Works by de Ridder, Dick

Results: 85

PanTools: representation, storage and exploration of pan-genomic data.

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i487, doi. 10.1093/bioinformatics/btw455

By:

Sheikhizadeh, Siavash;
Schranz, M. Eric;
Akdel, Mehmet;
de Ridder, Dick;
Smit, Sandra

Publication type:

Article

ACE: accurate correction of errors using K-mer tries.

Published in:

Bioinformatics, 2015, v. 31, n. 19, p. 3216, doi. 10.1093/bioinformatics/btv332

By:

Sheikhizadeh, Siavash;
de Ridder, Dick

Publication type:

Article

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.

Published in:

Bioinformatics, 2013, v. 29, n. 22, p. 2826, doi. 10.1093/bioinformatics/btt502

By:

Nijkamp, Jurgen F.;
Pop, Mihai;
Reinders, Marcel J. T.;
de Ridder, Dick

Publication type:

Article

De novo detection of copy number variation by co-assembly.

Published in:

Bioinformatics, 2012, v. 28, n. 24, p. 3195, doi. 10.1093/bioinformatics/bts601

By:

Nijkamp, Jurgen F.;
van den Broek, Marcel A.;
Geertman, Jan-Maarten A.;
Reinders, Marcel J. T.;
Daran, Jean-Marc G.;
de Ridder, Dick

Publication type:

Article

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

Published in:

Bioinformatics, 2012, v. 28, n. 11, p. 1429, doi. 10.1093/bioinformatics/bts175

By:

Gritsenko, Alexey A.;
Nijkamp, Jurgen F.;
Reinders, Marcel J.T.;
Ridder, Dick de

Publication type:

Article

Integrating genome assemblies with MAIA.

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. i433, doi. 10.1093/bioinformatics/btq366

By:

Nijkamp, Jurgen;
Winterbach, Wynand;
Van den Broek, Marcel;
Daran, Jean-Marc;
Reinders, Marcel;
De Ridder, Dick

Publication type:

Article

Maximum significance clustering of oligonucleotide microarrays.

Published in:

Bioinformatics, 2006, v. 22, n. 3, p. 326, doi. 10.1093/bioinformatics/bti788

By:

Dick de Ridder;
Frank J. T. Staal;
Jacques J. M. van Dongen;
Marcel J. T. Reinders

Publication type:

Article

Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration.

Published in:

Advanced Science, 2024, v. 11, n. 36, p. 1, doi. 10.1002/advs.202401899

By:

Yang, Meixin;
Smit, Sandra;
de Ridder, Dick;
Feng, Jie;
Liu, Taiguo;
Xu, Jinrong;
van der Lee, Theo A. J.;
Zhang, Hao;
Chen, Wanquan

Publication type:

Article

Allelic variants confer Arabidopsis adaptation to small regional environmental differences.

Published in:

Plant Journal, 2024, v. 120, n. 4, p. 1662, doi. 10.1111/tpj.17067

By:

Wijfjes, Raúl Y.;
Boesten, René;
Becker, Frank F. M.;
Theeuwen, Tom P. J. M.;
Snoek, Basten L.;
Mastoraki, Maria;
Verheijen, Jelle J.;
Güvencli, Nuri;
Denkers, Lissy‐Anne M.;
Koornneef, Maarten;
van Eeuwijk, Fred A.;
Smit, Sandra;
de Ridder, Dick;
Aarts, Mark G. M.

Publication type:

Article

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

Published in:

Plant Journal, 2024, v. 117, n. 4, p. 1281, doi. 10.1111/tpj.16546

By:

Correa Marrero, Miguel;
Capdevielle, Sylvain;
Huang, Weijie;
Al‐Subhi, Ali M.;
Busscher, Marco;
Busscher‐Lange, Jacqueline;
van der Wal, Froukje;
de Ridder, Dick;
van Dijk, Aalt D. J.;
Hogenhout, Saskia A.;
Immink, Richard G. H.

Publication type:

Article

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light‐use efficiency.

