Genomics
Proteomics
Metabolomics
Data analysis, integration & stewardship
The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases
Laurie, S. et al. (2022). Hum Mutat.
Road to FAIR genomes: a gap analysis of NGS data generation and sharing in the Netherlands
Belien, JAM. et al. (2022). BMJ Open Sci.
FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research
Velde, van der, KJ. et al. (2022). Sci Data.
Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS.
Hop, PJ. et al. (2022). Sci Transl Med.
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.
Lopera-Maya, EA. et al. (2022).
The power of genetic diversity in genome-wide association studies of lipids
Graham, SE. et al. (2021). Nature.
The Data Use Ontology to streamline responsible access to human biomedical datasets
Lawson, J. et al. (2021). Cell Genom.
Validating biomarkers and models for epigenetic inference of alcohol consumption from blood
Maas, SCE. et al. (2021). Clin Epigenetics.
Lessons learned from unsolicited findings in clinical exome sequencing of 16,482 individuals
Schoot, van der, V. et al (2021). Eur J Hum Genet.
Genetics and Not Shared Environment Explains Familial Resemblance in Adult Metabolomics Data
Pool, R. et al. (2020). Twin Res Hum Genet.
Metabolic Age Based on the BBMRI-NL 1 H-NMR Metabolomics Repository as Biomarker of Age-related Disease
Akker, van den, EB. (2020). Circ Genom Precis Med.
DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan
Dongen, van, J. (2021). Mol Psychiatry.
Identification of 371 genetic variants for age at first sex and birth linked to externalising behavior
Mills, MC. (2021). Nat Hum Behav.
Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms
Feng, X. (2021). Anal Chim Acta.
MSIWarp: A General Approach to Mass Alignment in Mass Spectrometry Imaging
Eriksson, JO. (2020). Anal Chem.
The 'un-shrunk' partial correlation in Gaussian graphical modelsThe 'un-shrunk' partial correlation in Gaussian graphical models
Bernal, V. (2021). BMC Bioinformatics.
Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation
Yang, Y. (2021). J Proteome Res.
Solving the unsolved rare diseases in Europe
Graessner, H. et al. (2021). Eur J Hum Genet.
Metabolomics-Based Screening of Inborn Errors of Metabolism: Enhancing Clinical Application with a Robust Computational Pipeline
Hoegen, B. et al. (2021). Metabolites.
The de novo FAIRification process of a registry for vascular anomalies
Groenen, KHJ. et al. (2021). Orphanet J Rare Dis.
Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations
Boer, CG. et al. (2021). Cell.
Long-term trajectories of decline in cognition and daily functioning before and after stroke
Heshmatollah, A. et al. (2021). J Neurol Neurosurg Psychiatry.
Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.
Zurek, B. et al. (2021). Eur J Hum Genet.
Learning mutational signatures and their multidimensional genomic properties with TensorSignatures
Vöhringer, H. et al. (2021). Nat Commun.
Benchmarking deep learning splice prediction tools using functional splice assays
Riepe, TV. et al. (2021). Hum Mutat.
Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection
Salz, R. et al. (2021). J Proteome Res.
Feasibility of predicting allele specific expression from DNA sequencing using machine learning
Zhang, Z. et al. (2021). Sci Rep.
Neuroproteomics of the synapse: subcellular quantification of protein networks and signaling dynamics
Gelder, van, CAGH. et al. (2021). Mol Cell Proteomics.
Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1
Brandsma, CA. et al. (2020). Thorax.
Lifelines COVID-19 cohort; investigating COVID-19 infection and its health and societal impacts in a Dutch population-based cohort
Mc Intyre, K. et al. (2021). BMJ Open.
Associations between the CADM2 gene, substance use, risky sexual behavior, and self-control: A phenome-wide association study
Arends RM, Pasman JA, Verweij KJH, Derks EM, Gordon SD, Hickie I, Thomas NS, Aliev F, Zietsch BP, van der Zee MD, Mitchell BL, Martin NG, Dick DM, Gillespie NA, de Geus EJC, Boomsma DI, Schellekens AFA, Vink JM.Addict Biol. 2021 Feb 18:e13015. doi: 10.1111/adb.13015. Online ahead of print.
Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science.
Weintraub, ST. et al. (2019). J Proteome Res. 18, 575.
PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis.
Ressa, A. et al. (2019). J Proteome Res. 18, 576-584.
The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases
Laurie, S. et al. (2022). Hum Mutat.
Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications
Schobers, G. et al. (2022). Genome Med.
How to proceed after “negative”exome: A review on genetic diagnostics, limitations, challenges, and emerging new multiomics techniques
Wortmann, SB. et al. (2022). J Inherit Metab Dis.
Clinical exome sequencing – mistakes and caveats
Corominas, J. et al. (2022). Hum Mutat.
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.
Lopera-Maya, EA. et al. (2022).
Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19
Sahajpal, NS. et al. (2022). iScience.
The power of genetic diversity in genome-wide association studies of lipids
Graham, SE. et al. (2021). Nature.
