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R. Lindeboom · SciRah

Researcher profile · Semantic Scholar

R. Lindeboom

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R. Lindeboom — researcher profile on SciRah

h-index: 26
Works: 69
Citations: 4,280

Most-cited papers

Single-cell multi-omics analysis of the immune response in COVID-19
E. Stephenson, G. Reynolds, R. Botting, F. Calero-Nieto +64 more
2021Nature Medicine652 citations Open access
Semantic Scholar
N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis
Raghu R. Edupuganti, Simon Geiger, R. Lindeboom, Hailing Shi +11 more
2017Nature Structural &Molecular Biology509 citations Open access
Semantic Scholar
The rules and impact of nonsense-mediated mRNA decay in human cancers
R. Lindeboom, F. Supek, Ben Lehner
2016Nature Genetics484 citations Open access
Semantic Scholar
Local and systemic responses to SARS-CoV-2 infection in children and adults
Masahiro Yoshida, K. Worlock, N. Huang, R. Lindeboom +52 more
2021Nature310 citations Open access
Semantic Scholar
The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy
R. Lindeboom, M. Vermeulen, Ben Lehner, F. Supek
2019Nature Genetics255 citations Open access
Semantic Scholar
To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases.
F. Supek, Ben Lehner, R. Lindeboom
2020Trends in Genetics215 citations Open access
Semantic Scholar
Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids.
B. Artegiani, Lisa van Voorthuijsen, R. Lindeboom, Danielle Seinstra +14 more
2019Cell Stem Cell200 citations Open access
Semantic Scholar
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche
E. Madissoon, A. Oliver, V. Kleshchevnikov, A. Wilbrey-Clark +36 more
2022Nature Genetics186 citations Open access
Semantic Scholar
Single-Molecule Imaging Uncovers Rules Governing Nonsense-Mediated mRNA Decay
Tim A. Hoek, D. Khuperkar, R. Lindeboom, Stijn Sonneveld +4 more
2019Molecules and Cells143 citations Open access
Semantic Scholar
Integrative multi‐omics analysis of intestinal organoid differentiation
R. Lindeboom, Lisa van Voorthuijsen, K. Oost, M. Rodriguez-Colman +8 more
2018Molecular Systems Biology128 citations Open access
Semantic Scholar
Human SARS-CoV-2 challenge uncovers local and systemic response dynamics
R. Lindeboom, K. Worlock, L. Dratva, M. Yoshida +40 more
2024Nature122 citations Open access
Semantic Scholar
ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage.
C. G. Spruijt, M. S. Luijsterburg, R. Menafra, R. Lindeboom +12 more
2016Cell Reports115 citations Open access
Semantic Scholar
Towards a Human Cell Atlas: Taking Notes from the Past.
R. Lindeboom, A. Regev, S. Teichmann
2021Trends in Genetics78 citations Open access
Semantic Scholar
Liver Colonization by Colorectal Cancer Metastases Requires YAP-Controlled Plasticity at the Micrometastatic Stage
Maria C. Heinz, N. A. Peters, K. Oost, R. Lindeboom +13 more
2022Cancer Research75 citations Open access
Semantic Scholar
Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins
Chen-Qu Suo, K. Polański, E. Dann, R. Lindeboom +8 more
2023Nature Biotechnology68 citations Open access
Semantic Scholar
Decoding chromatin states by proteomic profiling of nucleosome readers
Saulius Lukauskas, Andrey Tvardovskiy, Nhuong V. Nguyen, Mara Stadler +16 more
2024Nature60 citations Open access
Semantic Scholar
Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs
A. H. Smits, R. Lindeboom, M. Perino, S. J. van Heeringen +2 more
2014Nucleic Acids Research59 citations Open access
Semantic Scholar
Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation.
J. Bonnet, R. Lindeboom, D. Pokrovsky, Georg Stricker +6 more
2019Developmental Cell56 citations Open access
Semantic Scholar
Early human lung immune cell development and its role in epithelial cell fate
J. Barnes, Masahiro Yoshida, Peng He, K. Worlock +29 more
2022bioRxiv49 citations Open access
Semantic Scholar
Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
N. Rother, Cansu Yanginlar, R. Lindeboom, S. Bekkering +15 more
2020Cell Reports Medicine48 citations Open access
Semantic Scholar
RNF43 truncations trap CK1 to drive niche‐independent self‐renewal in cancer
M. Spit, Nicola Fenderico, Ingrid Jordens, Tomasz W. Radaszkiewicz +16 more
2020EMBO Journal46 citations Open access
Semantic Scholar
Age-specific nasal epithelial responses to SARS-CoV-2 infection
M. Woodall, A. Cujba, K. Worlock, K. Case +35 more
2024Nature Microbiology45 citations Open access
Semantic Scholar
Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131*
Radhika A. Varier, E. C. de Santa Pau, P. van der Groep, R. Lindeboom +12 more
2016Journal of Biological Chemistry43 citations Open access
Semantic Scholar
Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data
F. Drost, Yang An, Irene Bonafonte-Pardàs, L. Dratva +6 more
2024Nature Communications37 citations Open access
Semantic Scholar
Specific Labeling of Stem Cell Activity in Human Colorectal Organoids Using an ASCL2-Responsive Minigene
K. Oost, Lisa van Voorthuijsen, Arianna Fumagalli, R. Lindeboom +10 more
2018Cell Reports35 citations Open access
Semantic Scholar
NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells
S. Kloet, I. Karemaker, Lisa van Voorthuijsen, R. Lindeboom +5 more