Published in:

Plant Journal, 2022, v. 112, n. 5, p. 1298, doi. 10.1111/tpj.16005

By:

Garassino, Francesco;
Wijfjes, Raúl Y.;
Boesten, René;
Reyes Marquez, Francisca;
Becker, Frank F. M.;
Clapero, Vittoria;
van den Hatert, Iris;
Holmer, Rens;
Schranz, M. Eric;
Harbinson, Jeremy;
de Ridder, Dick;
Smit, Sandra;
Aarts, Mark G. M.

Publication type:

Article

DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom.

Published in:

Plant Journal, 2018, v. 95, n. 4, p. 686, doi. 10.1111/tpj.13979

By:

Demirci, Sevgin;
Peters, Sander A.;
de Ridder, Dick;
van Dijk, Aalt D. J.

Publication type:

Article

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 3, p. 1, doi. 10.1371/journal.pcbi.1008197

By:

Durairaj, Janani;
Melillo, Elena;
Bouwmeester, Harro J.;
Beekwilder, Jules;
de Ridder, Dick;
van Dijk, Aalt D. J.

Publication type:

Article

Exploring intra‐ and intergenomic variation in haplotype‐resolved pangenomes.

Published in:

Plant Biotechnology Journal, 2025, v. 23, n. 3, p. 874, doi. 10.1111/pbi.14545

By:

Jonkheer, Eef M.;
de Ridder, Dick;
van der Lee, Theo A. J.;
de Haan, Jorn R.;
Berke, Lidija;
Smit, Sandra

Publication type:

Article

Insight into Neutral and Disease-Associated Human Genetic Variants through Interpretable Predictors.

Published in:

PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0120729

By:

van den Berg, Bastiaan A.;
Reinders, Marcel J. T.;
de Ridder, Dick;
de Beer, Tjaart A. P.

Publication type:

Article

Exploring Sequence Characteristics Related to High-Level Production of Secreted Proteins in Aspergillus niger.

Published in:

PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0045869

By:

den Berg, Bastiaan A. van;
Reinders, Marcel J. T.;
Hulsman, Marc;
Liang Wu;
Pel, Herman J.;
Roubos, Johannes A.;
de Ridder, Dick

Publication type:

Article

Understanding Regulation of Metabolism through Feasibility Analysis.

Published in:

PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0039396

By:

Nikerel, Emrah;
Berkhout, Jan;
Fengyuan Hu;
Teusink, Bas;
Reinders, Marcel J. T.;
De Ridder, Dick

Publication type:

Article

GATA3 Expression Is Decreased in Psoriasis and during Epidermal Regeneration; Induction by Narrow-Band UVB and IL-4.

Published in:

PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0019806

By:

Rácz, Emõke;
Kurek, Dorota;
Kant, Marius;
Baerveldt, Ewout M.;
Florencia, Edwin;
Mourits, Sabine;
Ridder, Dick de;
Laman, Jon D.;
Fits, Leslie van der;
Prens, Errol P.

Publication type:

Article

Hecaton: reliably detecting copy number variation in plant genomes using short read sequencing data.

Published in:

BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-6153-8

By:

Wijfjes, Raúl Y.;
Smit, Sandra;
de Ridder, Dick

Publication type:

Article

Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction.

Published in:

BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06081-9

By:

Capela, João;
Zimmermann-Kogadeeva, Maria;
Dijk, Aalt D. J. van;
de Ridder, Dick;
Dias, Oscar;
Rocha, Miguel

Publication type:

Article

Shifts in growth strategies reflect tradeoffs in cellular economics.

Published in:

Molecular Systems Biology, 2009, v. 5, n. 1, p. 323, doi. 10.1038/msb.2009.82

By:

Molenaar, Douwe;
van Berlo, Rogier;
de Ridder, Dick;
Teusink, Bas

Publication type:

Article

Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD.

Published in:

PLoS Genetics, 2020, v. 16, n. 9, p. 1, doi. 10.1371/journal.pgen.1009027

By:

Groß, Christian;
Bortoluzzi, Chiara;
de Ridder, Dick;
Megens, Hendrik-Jan;
Groenen, Martien A. M.;
Reinders, Marcel;
Bosse, Mirte

Publication type:

Article

Uncovering the Role of Metabolism in Oomycete–Host Interactions Using Genome-Scale Metabolic Models.

