Marnix Medema
Professor Bio Informatics
- Name
- Prof.dr. M.H. Medema
- Telephone
- 071 5275672
- 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
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Over a million euros for two studies on solutions to antimicrobial resistance -
A computational tool that will transform bacterial genome analysis -
Awaken sleeping antibiotics with ERC Advanced grant -
These eleven Leiden Science researchers are among the most highly cited -
Discovery Leiden nominated for KIJK: Best Tech-idea of 2021 -
Artificial intelligence helps in the search for new antibiotics -
IBL coordinates project to search for new medicines in marine biodiversity
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Marnix Medema new visiting professor Van der Klaauw chair
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.
Professor Bio Informatics
- 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.
- Machushynets V., Al Ayed K., Terlouw R., Du C., Buijs P., Willemse J., Elsayed S., Schill J., Trebosc V.: Pieren M., Alexander F.M., Cochrane S.A., Liles M.R., Medema M.H., Martin N.I. & Wezel G.P. van (2024), Discovery and derivatization of tridecaptin antibiotics with altered host specificity and enhanced bioactivity, ACS Chemical Biology 19(5): 1106-1115.
- Augustijn H.E., Roseboom J.M., Medema M.H. & Wezel G.P. van (2024), Harnessing regulatory networks in Actinobacteria for natural product discovery, Journal of Industrial Microbiology and Biotechnology 51: kuae011.
- Augustijn H.E., Karapliafis D., Joosten K.M.M., Rigali S, Wezel G.P. van & Medema M.H. (2024), LogoMotif: a comprehensive database of transcription factor binding site profiles in actinobacteria, Journal of Molecular Biology 436(17): 168558.
- Bergeijk D.A. van, Augustijn H.E., Elsayed S.S.M.A., Willemse J.J., Carrion Bavo V.J., Du C., Urem M., Grigoreva L.V., Cheprasov M.Y., Grigoriev S., Jansen H., Wintermans B., Budding A.E., Spaink H.P., Medema M.H. & Wezel G.P. van (2024), Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth, Environmental Microbiology 26(2): e16589.
- 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.
- 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.
- 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].
- Augustijn H.E. & Medema M.H. (2022), Freedom of expression: A synthetic route to metabolites, Cell 185(9): 1449-1451.
- 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.
- 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