through surface display ofcombinatorially engineered cellulose-binding domains. Applied and environmental microbiology 2001
Directed immobilization of recombinant staphylococci on cotton fibers byfunctional display of a fungal cellulose-binding domain. FEMS microbiology letters 2001
Alpha-amylase inhibitors selected from a combinatorial library of a cellulosebinding domain scaffold. Proteins 2000
Trichoderma reesei cellobiohydrolase I with an endoglucanase cellulose-bindingdomain: action on bacterial microcrystalline cellulose. Journal of biotechnology 1997