Author

D. de Ridder

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 5 Plant Biology· 4 Evolutionary Biology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 5 Organism:Arabidopsis· 4 Assay:proteomics· 4 Approach:deep learning· 3 Research Focus:host-pathogen & immune response· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Assay:fluorescence / live-cell microscopy· 2

Frequent Co-Authors

C. de Lannoy· 4 shared C. Joo· 3 shared M. Filius· 3 shared B. L. Snoek· 2 shared H. Nijveen· 2 shared M. Hartanto· 2 shared R. van Wee· 2 shared S. H. Kim· 2 shared

Activity by Year

2020-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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4 shared papersBiophysics

C. de Lannoy

Mutual co-authors in cluster

Author profile →

11 papers

Recent·Most cited

Full-Length Single-Molecule Protein Fingerprinting

M. Filius, R. van Wee, C. de Lannoy, I. Westerlaken, Z. Li, S. H. Kim, C. de Agrela Pinto, Y. Wu, G.-J. Boons, M. Pabst, D. de Ridder, C. Joo

This paper introduces a method to map amino acid positions and post-translational modifications in single protein molecules with sub-nanometer resolution using FRET-based single-molecule protein fingerprinting.

bioRxiv · Sep 26, 2023Biophysics

Allelic variants confer Arabidopsis adaptation to mild environmental clines

R. Y. Wijfjes, R. Boesten, F. F. M. Becker, T. P. J. M. Theeuwen, B. L. Snoek, M. Mastoraki, J. J. Verheijen, N. Guvencli, L.-A. M. Denkers, M. Koornneef, F. A. van Eeuwijk, S. Smit, D. de Ridder, M. G. M. Aarts

This study identifies allelic variants in Arabidopsis thaliana that confer adaptation to mild environmental clines in the Netherlands.

bioRxiv · Sep 18, 2023Plant Biology

Nanopores reveal the stoichiometry of single oligo-adenylates produced by type III CRISPR-Cas

D. Fuentenebro-Navas, J. A. Steens, C. De Lannoy, B. Noordijk, D. de Ridder, R. H. J. Staals, S. Schmid

This study uses a nanopore assay with a CNN to detect and determine the stoichiometry of single cOAs produced by type III CRISPR-Cas systems.

bioRxiv · Aug 18, 2023 · PreprintBiophysics

Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems

D. Calderon-Franco, F. Corbera-Rubio, M. Cuesta-Sanz, B. Pieterse, D. de Ridder, M. van Loosdrecht, D. van Halem, M. Laureni, D. G. Weissbrodt

This study analyzes antibiotic resistance determinants in chlorine-free drinking water treatment plants using metagenomics and quantitative PCR, finding reduced ARGs and MGEs despite increases in disinfection sub-units.

Water Research · May 1, 2023Peer-reviewedMicrobiology

Prioritizing Candidate eQTL Causal Genes in Arabidopsis using Random Forests

M. Hartanto, A. A. Sani, D. de Ridder, H. Nijveen

This study improves eQTL causal gene prioritization in Arabidopsis using machine learning, achieving high accuracy in identifying potential causal genes.

bioRxiv · Apr 6, 2022Plant Biology

Inferring kinetic rate constants from single-molecule FRET trajectories - a blind benchmark of kinetic analysis tools

M. Götz, A. Barth, S. S.- R. Bohr, R. Börner, J. Chen, T. Cordes, D. A. Erie, C. Gebhardt, M. C. A. S. Hadzic, G. L. Hamilton, N. S. Hatzakis, T. Hugel, L. Kisley, D. C. Lamb, C. de Lannoy, , S. Schmid

This study benchmarks eleven tools for inferring kinetic rate constants from smFRET trajectories using simulated and experimental data with varying challenges.

bioRxiv · Nov 23, 2021Biophysics

Evaluation of FRET X for Single-Molecule Protein Fingerprinting

C. de Lannoy, M. Filius, R. van Wee, C. Joo, D. de Ridder

The paper evaluates FRET X fingerprinting for single-molecule protein identification through simulations and experiments, achieving 95% accuracy in identifying proteins from a complex mixture.

bioRxiv · Jun 30, 2021Biophysics

FRETboard: semi-supervised classification of FRET traces

C. V. de Lannoy, M. Filius, S. H. Kim, C. Joo, D. de Ridder

FRETboard is a semi-supervised tool for classifying FRET traces, improving efficiency and accuracy compared to manual methods and existing software.

bioRxiv · Aug 28, 2020Biophysics

Network analysis prioritizes DEWAX and ICE1 as the candidate genes for two major eQTL hotspots in seed germination

M. Hartanto, R. V. L. Joosen, B. L. Snoek, L. A. J. Willems, M. G. Sterken, D. de Ridder, H. W. M. Hilhorst, W. Ligterink, H. Nijveen

The paper identifies DEWAX and ICE1 as key regulatory genes for eQTL hotspots in seed germination through network analysis.

bioRxiv · Apr 29, 2020Plant Biology

Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors

M. Correa Marrero, S. Capdevielle, W. Huang, A. M. Al-Subhi, M. Busscher, J. Busscher-Lange, F. van der Wal, D. de Ridder, A. D. J. van Dijk, S. A. Hogenhout, R. G. H. Immink

The paper maps protein interactions between phytoplasma effectors and Arabidopsis transcription factors, revealing specific targeting of development-related factors and unique infection strategies.

bioRxiv · Feb 13, 2020Plant Biology

Oomycete metabolism is highly dynamic and reflects lifestyle adaptations

S. Y. A. Rodenburg, D. de Ridder, F. Govers, M. F. Seidl

This study compares oomycete metabolism across different lifestyles, finding that obligate biotrophs show convergent gene loss and reductive evolution in their metabolic networks.

bioRxiv · Feb 12, 2020Evolutionary Biology