M
Marnix H. Medema
Researcher at Wageningen University and Research Centre
Publications - 161
Citations - 20394
Marnix H. Medema is an academic researcher from Wageningen University and Research Centre. The author has contributed to research in topics: Biology & Genome. The author has an hindex of 47, co-authored 136 publications receiving 13720 citations. Previous affiliations of Marnix H. Medema include University of Groningen & Radboud University Nijmegen.
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Journal ArticleDOI
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
Kai Blin,Simon Shaw,Katharina Steinke,Rasmus Villebro,Nadine Ziemert,Sang Yup Lee,Sang Yup Lee,Marnix H. Medema,Tilmann Weber +8 more
TL;DR: AntiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-Ri PPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines and provides more detailed predictions for type II polyketide synthase-encoding gene clusters.
Journal ArticleDOI
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
Tilmann Weber,Kai Blin,Srikanth Duddela,Daniel Krug,Hyun Uk Kim,Robert E. Bruccoleri,Sang Yup Lee,Sang Yup Lee,Michael A. Fischbach,Rolf Müller,Wolfgang Wohlleben,Rainer Breitling,Eriko Takano,Marnix H. Medema,Marnix H. Medema +14 more
TL;DR: AntiSMASH as mentioned in this paper is a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.org.
Journal ArticleDOI
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
Marnix H. Medema,Kai Blin,Peter Cimermancic,Victor de Jager,Victor de Jager,Piotr Zakrzewski,Michael A. Fischbach,Tilmann Weber,Eriko Takano,Rainer Breitling +9 more
TL;DR: This work presents the first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view.
Journal ArticleDOI
Structure and function of the global topsoil microbiome.
Mohammad Bahram,Mohammad Bahram,Mohammad Bahram,Falk Hildebrand,Sofia K. Forslund,Sofia K. Forslund,Jennifer L. Anderson,Nadejda A. Soudzilovskaia,Peter M. Van Bodegom,Johan Bengtsson-Palme,Sten Anslan,Sten Anslan,Luis Pedro Coelho,Helery Harend,Jaime Huerta-Cepas,Marnix H. Medema,Mia R. Maltz,Sunil Mundra,Pål Axel Olsson,Mari Pent,Sergei Põlme,Shinichi Sunagawa,Martin Ryberg,Leho Tedersoo,Peer Bork,Peer Bork +25 more
TL;DR: It is shown that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance, and that the relative contributions of these microorganisms to global nutrient cycling varies spatially.
Journal ArticleDOI
antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.
Kai Blin,Thomas Wolf,Marc G. Chevrette,Xiaowen Lu,Christopher J. Schwalen,Satria A. Kautsar,Hernando G. Suarez Duran,Emmanuel L. C. de los Santos,Hyun Uk Kim,Mariana Nave,Jeroen S. Dickschat,Douglas A. Mitchell,Ekaterina Shelest,Rainer Breitling,Eriko Takano,Sang Yup Lee,Tilmann Weber,Marnix H. Medema +17 more
TL;DR: The thoroughly updated antiSMASH version 4 is presented, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, and several usability features have been updated and improved.