Published in:

Frontiers in Microbiology, 2021, p. 1, doi. 10.3389/fmicb.2021.748178

By:

Rodenburg, Sander Y. A.;
Seidl, Michael F.;
de Ridder, Dick;
Govers, Francine

Publication type:

Article

A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33023-3

By:

Götz, Markus;
Barth, Anders;
Bohr, Søren S.-R.;
Börner, Richard;
Chen, Jixin;
Cordes, Thorben;
Erie, Dorothy A.;
Gebhardt, Christian;
Hadzic, Mélodie C. A. S.;
Hamilton, George L.;
Hatzakis, Nikos S.;
Hugel, Thorsten;
Kisley, Lydia;
Lamb, Don C.;
de Lannoy, Carlos;
Mahn, Chelsea;
Dunukara, Dushani;
de Ridder, Dick;
Sanabria, Hugo;
Schimpf, Julia

Publication type:

Article

CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations.

Published in:

Genome Medicine, 2020, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13073-020-00775-w

By:

Li, Shuang;
van der Velde, K. Joeri;
de Ridder, Dick;
van Dijk, Aalt D. J.;
Soudis, Dimitrios;
Zwerwer, Leslie R.;
Deelen, Patrick;
Hendriksen, Dennis;
Charbon, Bart;
van Gijn, Marielle E.;
Abbott, Kristin;
Sikkema-Raddatz, Birgit;
van Diemen, Cleo C.;
Kerstjens-Frederikse, Wilhelmina S.;
Sinke, Richard J.;
Swertz, Morris A.

Publication type:

Article

The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool.

Published in:

BMC Genomics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12864-021-07583-5

By:

Jonkheer, Eef M.;
Brankovics, Balázs;
Houwers, Ilse M.;
van der Wolf, Jan M.;
Bonants, Peter J. M.;
Vreeburg, Robert A. M.;
Bollema, Robert;
de Haan, Jorn R.;
Berke, Lidija;
Smit, Sandra;
de Ridder, Dick;
van der Lee, Theo A. J.

Publication type:

Article

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 51, doi. 10.1186/s12859-016-1305-1

By:

van Dijk, Aalt D. J.;
Lähdesmäki, Harri;
de Ridder, Dick;
Rousu, Juho

Publication type:

Article

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/s12859-015-0806-7

By:

Aflitos, Saulo Alves;
Severing, Edouard;
Sanchez-Perez, Gabino;
Peters, Sander;
de Jong, Hans;
de Ridder, Dick

Publication type:

Article

Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients.

Published in:

2008

By:

Howe, Steven J.;
Mansour, Marc R.;
Schwarzwaelder, Kerstin;
Bartholomae, Cynthia;
Hubank, Michael;
Kempski, Helena;
Brugman, Martijn H.;
Pike-Overzet, Karin;
Chatters, Stephen J.;
de Ridder, Dick;
Gilmour, Kimberly C.;
Adams, Stuart;
Thornhill, Susannah I.;
Parsley, Kathryn L.;
Staal, Frank J.T.;
Gale, Rosemary E.;
Linch, David C.;
Bayford, Jinhua;
Brown, Lucie;
Quaye, Michelle

Publication type:

journal article

Gammaretrovirus-mediated correction of SCID-X1 is associated with skewed vector integration site distribution in vivo.

Published in:

2007

By:

Schwarzwaelder, Kerstin;
Howe, Steven J.;
Schmidt, Manfred;
Brugman, Martijn H.;
Deichmann, Annette;
Glimm, Hanno;
Schmidt, Sonja;
Prinz, Claudia;
Wissler, Manuela;
King, Douglas J. S.;
Fang Zhang;
Parsley, Kathryn L.;
Gilmour, Kimberly C.;
Sinclair, Joanna;
Bayford, Jinhua;
Peraj, Rachel;
Pike-Overzet, Karin;
Staal, Frank J. T.;
de Ridder, Dick;
Kinnon, Christine

Publication type:

journal article

Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy.

