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Integration of -omics data

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Research Projects

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Publications

Domestication Shapes Recombination Patterns in Tomato

Fuentes, R.R. , Ridder, D. de , Dijk, A.D.J. van , Peters, S.A. (2021) Molecular Biology and Evolution (2021). - ISSN 0737-4038
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases

Durairaj, J. , Melillo, E. , Bouwmeester, H.J. , Beekwilder, M.J. , Ridder, D. de , Dijk, A.D.J. van (2021) PLoS Computational Biology 17 (2021)3. - ISSN 1553-734X
Chasing breeding footprints through structural variations in Cucumis melo and wild relatives

Demirci, S. , Fuentes, Roven , Dooijeweert, W. van , Aflitos, S.A. , Schijlen, E.G.W.M. , Hesselink, T. , Ridder, D. de , Dijk, A.D.J. van , Peters, S.A. (2021) G3 : Genes Genomes Genetics 11 (2021)1. - ISSN 2160-1836
The santalene synthase from Cinnamomum camphora: Reconstruction of a sesquiterpene synthase from a monoterpene synthase

Girolamo, A. Di , Durairaj, J. , Houwelingen, A.M.M.L. van , Verstappen, F.W.A. , Bosch, H.J. , Cankar, K. , Bouwmeester, H.J. , Ridder, D. de , Dijk, A.D.J. van , Beekwilder, M.J. (2020) Archives of Biochemistry and Biophysics 695 (2020). - ISSN 0003-9861 - 12 p.
Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing

Rommel Fuentes, Roven , Hesselink, T. , Nieuwenhuis, Ronald , Bakker, L.V. , Schijlen, E.G.W.M. , Dooijeweert, W. van , Diaz Trivino, S. , Haan, Jorn R. de , Sanchez Perez, G.F. , Zhang, Xinyue , Fransz, Paul , Jong, J.H.S.G.M. de , Dijk, A.D.J. van , Ridder, D. de , Peters, S.A. (2020) The Plant Journal 102 (2020)3. - ISSN 0960-7412 - p. 480 - 492.
Integrative pangenome analysis of the Pectobacterium genus

Jonkheer, Eef , Brankovics, Balázs , Houwers, I.M. , Wolf, J.M. van der , Bonants, P.J.M. , Vreeburg, R.A.M. , Sheikhizadeh Anari, S. , Ridder, D. de , Smit, S. , Lee, T.A.J. van der (2019)
Profile hidden Markov models trained on aligned KEGG Orthology sequences for enzyme annotation

Rodenburg, Y.A. , Ridder, D. de , Govers, F. , Seidl, M.F. (2019) : Wageningen University & Research
The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters

Thines, M. , Sharma, R. , Rodenburg, Y.A. , Gogleva, A. , Judelson, H.S. , Xia, X. , Hoogen, D.J. van den , Kitner, M. , Klein, J. , Neilen, M. , Ridder, D. de , Seidl, M.F. , Ackerveken, G. van den , Govers, F. , Schornack, S. , Studholme, D.J. (2019) : BioRxiv
poreTally: run and publish de novo nanopore assembler benchmarks

Lannoy, Carlos de , Risse, J.E. , Ridder, D. de (2019) Bioinformatics 35 (2019)15. - ISSN 1367-4803 - p. 2663 - 2664.
Improved inference of intermolecular contacts through protein–protein interaction prediction using coevolutionary analysis

Correa Marrero, M. , Immink, G.H. , Ridder, D. de , Dijk, A.D.J. van (2019) Bioinformatics 35 (2019)12. - ISSN 1367-4803 - p. 2036 - 2042.

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