Lessons learned from unsolicited findings in clinical exome sequencing of 16,482 individuals
Schoot, van der, V. et al (2021). Eur J Hum Genet.
Multiple Myeloma Minimal Residual Disease Detection: Targeted Mass Spectrometry in Blood vs Next-Generation Sequencing in Bone Marrow
Langerhorst, P. et al. (2021). Clin Chem.
DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan
Dongen, van, J. (2021). Mol Psychiatry.
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation
Min, JL. (2021). Nat Genet.
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
Võsa, U. (2021). Nat Genet.
Identification of 371 genetic variants for age at first sex and birth linked to externalising behavior
Mills, MC. (2021). Nat Hum Behav.
Solving the unsolved rare diseases in Europe
Graessner, H. et al. (2021). Eur J Hum Genet.
Identical twins carry a persistent epigenetic signature of early genome programming
Dongen, van, J. et al. (2021). Nat Commun.
Metabolomic and lipidomic signatures associated with activation of human cDC1 (BDCA3+ /CD141+ ) dendritic cells
Basit, F. et al. (2021). Immunology.
Genetic insights into biological mechanisms governing human ovarian ageing
Ruth, K.S. et al. (2021). Nature.
Genetic predisposition (HLA-SE) is associated with ACPA-IgG variable domain glycosylation in the predisease phase of RA
Kissel, T. et al. (2021). Ann Rheum Dis.
The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets
Riet, van, J. et al. (2021). Nat Commun.
Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns
Bollen, Y. et al. (2021).Nat Genet.
Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors
Sabatella, M. et al. (2021). J Pathol.
Next generation cytogenetics: comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping
Neveling, K. et al. (2021). Am J Hum Genet.
Optical genome mapping enables constitutional chromosomal aberration detection
Mantere, T. et al. (2021). Am J Hum Genet.
A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids
Jhun, MA. et al. (2021). Nat Commun.
Clinical Validation of Whole Genome Sequencing for Cancer Diagnostics
Roepman, P. et al. (2021). J Mol Diagn.
Early technology assessment of using whole genome sequencing in personalised oncology
Simons, M. et al. (2021). Expert Rev Pharmacoecon Outcomes Res.
Single-cell derived tumor organoids display diversity in HLA class I peptide presentation
Demmers, L.C. et al. (2020). Nat Commun.
Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1
Brandsma, CA. et al. (2020). Thorax.
Long-read trio sequencing of individuals with unsolved intellectual disability
Pauper, M. et al. (2021). Eur J Hum Genet. 637 – 648.
Presence of Genetic Variants Among Young Men With COVID-19.
Van der Made, Cl. (2020). JAMA.
Mutational signature in colorectal cancer caused by genotoxic pks + E. coli.
Pleguezuelos-Manzano, C. et al. (2020). Nature.
SARS-CoV-2 productively infects human gut enterocytes.
Lamers, MM. et al. (2020). Science.
The Immunometabolic Atlas: A tool for design and interpretation of metabolomics studies in immunology
Maas, P. et al. (2022). PLoS One.
Preparing ductal epithelial organoids for high-spatial-resolution molecular profiling using mass spectrometry imaging.
Bakker, B. et al. (2022). Nat Protoc.
Metabolite Identification Using Infrared Ion Spectroscopy─Novel Biomarkers for Pyridoxine-Dependent Epilepsy
Outersterp, van, RE. et al. (2021). Anal Chem.
Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring
Ghorasaini, M. et al. (2021). Anal Chem.
Genetics and Not Shared Environment Explains Familial Resemblance in Adult Metabolomics Data
Pool, R. et al. (2020). Twin Res Hum Genet.
Metabolic Age Based on the BBMRI-NL 1 H-NMR Metabolomics Repository as Biomarker of Age-related Disease
Akker, van den, EB. (2020). Circ Genom Precis Med.
Combined Metabolic and Chemical (CoMetChem) Labeling Using Stable Isotopes-a Strategy to Reveal Site-Specific Histone Acetylation and Deacetylation Rates by LC-MS
Pijkeren, van, A. (2021). Anal Chem.
Metabolomic and lipidomic signatures associated with activation of human cDC1 (BDCA3+ /CD141+ ) dendritic cells
Basit, F. et al. (2021). Immunology.
A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids
Jhun, MA. et al. (2021). Nat Commun.
Untargeted metabolomics and infrared ion spectroscopy identify biomarkers for pyridoxine-dependent epilepsy
Engelke, UFG. et al. (2021). J Clin Invest.
Results of an explorative clinical evaluation suggest immediate and persistent post-reperfusion metabolic paralysis drives kidney ischemia reperfusion injury
Lindeman J.H. et al. (2020). Kidney Int.
Effect of metabolic genetic variants on long-term disease comorbidity in patients with type 2 diabetes
Abedian S et al. 2021. Sci Rep 11(1):2794.
Reproducibility of Targeted Lipidome Analyses (Lipidyzer) in Plasma and Erythrocytes over a 6-Week Period
Loef, M. et al. (2020). Metabolites.
