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Integration of -omics data

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Research Projects

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Publications

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.
Pangenome analysis and its application on Pectobacterium
Jonkheer, Eef , Smit, S. , Ridder, D. de , Brankovics, Balázs , Houwers, I.M. , Wolf, J.M. van der , Bonants, P.J.M. , Vreeburg, R.A.M. , Lee, T.A.J. van der (2018)
Comparative genomics including the basal pathogen Peronospora belbahrii reveal common evolutionary patterns and the monophyly of downy mildews in a paraphyletic Phytophthora
Thines, M. , Sharma, R. , Rodenburg, Y.A. , Gogleva, A. , Judelson, H.S. , Xia, X. , Hoogen, D.J. van den , Kitner, M. , Klein, J. , Ridder, D. de , Seidl, M.F. , Ackerveken, G. van den , Govers, F. , Schornack, S. , Studholme, D.J. (2018) : IPF
In silico predictions of variant deleteriousness in the genomes of pig species
Gross, Christian , Derks, M. , Ridder, D. de , Reinders, M. (2018)
Correcting palindromes in long reads after whole-genome amplification
Warris, S. , Schijlen, E.G.W.M. , Geest, H.C. van de , Vegesna, R. , Hesselink, T. , Lintel Hekkert, B. te , Sanchez Perez, G.F. , Medvedev, P. , Makova, K.D. , Ridder, D. de (2018) BMC Genomics 19 (2018). - ISSN 1471-2164
Genome-wide characterization of Phytophthora infestans metabolism : a systems biology approach
Rodenburg, Y.A. , Seidl, M.F. , Ridder, D. de , Govers, F. (2018) Molecular Plant Pathology 19 (2018)6. - ISSN 1464-6722 - p. 1403 - 1413.

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