Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

by Marnix H. Medema
Published 2018-03-01

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus

by Ana Ceniceros, Lubbert Dijkhuizen, Mirjan Petrusma, Marnix H. Medema
Published 2017-08-01

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences

by Samuel C. Epstein, Louise K. Charkoudian, Marnix H. Medema
Published 2018-07-01

luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria

by Carolyn A. Brotherton, Marnix H. Medema, E. Peter Greenberg
Published 2018-03-01

A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis.

by Marnix H Medema, Peter Cimermancic, Andrej Sali, Eriko Takano, Michael A Fischbach
Published 2014-12-01

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models.

by Piotr Zakrzewski, Marnix H Medema, Albert Gevorgyan, Andrzej M Kierzek, Rainer Breitling, Eriko Takano
Published 2012-01-01

Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.

by Marnix H Medema, Yared Paalvast, Don D Nguyen, Alexey Melnik, Pieter C Dorrestein, Eriko Takano, Rainer Breitling
Published 2014-09-01

Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium

by Koen Hoogendoorn, Koen Hoogendoorn, Lena Barra, Cees Waalwijk, Jeroen S. Dickschat, Theo A. J. van der Lee, Marnix H. Medema
Published 2018-06-01

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides.

by Alexander M Kloosterman, Peter Cimermancic, Somayah S Elsayed, Chao Du, Michalis Hadjithomas, Mohamed S Donia, Michael A Fischbach, Gilles P van Wezel, Marnix H Medema
Published 2020-12-01

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

by Lotte Witjes, Rik Kooke, Justin J. J. van der Hooft, Ric C. H. de Vos, Joost J. B. Keurentjes, Marnix H. Medema, Harm Nijveen
Published 2019-04-01

The role of strigolactones in P deficiency induced transcriptional changes in tomato roots

by Yanting Wang, Hernando G. Suárez Duran, Jan C. van Haarst, Elio G.W.M Schijlen, Carolien Ruyter-Spira, Marnix H. Medema, Lemeng Dong, Harro J. Bouwmeester
Published 2021-07-01

Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes

by Ben O. Oyserman, Ben O. Oyserman, Viviane Cordovez, Viviane Cordovez, Stalin Sarango Flores, Marcio F. A. Leite, Harm Nijveen, Marnix H. Medema, Jos M. Raaijmakers, Jos M. Raaijmakers
Published 2021-01-01

Evolution of combinatorial diversity in trans-acyltransferase polyketide synthase assembly lines across bacteria

by Eric J. N. Helfrich, Reiko Ueoka, Marc G. Chevrette, Franziska Hemmerling, Xiaowen Lu, Stefan Leopold-Messer, Hannah A. Minas, Adrien Y. Burch, Steven E. Lindow, Jörn Piel, Marnix H. Medema
Published 2021-03-01

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

by Madeleine Ernst, Kyo Bin Kang, Andrés Mauricio Caraballo-Rodríguez, Louis-Felix Nothias, Joe Wandy, Christopher Chen, Mingxun Wang, Simon Rogers, Marnix H. Medema, Pieter C. Dorrestein, Justin J.J. van der Hooft
Published 2019-07-01

The Surfactin-Like Lipopeptides From Bacillus spp.: Natural Biodiversity and Synthetic Biology for a Broader Application Range

by Ariane Théatre, Carolina Cano-Prieto, Marco Bartolini, Yoann Laurin, Yoann Laurin, Magali Deleu, Joachim Niehren, Tarik Fida, Saïcha Gerbinet, Mohammad Alanjary, Marnix H. Medema, Angélique Léonard, Laurence Lins, Ana Arabolaza, Hugo Gramajo, Harald Gross, Philippe Jacques
Published 2021-03-01

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

by Vittorio Tracanna, Adam Ossowicki, Marloes L. C. Petrus, Sam Overduin, Barbara R. Terlouw, George Lund, Serina L. Robinson, Sven Warris, Elio G. W. M. Schijlen, Gilles P. van Wezel, Jos M. Raaijmakers, Paolina Garbeva, Marnix H. Medema
Published 2021-06-01

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.

by Madeleine Ernst, Madeleine Ernst, Madeleine Ernst, Louis-Félix Nothias, Louis-Félix Nothias, Justin J. J. van der Hooft, Ricardo R. Silva, Ricardo R. Silva, C. Haris Saslis-Lagoudakis, Olwen M. Grace, Karen Martinez-Swatson, Gustavo Hassemer, Gustavo Hassemer, Luís A. Funez, Henrik T. Simonsen, Marnix H. Medema, Dan Staerk, Niclas Nilsson, Paola Lovato, Pieter C. Dorrestein, Pieter C. Dorrestein, Pieter C. Dorrestein, Nina Rønsted
Published 2019-07-01

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

by Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou-Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul Zierep, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere T. Ebob, Jonathan A. Metuge, Boris D. Bekono, Mustafa A. Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, José L. Medina-Franco, Johannes Kirchmair, Tilmann Weber, Özlem Tastan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig-Müller
Published 2021-09-01