Marnix Medema
Assistant Professor
- Name
- Dr. M.H. Medema
- Telephone
- +31 71 527 5672
- m.h.medema@biology.leidenuniv.nl
From May 2020 to April 2021, Marnix Medema will be Van der Klaauw visiting professor at Leiden University. His research focuses on the development of computational algorithms to explore metabolic diversity and the associated functions in microbiomes.
More information about Marnix Medema
News
Bacteria, fungi and plants produce large numbers of small molecules, which mediate key interactions between these organisms at the molecular level, and are responsible for many important microbiome-associated phenotypes. Many of these molecules are also applied as antibiotics, chemotherapeutics, and crop protection agents. Marnix Medema and his research group in Wageningen develop and apply computational tools to study the functional diversity of such molecules based on large-scale (meta)genomic, transcriptomic and metabolomic data.
Assistant Professor
- Science
- Instituut Biologie Leiden
- IBL Microbial Sciences
- Guerrero Egio G., Pintado A., Bretscher K.M., Arias-Giraldo L.M., Paulson J.N., Spaink H.P., Claessen D., Ramos C., Cazorla F.M., Medema M.H., Raaijmakers J.M. & Carrion Bravo V.J. (2024), bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria, Nature Communications 15: 2072.
- Liu Y., Jarman B., Low Y.S., Augustijn H.E., Huang S., Chen H, DeFeo M.E., Sekiba K., Hou B., Meng X., Weakley A.M., Cabrera A.V., Zhou Z., Wezel G.P. van, Medema M.H., Ganesan C., Pao A.C., Gombar S. & Dodd D. (2023), A widely distributed gene cluster compensates for uricase loss in hominids, Cell 186(16): 3400-3413 (e20).
- Blin K., Shaw S., Augustijn H.E., Reitz Z.L., Biermann F., Alanjary M., Fetter A., Terlouw B.R., Metcalf W.W., Helfrich E.J.N., Wezel G.P. van & Medema M.H. Weber T. (2023), antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation, Nucleic Acids Research 51(W1): W46–W50.
- Zdouc M., Bayona Maldonado L.M., Augustijn H., Soldatou S., Jonge N. de, Jaspars M., Wezel G.P. van, Medema M.H. & Hooft J.J.J. van der (2023), FERMO v.0.8.11. Zenodo (version 0.8.11). Zenodo. [software].
- Terlouw B.R., Blin K., Navarr-Munoz J.C., Avalon N.E., Chevrette M.G., Egbert S., Lee S., Meijer D., Recchia M.J.J., Reitz Z.L., Santen J.A. van, Selem-Mojica N., Torring T., Zaroubi L., Alaniary M., Aleti G., Aguilar C., Al-Salihi S.A.A., Augustijn H.E., Avalar-Rivas J.A., Avitia Dominguez L.A., Barona Gomez F., Bernaldo-Agüero J., Bielinski V.A., Biermann F., Booth T.J., Carrion Bravo V.J., Castelo-Branco R., Chagas F.O., Cruz-Moreles P., Du C., Duncan K.R., Gavriilidou A., Gayrard D., Gutiérez-Garcia K., Haslinger K., Helfrich E.J.N., Hooft J.J.J. van der, Jati A.P., Kalkreuter E., Kalyvas N., Kang K.B., Kautsar S., Kim. W., Kunjapur A.M., Li Y.X., Lin G., Loureiro C., Louwen J.J.R., Louwen N.L.L., Lung G., Parra J., Philmus B., Purmohsenin B., Prong L.J.U., Rego A., Rex D.A.B., Robinson S., Rosas Becerra L.R., Roxborough E.T., Schorn M.A., Scobie D.J., Singh K.S., Sokolova N., Tang X., Udwary D., Vigneshwari A., Vind K., Vromans S.P.J.M., Waschulin V., Williams S.E., Winter J.M., Witte T.E., Xie H., Yang D., Yu J., Zdouc M., Zhong Z., Collemare J., Linington R.G., Weber T. & Medema M.H. (2023), MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters, Nucleic Acids Research 51(D1): D603-D610.
- Mullowney M.W., Duncan K.R., Elsayed S.S., Garg N., Hooft J.J.J. van der, Martin N.I., Meijer D., Terlouw B.R., Biermann F., Blin K., Durairaj J., Gorostiola González M., Helfrich E.J.N., Huber F., Leopold-Messer S., Rajan K., Rond T. de, Santen J.A. van, Sorokina M., Balunas M.J., Beniddir M.A., Bergeijk D.A. van, Carroll L.M., Clark C.M., Clevert D.A., Dejong C.A., Du C., Ferrinho S., Grisoni F., Hofstetter A., Jespers W., Kalinina O.V., Kautsar S.A., Kim H., Leao T.F., Masschelein J., Rees E.R., Reher R., Reker D., Schwaller P., Segler M., Skinnider M.A., Walker A.S., Willighagen E.L., Zdrazil B., Ziemert N., Goss R.J.M., Guyomard P., Volkamer A., Gerwick W.H., Kim H.U., Müller R., Wezel G.P. van, Westen G.J.P. van, Hirsch A.K.H., Linington R.G., Robinson S.L. & Medema M.H. (2023), Artificial intelligence for natural product drug discovery, Nature Reviews Drug Discovery 22: 895-916.
- Oyserman B.O., Flores S.S., Griffioen T., Pan X., Wijk E. van der, Pronk L., Lokhorst W., Nurfikari A., Paulson J.N., Movassagh M., Stopnisek N., Kupczok A., Cordovez V., Carrión V.J., Ligterink W., Snoek B.L., Medema M.H. & Raaijmakers J.M. (2022), Disentangling the genetic basis of rhizosphere microbiome assembly in tomato, Nature Communications 13: 3228.
- Augustijn H.E. & Medema M.H. (2022), Freedom of expression: A synthetic route to metabolites, Cell 185(9): 1449-1451.
- Kloosterman A.M., Medema M.H. & Wezel G.P. van (2021), Omics-based strategies to discover novel classes of RiPP natural products, Current Opinion in Biotechnology 69: 60-67.
- Blin K., Shaw S., Kloosterman A.M., Charlop-Powers Z., Wezel G.P. van, Medema M.H. & Tilmann W. (2021), antiSMASH 6.0: improving cluster detection and comparison capabilities, Nucleic Acids Research 49(W1): W29-W35.
- Scientific Advisory Board member
- Assistant Professor