Dick de Ridder

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 30

Top Topics

Machine Learning

Atomic Force Microscopy

Dna Methylation

Single Molecule

Top Venues

Nature communications

Nature nanotechnology

Nucleic acids research

This page only lists publications with an associated author ORCID identifier.

Publications

Roven Rommel Fuentes, Ronald Nieuwenhuis, Jihed Chouaref, Thamara Hesselink, Willem van Dooijeweert, Hetty C van den Broeck, Elio Schijlen, Henk J Schouten, Yuling Bai, Paul Fransz, Maike Stam, Hans de Jong, Sara Diaz Trivino, Dick de Ridder, Aalt D J van Dijk, Sander A Peters
A catalogue of recombination coldspots in interspecific tomato hybrids. PLoS genetics 20 (7) (2024)
Sander Y A Rodenburg, Dick de Ridder, Francine Govers, Michael F Seidl
Oomycete Metabolism Is Highly Dynamic and Reflects Lifestyle Adaptations. Molecular plant-microbe interactions : MPMI (2024)
Roven Rommel Fuentes, Ronald Nieuwenhuis, Jihed Chouaref, Thamara Hesselink, Willem van Dooijeweert, Hetty C van den Broeck, Elio Schijlen, Henk J Schouten, Yuling Bai, Paul Fransz, Maike Stam, Hans de Jong, Sara Diaz Trivino, Dick de Ridder, Aalt D J van Dijk, Sander A Peters
A catalogue of recombination coldspots in interspecific tomato hybrids. PLoS genetics 20 (7) (2024)
Mike Filius, Raman van Wee, Carlos de Lannoy, Ilja Westerlaken, Zeshi Li, Sung Hyun Kim, Cecilia de Agrela Pinto, Yunfei Wu, Geert-Jan Boons, Martin Pabst, Dick de Ridder, Chirlmin Joo
Full-length single-molecule protein fingerprinting. Nature nanotechnology 19 (5) (2024)
Sander Y A Rodenburg, Dick de Ridder, Francine Govers, Michael F Seidl
Oomycete Metabolism Is Highly Dynamic and Reflects Lifestyle Adaptations. Molecular plant-microbe interactions : MPMI 37 (7) (2024)
Roven Rommel Fuentes, Ronald Nieuwenhuis, Jihed Chouaref, Thamara Hesselink, Willem van Dooijeweert, Hetty C van den Broeck, Elio Schijlen, Henk J Schouten, Yuling Bai, Paul Fransz, Maike Stam, Hans de Jong, Sara Diaz Trivino, Dick de Ridder, Aalt D J van Dijk, Sander A Peters
A catalogue of recombination coldspots in interspecific tomato hybrids. PLoS genetics 20 (7) (2024)
Roven Rommel Fuentes, Ronald Nieuwenhuis, Jihed Chouaref, Thamara Hesselink, Willem van Dooijeweert, Hetty C van den Broeck, Elio Schijlen, Henk J Schouten, Yuling Bai, Paul Fransz, Maike Stam, Hans de Jong, Sara Diaz Trivino, Dick de Ridder, Aalt D J van Dijk, Sander A Peters
A catalogue of recombination coldspots in interspecific tomato hybrids. PLoS genetics 20 (7) (2024)
Mike Filius, Raman van Wee, Carlos de Lannoy, Ilja Westerlaken, Zeshi Li, Sung Hyun Kim, Cecilia de Agrela Pinto, Yunfei Wu, Geert-Jan Boons, Martin Pabst, Dick de Ridder, Chirlmin Joo
Full-length single-molecule protein fingerprinting. Nature nanotechnology (2024)
Markus Götz, Anders Barth, Søren S-R Bohr, Richard Börner, Jixin Chen, Thorben Cordes, Dorothy A Erie, Christian Gebhardt, Mélodie C A S Hadzic, George L Hamilton, Nikos S Hatzakis, Thorsten Hugel, Lydia Kisley, Don C Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A M Seidel, Roland K O Sigel, Magnus B Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R Weninger, Pengning Xu, Sonja Schmid
Reply to: On the statistical foundation of a recent single molecule FRET benchmark. Nature communications 15 (1) (2024)
Markus Götz, Anders Barth, Søren S-R Bohr, Richard Börner, Jixin Chen, Thorben Cordes, Dorothy A Erie, Christian Gebhardt, Mélodie C A S Hadzic, George L Hamilton, Nikos S Hatzakis, Thorsten Hugel, Lydia Kisley, Don C Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A M Seidel, Roland K O Sigel, Magnus B Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R Weninger, Pengning Xu, Sonja Schmid
Reply to: On the statistical foundation of a recent single molecule FRET benchmark. Nature communications 15 (1) (2024)
Markus Götz, Anders Barth, Søren S-R Bohr, Richard Börner, Jixin Chen, Thorben Cordes, Dorothy A Erie, Christian Gebhardt, Mélodie C A S Hadzic, George L Hamilton, Nikos S Hatzakis, Thorsten Hugel, Lydia Kisley, Don C Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A M Seidel, Roland K O Sigel, Magnus B Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R Weninger, Pengning Xu, Sonja Schmid
Reply to: On the statistical foundation of a recent single molecule FRET benchmark. Nature communications 15 (1) (2024)
Mike Filius, Raman van Wee, Carlos de Lannoy, Ilja Westerlaken, Zeshi Li, Sung Hyun Kim, Cecilia de Agrela Pinto, Yunfei Wu, Geert-Jan Boons, Martin Pabst, Dick de Ridder, Chirlmin Joo