2018Nature Communications26 citations Open access
Semantic Scholar
Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq
Hannah K. Neikes, Katarzyna W. Kliza, Cathrin Gräwe, Roelof A. Wester +8 more
2023Nature Biotechnology25 citations
Semantic Scholar
Retinoic acid signaling drives differentiation toward the absorptive lineage in colorectal cancer
Roelof A. Wester, Lisa van Voorthuijsen, Hannah K. Neikes, J. Dijkstra +6 more
2021iScience23 citations Open access
Semantic Scholar
Proteomic landscape of the primary somatosensory cortex upon sensory deprivation
K. Kole, R. Lindeboom, Marijke P. A. Baltissen, P. Jansen +3 more
2017GigaScience20 citations Open access
Semantic Scholar
The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres
E. Stephenson, Gary Reynolds, R. Botting, F. Calero-Nieto +64 more
2021medRxiv19 citations Open access
Semantic Scholar
Obesity Is Associated with Attenuated Tissue Immunity in COVID-19
S. Guo, Georgina S. Bowyer, J. Ferdinand, M. Maes +22 more
2022American Journal of Respiratory and Critical Care Medicine17 citations Open access
Semantic Scholar
Acid ceramidase regulates innate immune memory
N. Rother, Cansu Yanginlar, Geoffrey Prévot, Inge Jonkman +21 more
2023Cell Reports16 citations Open access
Semantic Scholar
Multi-omics profiling reveals a distinctive epigenome signature for high-risk acute promyelocytic leukemia
Abhishek A. Singh, F. Petraglia, A. Nebbioso, Guoqiang Yi +27 more
2018OncoTarget15 citations Open access
Semantic Scholar
SARS-CoV-2 human challenge reveals biomarkers that discriminate early and late phases of respiratory viral infections
J. Rosenheim, Rishi K. Gupta, C. Thakker, Tiffeney Mann +31 more
2024Nature Communications14 citations Open access
Semantic Scholar
Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis
F. Drost, Yang An, L. Dratva, R. Lindeboom +5 more
2021bioRxiv13 citations Open access
Semantic Scholar
ZMYND 8 Co-localizes with NuRD on Target Genes and Regulates Poly ( ADP-Ribose )-Dependent Recruitment of GATAD 2 A / NuRD to Sites of DNA Damage Graphical
C. G. Spruijt, M. S. Luijsterburg, R. Menafra, R. Lindeboom +12 more
201612 citations
Semantic Scholar
Human SARS-CoV-2 challenge resolves local and systemic response dynamics
R. Lindeboom, Kaylee B. Worlock, Lisa M. Dratva, M. Yoshida +34 more
2023medRxiv11 citations Open access
Semantic Scholar
Hydroxychloroquine inhibits trained immunity - implications for COVID-19
N. Rother, Cansu Yanginlar, R. Lindeboom, S. Bekkering +15 more
2020medRxiv9 citations Open access
Semantic Scholar
SARS-CoV-2 human challenge reveals single-gene blood transcriptional biomarkers that discriminate early and late phases of acute respiratory viral infections.
J. Rosenheim, Rishi K. Gupta, C. Thakker, Tiffeney Mann +31 more
2023medRxiv7 citations Open access
Semantic Scholar
Pre-existing and early cellular immune factors correlate with functionally complete protection against primary controlled human SARS-CoV-2 infection
H. Wagstaffe, R. Thwaites, J. Sidhu, R. Lindeboom +22 more
2025Nature Communications6 citations
Semantic Scholar
Modelling Technical and Biological Effects in scRNA-seq data with Scalable GPLVMs
Vidhi Lalchand, Aditya Ravuri, E. Dann, N. Kumasaka +5 more
20226 citations
Semantic Scholar
Modelling Technical and Biological Effects in scRNA-seq data with Scalable GPLVMs
Vidhi Lalchand, Aditya Ravuri, E. Dann, N. Kumasaka +5 more
2022MLCB5 citations Open access
Semantic Scholar
Early Human Lung Immune Cell Development and Its Role in Epithelial Cell Fate
M. Nikolič, J. Barnes, M. Yoshida, P. He +29 more
2024D108. SIGNALING PATHWAYS IN AIRWAY REGENERATION AND REPAIR4 citations Open access
Semantic Scholar
Mass Spectrometry-Based Absolute Quantification of Single Xenopus Embryo Proteomes.
R. Lindeboom, A. H. Smits, M. Perino, G. J. Veenstra +1 more
2018Cold Spring Harbor Protocols4 citations Open access
Semantic Scholar
MHC1-TIP enables single-tube multimodal immunopeptidome profiling and uncovers intratumoral heterogeneity in antigen presentation
Mayukha Bathini, Diana Bocaniciu, F. Johnson, Rick C. P. de Jong +12 more
2025bioRxiv3 citations Open access
Semantic Scholar
Temporal multi-omics analysis of COVID-19 in end-stage kidney disease
Emily Stephenson, E. Macdonald-Dunlop, L. Dratva, R. Lindeboom +26 more
2025Cell Genomics3 citations Open access
Semantic Scholar
Quantifying genome-wide transcription factor binding affinities for chromatin using BANC-seq
Roelof A. Wester, Hannah K. Neikes, R. Lindeboom, M. Vermeulen
2024Nature Protocols2 citations Open access
Semantic Scholar
Dandelion utilizes single cell adaptive immune receptor repertoire to explore lymphocyte developmental origins
Chen-Qu Suo, K. Polański, E. Dann, R. Lindeboom +8 more
2023bioRxiv2 citations Open access
Semantic Scholar
The emergence of goblet inflammatory or ITGB6hi nasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis
M. Woodall, A. Cujba, K. Worlock, K. Case +33 more
2023bioRxiv2 citations Open access
Semantic Scholar
Chromatin regulates genome-wide transcription factor binding affinities
Hannah K. Neikes, R. Lindeboom, Cathrin Gräwe, L. Lamers +6 more
2022bioRxiv2 citations Open access
Semantic Scholar

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