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Integration of -omics data

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Research Projects

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Publications

PanTools v3: functional annotation, classification and phylogenomics

Jonkheer, E.M. , Workum, F.J.M. van , Sheikhizadeh Anari, S. , Brankovics, B. , Haan, J.R. de , Berke, Lidija , Lee, T.A.J. van der , Ridder, D. de , Smit, S. (2022) Bioinformatics 38 (2022)18. - ISSN 1367-4803 - p. 4403 - 4405.
Domestication Shapes Recombination Patterns in Tomato

Fuentes, R.R. , Ridder, D. de , Dijk, A.D.J. van , Peters, S.A. (2022) Molecular Biology and Evolution 39 (2022)1. - 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
Oomycete metabolism is highly dynamic and reflects lifestyle adaptations

Rodenburg, Y.A. , Ridder, D. de , Govers, F. , Seidl, M.F. (2020) : BioRxiv - p.
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.
PanTools

Nijveen, H. , Smit, S. , Medema, M.H. , Ridder, D. de , Dijk, A.D.J. van , Jonkheer, E.M. , Hooft, J.J.J. van der , Lankveld, T. van , Moed, M. , Workum, F.J.M. van (2019) Wageningen : Wageningen University & Research
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

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