Full-length single-molecule protein fingerprinting. Nature nanotechnology (2024)
Thijs Nieuwkoop, Barbara R Terlouw, Katherine G Stevens, Richard A Scheltema, Dick de Ridder, John van der Oost, Nico J Claassens
Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning. Nucleic acids research 51 (5) (2023)
Ben Noordijk, Reindert Nijland, Victor J Carrion, Jos M Raaijmakers, Dick de Ridder, Carlos de Lannoy
baseLess: lightweight detection of sequences in raw MinION data. Bioinformatics advances 3 (1) (2023)
Thijs Nieuwkoop, Barbara R Terlouw, Katherine G Stevens, Richard A Scheltema, Dick de Ridder, John van der Oost, Nico J Claassens
Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning. Nucleic acids research 51 (5) (2023)
Ben Noordijk, Reindert Nijland, Victor J Carrion, Jos M Raaijmakers, Dick de Ridder, Carlos de Lannoy
baseLess: lightweight detection of sequences in raw MinION data. Bioinformatics advances 3 (1) (2023)
Thijs Nieuwkoop, Barbara R Terlouw, Katherine G Stevens, Richard A Scheltema, Dick de Ridder, John van der Oost, Nico J Claassens
Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning. Nucleic acids research (2023)
Markus Götz, Anders Barth, Søren S-R Bohr, Richard Börner, Jixin Chen, Thorben Cordes, Dorothy A Erie, Christian Gebhardt, Mélodie C A S Hadzic, George L Hamilton, Nikos S Hatzakis, Thorsten Hugel, Lydia Kisley, Don C Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A M Seidel, Roland K O Sigel, Magnus Berg Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R Weninger, Pengning Xu, Sonja Schmid
A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories. Nature communications 13 (1) (2022)
Eef M Jonkheer, Dirk-Jan M van Workum, Siavash Sheikhizadeh Anari, Balázs Brankovics, Jorn R de Haan, Lidija Berke, Theo A J van der Lee, Dick de Ridder, Sandra Smit
PanTools v3: functional annotation, classification and phylogenomics. Bioinformatics (Oxford, England) 38 (18) (2022)
Margi Hartanto, Asif Ahmed Sami, Dick de Ridder, Harm Nijveen
Prioritizing candidate eQTL causal genes in Arabidopsis using RANDOM FORESTS. G3 (Bethesda, Md.) 12 (11) (2022)
Janani Durairaj, Elena Melillo, Harro J Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D J van Dijk
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. PLoS computational biology 17 (3) (2021)
Margi Hartanto, Ronny V L Joosen, Basten L Snoek, Leo A J Willems, Mark G Sterken, Dick de Ridder, Henk W M Hilhorst, Wilco Ligterink, Harm Nijveen
Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana. G3 (Bethesda, Md.) 10 (11) (2020)
Christian Groß, Chiara Bortoluzzi, Dick de Ridder, Hendrik-Jan Megens, Martien A M Groenen, Marcel J T Reinders, Mirte Bosse
Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD. PLoS genetics 16 (9) (2020)
Raúl Y Wijfjes, Sandra Smit, Dick de Ridder
Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data. BMC genomics 20 (1) (2019)
Sander Y A Rodenburg, Michael F Seidl, Howard S Judelson, Andrea L Vu, Francine Govers, Dick de Ridder
Metabolic Model of the Phytophthora infestans-Tomato Interaction Reveals Metabolic Switches during Host Colonization. mBio 10 (4) (2019)
Dick de Ridder
Artificial intelligence in the lab: ask not what your computer can do for you. Microbial biotechnology 12 (1) (2018)
Miguel Correa Marrero, Aalt D J van Dijk, Dick de Ridder
Sequence-based analysis of protein degradation rates. Proteins 85 (9) (2017)
Harm Nijveen, Wilco Ligterink, Joost J B Keurentjes, Olivier Loudet, Jiao Long, Mark G Sterken, Henk W M Hilhorst, Dick de Ridder, Jan E Kammenga, Basten L Snoek
AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana. The Plant journal : for cell and molecular biology 89 (6) (2017)
Alexey A Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal
Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity. PLoS computational biology 13 (9) (2017)
Luca Santuari, Gabino F Sanchez-Perez, Marijn Luijten, Bas Rutjens, Inez Terpstra, Lidija Berke, Maartje Gorte, Kalika Prasad, Dongping Bao, Johanna L P M Timmermans-Hereijgers, Kenichiro Maeo, Kenzo Nakamura, Akie Shimotohno, Ales Pencik, Ondřej Novák, Karen Ljung, Sebastiaan van Heesch, Ewart de Bruijn, Edwin Cuppen, Viola Willemsen, Anne-Maarit Bågman, Wolfgang Lukowitz, Berend Snel, Dick de Ridder, Ben Scheres, Renze Heidstra
The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots. The Plant cell 28 (12) (2016)