Publications

In this section the scientific publications of the X-omics partners are displayed. The X-omics consortium is a very large consortium and therefor generates a lot of publications (on average 50 publications per month). To inform you about the most important publications with a high impact, we have added a selection of publications below (displayed individually and searchable per expertise).

The de novo FAIRification process of a registry for vascular anomalies

Groenen, KHJ. et al. (2021). Orphanet J Rare Dis.

PMID: 34481493

Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations

Boer, CG. et al. (2021). Cell.

PMID: 34450027

Long-term trajectories of decline in cognition and daily functioning before and after stroke

Heshmatollah, A. et al. (2021). J Neurol Neurosurg Psychiatry.

PMID: 34230107

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases.

Zurek, B. et al. (2021). Eur J Hum Genet.

PMID: 34075208

Learning mutational signatures and their multidimensional genomic properties with TensorSignatures

Vöhringer, H. et al. (2021). Nat Commun.

PMID: 34131135

Benchmarking deep learning splice prediction tools using functional splice assays

Riepe, TV. et al. (2021). Hum Mutat.

PMID: 33942434

Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection

Salz, R. et al. (2021). J Proteome Res.

PMID: 33998808

Feasibility of predicting allele specific expression from DNA sequencing using machine learning

Zhang, Z. et al. (2021). Sci Rep.

PMID: 34012022

Neuroproteomics of the synapse: subcellular quantification of protein networks and signaling dynamics

Gelder, van, CAGH. et al. (2021). Mol Cell Proteomics.

PMID: 33933679

Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1

Brandsma, CA. et al. (2020). Thorax.

PMID: 31937552

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.

PMID: 33737436

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.

PMID: 33604983

Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science.

Weintraub, ST. et al. (2019). J Proteome Res. 18, 575.

PMID: 30704244

PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis.

Ressa, A. et al. (2019). J Proteome Res. 18, 576-584.

PMID: 30525654

Metabolomic and lipidomic signatures associated with activation of human cDC1 (BDCA3+ /CD141+ ) dendritic cells

Basit, F. et al. (2021). Immunology.

PMID: 34431087

Genetic insights into biological mechanisms governing human ovarian ageing

Ruth, K.S. et al. (2021). Nature.

PMID: 34349265

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.

PMID: 34385139

The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets

Riet, van, J. et al. (2021). Nat Commun.

PMID: 34326338

Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Bollen, Y. et al. (2021).Nat Genet.

PMID: 34211178

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.

PMID: 34231212

Next generation cytogenetics: comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping

Neveling, K. et al. (2021). Am J Hum Genet.

PMID: 34237281

Optical genome mapping enables constitutional chromosomal aberration detection

Mantere, T. et al. (2021). Am J Hum Genet.

PMID: 34237280

A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids

Jhun, MA. et al. (2021). Nat Commun.

PMID: 34183656

Clinical Validation of Whole Genome Sequencing for Cancer Diagnostics

Roepman, P. et al. (2021). J Mol Diagn.

PMID: 33964451

Early technology assessment of using whole genome sequencing in personalised oncology

Simons, M. et al. (2021). Expert Rev Pharmacoecon Outcomes Res.

PMID: 33910430

Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

Demmers, L.C. et al. (2020). Nat Commun.

PMID: 33087703

Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1

Brandsma, CA. et al. (2020). Thorax.

PMID: 31937552

Long-read trio sequencing of individuals with unsolved intellectual disability

Pauper, M. et al. (2021). Eur J Hum Genet. 637 – 648.

PMID: 33257779

Presence of Genetic Variants Among Young Men With COVID-19.

Van der Made, Cl. (2020). JAMA.

PMID: 32706371

Mutational signature in colorectal cancer caused by genotoxic pks + E. coli.

Pleguezuelos-Manzano, C. et al. (2020). Nature.

PMID: 32106218

SARS-CoV-2 productively infects human gut enterocytes.

Lamers, MM. et al. (2020). Science.

PMID: 32358202

Metabolomic and lipidomic signatures associated with activation of human cDC1 (BDCA3+ /CD141+ ) dendritic cells

Basit, F. et al. (2021). Immunology.

PMID: 34431087

A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids

Jhun, MA. et al. (2021). Nat Commun.

PMID: 34183656

Untargeted metabolomics and infrared ion spectroscopy identify biomarkers for pyridoxine-dependent epilepsy

Engelke, UFG. et al. (2021). J Clin Invest.

PMID: 34138754

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.

PMID: 32781105

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.

PMID: 33531528

Reproducibility of Targeted Lipidome Analyses (Lipidyzer) in Plasma and Erythrocytes over a 6-Week Period

Loef, M. et al. (2020). Metabolites.

PMID: 33396510

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.

PMID: 31548397

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.

PMID: 30686764

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.

PMID: 31451722

High sensitivity glycomics in biomedicine

Lageveen-Kammeijer, GSM. et al. (2021). Mass Spectrom Rev.

PMID: 34494287

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.

PMID: 34385139

Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer

Prekovic, S. et al. (2021). Nat Commun.

PMID: 34272384

Neuroproteomics of the synapse: subcellular quantification of protein networks and signaling dynamics

Gelder, van, CAGH. et al. (2021). Mol Cell Proteomics.

PMID: 33933679

Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

Demmers, L.C. et al. (2020). Nat Commun.

PMID: 33087703

Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1

Brandsma, CA. et al. (2020). Thorax.

PMID: 31937552

Adeno-associated virus capsid assembly is divergent and stochastic

Wörner, TP. et al. (2021). Nat Commun. 1642.

PMID: 33712599

Clonotypic Features of Rearranged Immunoglobulin Genes Yield Personalized Biomarkers for Minimal Residual Disease Monitoring in Multiple Myeloma

Langerhorst, P. et al. (2021). Clin Chem.

PMID: 33709101

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.

PMID: 33618028

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.

PMID: 33571451

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells.

Beumer, J. et al. (2020). Cell.

PMID: 32407674

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.

PMID: 31960518

SARS-CoV-2 productively infects human gut enterocytes.

Lamers, MM. et al. (2020). Science.

PMID: 32358202

Integrating Serum Protein Electrophoresis with Mass Spectrometry, A New Workflow for M-Protein Detection and Quantification.

Zajec, M. et al. (2020). J Proteome Res.

PMID: 31895568

Highly sensitive CE-ESI-MS analysis of N-glycans from complex biological samples.

Lageveen-Kammeijer, GSM. et al. (2019). Nat Commun. 10, 2137.

PMID: 31086181

Automated workflow composition in mass spectrometry-based proteomics.

Palmblad, M. et al. (2019). Bioinformatics. 35, 656 – 664.

PMID: 30060113

Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science.

Weintraub, ST. et al. (2019). J Proteome Res. 18, 575.

PMID: 30704244

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

Lacobucci, C. et al. (2019). Anal Chem. 91, 6953-6961.

PMID: 31045356

Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments.

Masson, GR. et al. (2019). Nat Methods. 16, 595-602.

PMID: 31249422

PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis.

Ressa, A. et al. (2019). J Proteome Res. 18, 576-584.

PMID: 30525654

Expanding the mass range for UVPD-based native top-down mass spectrometry.

Greisch, JF. et al. (2019). Chem Sci. 10, 7163-7171.

PMID: 31588283

Targeting proline in (phospho)proteomics.

van der Laarse, SAM. et al. (2019). FEBS J.

PMID: 31863553

NWO logoThis research was (partially) funded by NWO, project 184.034.019