Published in:

2007

By:

Deichmann, Annette;
Hacein-Bey-Abina, Salima;
Schmidt, Manfred;
Garrigue, Alexandrine;
Brugman, Martijn H.;
Jingqiong Hu;
Glimm, Hanno;
Gyapay, Gabor;
Prum, Bernard;
Fraser, Christopher C.;
Fischer, Nicolas;
Schwarzwaelder, Kerstin;
Siegler, Maria-Luise;
de Ridder, Dick;
Pike-Overzet, Karin;
Howe, Steven J.;
Thrasher, Adrian J.;
Wagemaker, Gerard;
Abel, Ulrich;
Staal, Frank J. T.

Publication type:

journal article

pCADD: SNV prioritisation in Sus scrofa.

Published in:

Genetics Selection Evolution, 2020, v. 52, n. 1, p. 1, doi. 10.1186/s12711-020-0528-9

By:

Groß, Christian;
Derks, Martijn;
Megens, Hendrik-Jan;
Bosse, Mirte;
Groenen, Martien A. M.;
Reinders, Marcel;
de Ridder, Dick

Publication type:

Article

How Biochemical Constraints of Cellular Growth Shape Evolutionary Adaptations in Metabolism.

Published in:

Genetics, 2013, v. 194, n. 2, p. 505, doi. 10.1534/genetics.113.150631

By:

Berkhout, Jan;
Bosdriesz, Evert;
Nikerel, Emrah;
Molenaar, Douwe;
de Ridder, Dick;
Teusink, Bas;
Bruggeman, Frank J.

Publication type:

Article

Genome‐wide characterization of <italic>Phytophthora infestans</italic> metabolism: a systems biology approach.

Published in:

Molecular Plant Pathology, 2018, v. 19, n. 6, p. 1403, doi. 10.1111/mpp.12623

By:

Rodenburg, Sander Y. A.;
Seidl, Michael F.;
de Ridder, Dick;
Govers, Francine

Publication type:

Article

Dysregulated signaling, proliferation and apoptosis impact on the pathogenesis of TCRγδ+ T cell large granular lymphocyte leukemia.

Published in:

PLoS ONE, 2017, v. 12, n. 4, p. 1, doi. 10.1371/journal.pone.0175670

By:

Kallemeijn, Martine J.;
de Ridder, Dick;
Schilperoord-Vermeulen, Joyce;
van der Klift, Michèle Y.;
Sandberg, Yorick;
van Dongen, Jacques J. M.;
Langerak, Anton W.

Publication type:

Article

Topology of molecular interaction networks.

Published in:

BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-90

By:

Winterbach, Wynand;
Van Mieghem, Piet;
Reinders, Marcel;
Huijuan Wang;
de Ridder, Dick

Publication type:

Article

baseLess: lightweight detection of sequences in raw MinION data.

Published in:

Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbad017

By:

Noordijk, Ben;
Nijland, Reindert;
Carrion, Victor J;
Raaijmakers, Jos M;
Ridder, Dick de;
Lannoy, Carlos de

Publication type:

Article

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study.

Published in:

Briefings in Bioinformatics, 2018, v. 19, n. 3, p. 387, doi. 10.1093/bib/bbw126

By:

Motazedi, Ehsan;
Finkers, Richard;
Maliepaard, Chris;
de Ridder, Dick

Publication type:

Article

Making the difference: integrating structural variation detection tools.

Published in:

Briefings in Bioinformatics, 2015, v. 16, n. 5, p. 852, doi. 10.1093/bib/bbu047

By:

Ke Lin;
Smit, Sandra;
Bonnema, Guusje;
Sanchez-Perez, Gabino;
de Ridder, Dick

Publication type:

Article

Pattern recognition in bioinformatics.

Published in:

Briefings in Bioinformatics, 2013, v. 14, n. 5, p. 633, doi. 10.1093/bib/bbt020

By:

de Ridder, Dick;
de Ridder, Jeroen;
Reinders, Marcel J. T.

Publication type:

Article

Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.609117

By:

Farooq, Muhammad;
van Dijk, Aalt D. J.;
Nijveen, Harm;
Aarts, Mark G. M.;
Kruijer, Willem;
Nguyen, Thu-Phuong;
Mansoor, Shahid;
de Ridder, Dick

Publication type:

Article

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans.

