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Publications of the Bioinformatics Group

View the complete publication list of the Bioinformatics Group in the Research@WUR database.

Latest Peer Reviewed Publications

Machine learning in plant science and plant breeding

Dijk, Aalt Dirk Jan van , Kootstra, Gert , Kruijer, Willem , Ridder, Dick de (2021) iScience 24 (2021)1. - ISSN 2589-0042
Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines

Wang, Yan , Correa Marrero, Miguel , Medema, Marnix H. , Dijk, Aalt D.J. van (2020) Bioinformatics 36 (2020)19. - ISSN 1367-4803 - p. 4846 - 4853.
Pan-genome analysis and ancestral state reconstruction of class halobacteria : probability of a new super-order

Gaba, Sonam , Kumari, Abha , Medema, Marnix , Kaushik, Rajeev (2020) Scientific Reports 10 (2020)1. - ISSN 2045-2322
Restoring degraded microbiome function with self-assembled communities

Landazuri, Carlos Fernando Gutierrez , Gomez, Janeth Sanabria , Raaijmakers, Jos M. , Oyserman, Ben O. (2020) FEMS microbiology ecology 96 (2020)12. - ISSN 0168-6496
Bracon brevicornis genome showcases the potential of linked-read sequencing in identifying a putative Complementary sex determiner gene

Ferguson, Kim B. , Pannebakker, Bart A. , Centurión, Alejandra , Heuvel, Joost van den , Nieuwenhuis, Ronald , Becker, Frank F.M. , Schijlen, Elio , Thiel, Andra , Zwaan, Bas J. , Verhulst, Eveline C. (2020) Genes 11 (2020)12. - ISSN 2073-4425 - p. 1 - 13.
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Tripathi, Anupriya , Vázquez-Baeza, Yoshiki , Gauglitz, Julia M. , Wang, Mingxun , Dührkop, Kai , Nothias-Esposito, Mélissa , Acharya, Deepa D. , Ernst, Madeleine , Hooft, Justin J.J. van der , Zhu, Qiyun , McDonald, Daniel , Brejnrod, Asker D. , Gonzalez, Antonio , Handelsman, Jo , Fleischauer, Markus , Ludwig, Marcus , Böcker, Sebastian , Nothias, Louis Félix , Knight, Rob , Dorrestein, Pieter C. (2020) Nature Chemical Biology (2020). - ISSN 1552-4450
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

Aksenov, Alexander A. , Laponogov, Ivan , Zhang, Zheng , Doran, Sophie L.F. , Belluomo, Ilaria , Veselkov, Dennis , Bittremieux, Wout , Nothias, Louis Felix , Nothias-Esposito, Mélissa , Maloney, Katherine N. , Misra, Biswapriya B. , Melnik, Alexey V. , Smirnov, Aleksandr , Du, Xiuxia , Jones, Kenneth L. , Dorrestein, Kathleen , Panitchpakdi, Morgan , Ernst, Madeleine , Hooft, Justin J.J. van der , Gonzalez, Mabel , Carazzone, Chiara , Amézquita, Adolfo , Callewaert, Chris , Morton, James T. , Quinn, Robert A. , Bouslimani, Amina , Orio, Andrea Albarracín , Petras, Daniel , Smania, Andrea M. , Couvillion, Sneha P. , Burnet, Meagan C. , Nicora, Carrie D. , Zink, Erika , Metz, Thomas O. , Artaev, Viatcheslav , Humston-Fulmer, Elizabeth , Gregor, Rachel , Meijler, Michael M. , Mizrahi, Itzhak , Eyal, Stav , Anderson, Brooke , Dutton, Rachel , Lugan, Raphaël , Boulch, Pauline Le , Guitton, Yann , Prevost, Stephanie , Poirier, Audrey , Dervilly, Gaud , Bizec, Bruno Le , Fait, Aaron , Persi, Noga Sikron , Song, Chao , Gashu, Kelem , Coras, Roxana , Guma, Monica , Manasson, Julia , Scher, Jose U. , Barupal, Dinesh Kumar , Alseekh, Saleh , Fernie, Alisdair R. , Mirnezami, Reza , Vasiliou, Vasilis , Schmid, Robin , Borisov, Roman S. , Kulikova, Larisa N. , Knight, Rob , Wang, Mingxun , Hanna, George B. , Dorrestein, Pieter C. , Veselkov, Kirill (2020) Nature Biotechnology (2020). - ISSN 1087-0156
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

Robinson, Serina L. , Terlouw, Barbara R. , Smith, Megan D. , Pidot, Sacha J. , Stinear, Timothy P. , Medema, Marnix H. , Wackett, Lawrence P. (2020) Journal of Biological Chemistry 295 (2020)44. - ISSN 0021-9258 - p. 14826 - 14839.
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.
Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD

Groß, Christian , Bortoluzzi, Chiara , Ridder, Dick de , Megens, Hendrik-Jan , Groenen, Martien A.M. , Reinders, Marcel , Bosse, Mirte (2020) Plos Genetics 16 (2020)9. - ISSN 1553-7390