Inhibition of ∆24-dehydrocholesterol reductase activates pro-resolving lipid mediator biosynthesis and inflammation resolution.
Körner, A. et al. (2019). Proc Natl Acad Sci U S A. 116, 20623 – 20634.
Cholesterol Metabolism Is a Druggable Axis that Independently Regulates Tau and Amyloid-β in iPSC-Derived Alzheimer’s Disease Neurons.
van der Kant, R. et al. (2019). Cell Stem Cell. 24, 363-275.
Fast LC-ESI-MS/MS analysis and influence of sampling conditions for gut metabolites in plasma and serum.
van der Laan, T. et al. (2019). Sci Rep. 9, 12370.
Histidine phosphorylation in human cells; a needle or phantom in the haystack?
Leijten, NM. et al. (2022). Nat Methods.
Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology
Klykov, O. et al. (2022). Mol Cell.
Combined Quantitative (Phospho)proteomics and Mass Spectrometry Imaging Reveal Temporal and Spatial Protein Changes in Human Intestinal Ischemia-Reperfusion
Kip, AM. et al. (2021). J Proteome Res.
Structural basis of soluble membrane attack complex packaging for clearance
Menny, A. et al. (2021). Nat Commun.
Multiple Myeloma Minimal Residual Disease Detection: Targeted Mass Spectrometry in Blood vs Next-Generation Sequencing in Bone Marrow
Langerhorst, P. et al. (2021). Clin Chem.
Active site variants in STT3A cause of dominant type I congenital disorder of glycosylation with neuromusculoskeletal findings
Wilson, MP. (2021). Am J Hum Genet.
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
Võsa, U. (2021). Nat Genet.
Human plasma IgG1 repertoires are simple, unique, and dynamic
Bondt, A. (2021). Cell Syst.
High sensitivity glycomics in biomedicine
Lageveen-Kammeijer, GSM. et al. (2021). Mass Spectrom Rev.
Genetic predisposition (HLA-SE) is associated with ACPA-IgG variable domain glycosylation in the predisease phase of RA
Kissel, T. et al. (2021). Ann Rheum Dis.
Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer
Prekovic, S. et al. (2021). Nat Commun.
Neuroproteomics of the synapse: subcellular quantification of protein networks and signaling dynamics
Gelder, van, CAGH. et al. (2021). Mol Cell Proteomics.
Single-cell derived tumor organoids display diversity in HLA class I peptide presentation
Demmers, L.C. et al. (2020). Nat Commun.
Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1
Brandsma, CA. et al. (2020). Thorax.
Adeno-associated virus capsid assembly is divergent and stochastic
Wörner, TP. et al. (2021). Nat Commun. 1642.
Clonotypic Features of Rearranged Immunoglobulin Genes Yield Personalized Biomarkers for Minimal Residual Disease Monitoring in Multiple Myeloma
Langerhorst, P. et al. (2021). Clin Chem.
Profiling the proteoforms of urinary prostate-specific antigen by capillary electrophoresis - mass spectrometry
Moran AB, Domínguez-Vega E, Nouta J, Pongracz T, de Reijke TM, Wuhrer M, Lageveen-Kammeijer GSM.J Proteomics. 2021 Feb 19;238:104148. doi: 10.1016/j.jprot.2021.104148. Online ahead of print.
Combined kinesin-1 and kinesin-3 activity drives axonal trafficking of TrkB receptors in Rab6 carriers
Zahavi EE et al. (2021). Dev Cell. S1534-5807(21)00068-X. Online ahead of print.
High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells.
Beumer, J. et al. (2020). Cell.
Metabolic changes related to the IDH1 mutation in gliomas preserve TCA-cycle activity: An investigation at the protein level.
Dekker, LJM. et al. (2020). FASEB J. 34, 3646 – 3657.
SARS-CoV-2 productively infects human gut enterocytes.
Lamers, MM. et al. (2020). Science.
Integrating Serum Protein Electrophoresis with Mass Spectrometry, A New Workflow for M-Protein Detection and Quantification.
Zajec, M. et al. (2020). J Proteome Res.
Highly sensitive CE-ESI-MS analysis of N-glycans from complex biological samples.
Lageveen-Kammeijer, GSM. et al. (2019). Nat Commun. 10, 2137.
Automated workflow composition in mass spectrometry-based proteomics.
Palmblad, M. et al. (2019). Bioinformatics. 35, 656 – 664.
Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science.
Weintraub, ST. et al. (2019). J Proteome Res. 18, 575.
First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.
Lacobucci, C. et al. (2019). Anal Chem. 91, 6953-6961.
Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.
Masson, GR. et al. (2019). Nat Methods. 16, 595-602.
PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis.
Ressa, A. et al. (2019). J Proteome Res. 18, 576-584.
Expanding the mass range for UVPD-based native top-down mass spectrometry.
Greisch, JF. et al. (2019). Chem Sci. 10, 7163-7171.
Targeting proline in (phospho)proteomics.
van der Laarse, SAM. et al. (2019). FEBS J.
This research was (partially) funded by NWO, project 184.034.019