Published in:

Database: The Journal of Biological Databases & Curation, 2020, v. 2020, p. 1, doi. 10.1093/database/baz149

By:

Snoek, Basten L;
Sterken, Mark G;
Hartanto, Margi;
Zuilichem, Albert-Jan van;
Kammenga, Jan E;
Ridder, Dick de;
Nijveen, Harm

Publication type:

Article

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2524-6

By:

Ferreira de Carvalho, Julie;
Oplaat, Carla;
Pappas, Nikolaos;
Derks, Martijn;
de Ridder, Dick;
Verhoeven, Koen J. F.

Publication type:

Article

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage.

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 250, doi. 10.1186/1471-2164-15-250

By:

Ke Lin;
Ningwen Zhang;
Severing, Edouard I;
Nijveen, Harm;
Feng Cheng;
Visser, Richard GF;
Xiaowu Wang;
de Ridder, Dick;
Bonnema, Guusje

Publication type:

Article

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 8, p. 1, doi. 10.1371/journal.pcbi.1004336

By:

Gritsenko, Alexey A.;
Hulsman, Marc;
Reinders, Marcel J. T.;
de Ridder, Dick

Publication type:

Article

Computational Estimation of the Composition of Fat/Oil Mixtures Containing Interesterifications from Gas and Liquid Chromatography Data.

Published in:

Journal of the American Oil Chemists' Society (JAOCS), 2005, v. 82, n. 10, p. 707, doi. 10.1007/s11746-005-1132-z

By:

Van Vliet, Martin H.;
Van Kempen, Geert M. P.;
Reinders, Marcel J. T.;
De Ridder, Dick

Publication type:

Article

91. Retroviral Vector Integrations Relate to Hematopoietic Stem Cell Gene Expression Patterns.

Published in:

Molecular Therapy, 2006, v. 13, p. S37, doi. 10.1016/j.ymthe.2006.08.110

By:

Brugman, Martijn H.;
Pike-Overzet, Karin;
Oerlemans-Bergs, Carla;
Swagemakers, Sigrid;
de Ridder, Dick;
Staal, Frank J. T.;
Verstegen, Monique M. A.;
Wagemaker, Gerard

Publication type:

Article

350. Ectopic Retroviral Expression of LMO2, but Not IL2Rγ, Blocks Human T-Cell Development from CD34+ Progenitor Cells: Implications for Gene Therapy.

Published in:

Molecular Therapy, 2006, v. 13, p. S133, doi. 10.1016/j.ymthe.2006.08.408

By:

Pike-Overzet, Karin;
de Ridder, Dick;
Weerkamp, Floor;
Baert, Miranda R. M.;
Verstegen, Monique M.;
Howe, Steven J.;
Thrasher, Adrian J.;
Wagemaker, Gerard;
van Dongen, Jacques J. M.;
Staal, Frank J. T.

Publication type:

Article

The use of proton transfer reaction mass spectrometry for high throughput screening of terpene synthases.

Published in:

Journal of Mass Spectrometry, 2023, v. 58, n. 6, p. 1, doi. 10.1002/jms.4951

By:

Di Girolamo, Alice;
Pedrotti, Michele;
Koot, Alex;
Verstappen, Francel;
van Houwelingen, Adèle;
Vossen, Celina;
Bouwmeester, Harro;
de Ridder, Dick;
Beekwilder, Jules

Publication type:

Article

Effective Treatment of Psoriasis with Narrow-Band UVB Phototherapy Is Linked to Suppression of the IFN and Th17 Pathways.

Published in:

Journal of Investigative Dermatology, 2011, v. 131, n. 7, p. 1547, doi. 10.1038/jid.2011.53

By:

Rácz, Emőke;
Prens, Errol P.;
Kurek, Dorota;
Kant, Marius;
de Ridder, Dick;
Mourits, Sabine;
Baerveldt, Ewout M.;
Ozgur, Zeliha;
van IJcken, Wilfred F. J.;
Laman, Jon D.;
Staal, Frank J.;
van der Fits, Leslie

Publication type:

Article