Publications

Publications from the Claringbould Lab.

2026

  1. Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells
    D.P.I. Moonen*, A. Claringbould*, A.R. Gschwind, S. Schrod, and others
    bioRxiv, 2026
    DOI
  2. Single-cell ultra-high-throughput multiplexed chromatin accessibility and gene expression sequencing (SUM-seq)
    U. Yildiz*, S. Lobato-Moreno*, A. Claringbould, and others
    Nature Protocols, 2026
    DOI
  3. Trans-eQTLs reveal the architecture of human gene regulatory networks
    C.A.R. Warmerdam, H.J. Westra, A. Graaf, and others
    medRxiv, 2026
    DOI

2025

  1. Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics
    S. Lobato-Moreno*, U. Yildiz*, A. Claringbould*, and others
    Nature Methods, 2025
    DOI
  2. High-throughput single-cell CRISPRi screens stratify neurodevelopmental functions of schizophrenia-associated genes
    U. Yildiz, A. Claringbould*, M. Marttinen*, and others
    bioRxiv, 2025
    DOI
  3. High-Sensitivity C Reactive Protein Mediates Age-Related Vascular Dysfunction: The Rotterdam Study
    S. Mohammadi Jouabadi, A. Claringbould, A.H.J. Danser, and others
    European Journal of Preventive Cardiology, 2025
    DOI
  4. Integrative Multi-Omics Identifies CDK1 as a Key Signaling Regulator of CD4+ T Cell Effector Function
    N.H. Servaas, H.G. Bauersachs, L. Abreu, A. Claringbould, and others
    bioRxiv, 2025
    DOI

2024

  1. Identification of rare disease genes as drivers of common diseases through tissue-specific gene regulatory networks
    O.B. Bakker*, A. Claringbould*, H.J. Westra, and others
    Scientific Reports, 2024
    DOI
  2. Using parent-offspring pairs and trios to estimate indirect genetic effects in education
    V. Trindade Pons, A. Claringbould, P. Kamphuis, A.J. Oldehinkel, and H.M. Loo
    Genetic Epidemiology, 2024
    DOI
  3. Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes
    C.G. Urzúa-Traslaviña, T. Lieshout, F. Boulogne, and others
    BMC Medical Genomics, 2024
    DOI

2023

  1. GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks
    A. Kamal*, C. Arnold*, A. Claringbould, and others
    Molecular Systems Biology, 2023
    DOI

2022

  1. Limited evidence for blood eQTLs in human sexual dimorphism
    E. Porcu, A. Claringbould, A. Weihs, and others
    Genome Medicine, 2022
    DOI
  2. Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations
    M. Lepamets, C. Auwerx, M. Nõukas, A. Claringbould, and others
    Human Genetics and Genomics Advances, 2022
    DOI

2021

  1. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
    U. Võsa*, A. Claringbould*, H.J. Westra, and others
    Nature Genetics, 2021
    DOI
  2. Enhancers in disease: molecular basis and emerging treatment strategies
    A. Claringbould and J.B. Zaugg
    Trends in Molecular Medicine, 2021
    DOI
  3. Correction for both common and rare cell types in blood is important to identify genes that correlate with age
    D. Pellegrino-Coppola*, A. Claringbould*, M. Stutvoet, and others
    BMC Genomics, 2021
    DOI
  4. Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγSignaling in Celiac Disease
    A. Graaf, M.M. Zorro, A. Claringbould, and others
    Frontiers in Genetics, 2021
    DOI
  5. Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility
    I.V. Blokland, P. Lanting, A.P.S. Ori, and others
    PLOS ONE, 2021
    DOI
  6. The trans-ancestral genomic architecture of glycemic traits
    J. Chen, C.N. Spracklen, G. Marenne, and others
    Nature genetics, 2021
    DOI
  7. Lifelines COVID-19 cohort: investigating COVID-19 infection and its health and societal impacts in a Dutch population-based cohort
    K. Mc Intyre, P. Lanting, P. Deelen, and others
    BMJ open, 2021
    DOI
  8. Pathological LSD1 mutations repress enhancer-mediated gene regulatory networks in early differentiation
    D. Bunina, P. Germain, Lopez T., and others
    bioRxiv, 2021
    DOI
  9. Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits
    M.C. Lai, M. Ruiz-Velasco, C. Arnold, and others
    bioRxiv, 2021
    DOI
  10. Mapping the human genetic architecture of COVID-19
    COVID-19 Host Genetics Initiative
    Nature, 2021
    DOI

2020

  1. Deconvolution of bulk blood eQTL effects into immune cell subpopulations
    R. Aguirre-Gamboa*, N. Klein*, J. Tommaso*, A. Claringbould, and others
    BMC Bioinformatics, 2020
    DOI
  2. Mendelian randomization while jointly modeling cis genetics identifies causal relationships between gene expression and lipids
    A. Graaf, A. Claringbould, A. Rimbert, and others
    Nature Communications, 2020
    DOI
  3. Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals
    L. Folkersen, S. Gustafsson, Q. Wang, and others
    Nature Metabolism, 2020
    DOI
  4. Imbalanced expression for predicted high-impact, autosomal-dominant variants in a cohort of 3,818 healthy samples
    N. Klein*, F. Dijk*, P. Deelen, and others
    bioRxiv, 2020
    DOI
  5. A characterization of cis- and trans-heritability of RNA-Seq-based gene expression
    K.G. Ouwens, R. Jansen, M.G. Nivard, and others
    European Journal of Human Genetics, 2020
    DOI
  6. Core gene identification using gene expression
    Annique Claringbould
    University of Groningen, 2020
    DOI

2019

  1. GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI
    A.C. Alves, N.M.G. De Silva, V. Karhunen, and others
    Science Advances, 2019
    DOI
  2. Alzheimer’s disease pathology explains association between dementia with Lewy bodies and APOE-\varepsilon4/TOMM40 long poly-T repeat allele variants
    I. Prokopenko, G. Miyakawa, B. Zheng, and others
    Alzheimer’s & Dementia: Translational Research & Clinical Interventions, 2019
    DOI
  3. The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus
    K. Schlicht, P. Nyczka, A. Caliebe, and others
    Human Genetics, 2019
    DOI
  4. Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
    J. Rooij*, P.R. Mandaviya*, A. Claringbould*, and others
    Genome Biology, 2019
    DOI
  5. Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation
    B. Zeng, L.R. Lloyd-Jones, G.W. Montgomery, and others
    Genetics, 2019
    DOI

2018

  1. Genome-wide identification of directed gene networks using large-scale population genomics data
    R. Luijk, K.F. Dekkers, M. Iterson, and others
    Nature Communications, 2018
    DOI
  2. A SNP panel for identification of DNA and RNA specimens
    S. Yousefi, T. Abbassi-Daloii, T. Kraaijenbrink, and others
    BMC Genomics, 2018
    DOI
  3. Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome
    D.V. Zhernakova, T.H. Le, A. Kurilshikov, and others
    Nature Genetics, 2018
    DOI

2017

  1. The genetic architecture of molecular traits
    A. Claringbould*, N. Klein*, and L. Franke
    Current Opinion in Systems Biology, 2017
    DOI