Works matching AU Medema, Marnix H.

Results: 74

Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.

Published in:

PLoS Biology, 2025, v. 23, n. 6, p. 1, doi. 10.1371/journal.pbio.3003183

By:

Augustijn, Hannah E.;
Reitz, Zachary L.;
Zhang, Le;
Boot, Jeanine A.;
Elsayed, Somayah S.;
Challis, Gregory L.;
Medema, Marnix H.;
van Wezel, Gilles P.

Publication type:

Article

Computational tools for the synthetic design of biochemical pathways.

Published in:

Nature Reviews Microbiology, 2012, v. 10, n. 3, p. 191, doi. 10.1038/nrmicro2717

By:

Medema, Marnix H.;
van Raaphorst, Renske;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms.

Published in:

Nature Reviews Microbiology, 2011, v. 9, n. 2, p. 131, doi. 10.1038/nrmicro2478

By:

Medema, Marnix H.;
Breitling, Rainer;
Bovenberg, Roel;
Takano, Eriko

Publication type:

Article

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

Published in:

Bioinformatics, 2017, v. 33, n. 20, p. 3202, doi. 10.1093/bioinformatics/btx400

By:

Chevrette, Marc G.;
Aicheler, Fabian;
Kohlbacher, Oliver;
Currie, Cameron R.;
Medema, Marnix H.

Publication type:

Article

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

Published in:

Metabolites (2218-1989), 2019, v. 9, n. 7, p. 144, doi. 10.3390/metabo9070144

By:

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

Publication type:

Article

Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000‐year‐old mammoth.

Published in:

Environmental Microbiology, 2024, v. 26, n. 2, p. 1, doi. 10.1111/1462-2920.16589

By:

van Bergeijk, Doris A.;
Augustijn, Hannah E.;
Elsayed, Somayah S.;
Willemse, Joost;
Carrión, Victor J.;
Du, Chao;
Urem, Mia;
Grigoreva, Lena V.;
Cheprasov, Maksim Y.;
Grigoriev, Semyon;
Jansen, Hans;
Wintermans, Bas;
Budding, Andries E.;
Spaink, Herman P.;
Medema, Marnix H.;
van Wezel, Gilles P.

Publication type:

Article

Comprehensive mass spectrometry‐guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae.

Published in:

Plant Journal, 2019, v. 98, n. 6, p. 1134, doi. 10.1111/tpj.14292

By:

Kang, Kyo Bin;
Ernst, Madeleine;
Hooft, Justin J. J.;
Silva, Ricardo R.;
Park, Junha;
Medema, Marnix H.;
Sung, Sang Hyun;
Dorrestein, Pieter C.

Publication type:

Article

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters.

Published in:

BMC Research Notes, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13104-019-4222-3

By:

Witjes, Lotte;
Kooke, Rik;
van der Hooft, Justin J. J.;
de Vos, Ric C. H.;
Keurentjes, Joost J. B.;
Medema, Marnix H.;
Nijveen, Harm

Publication type:

Article

A predicted physiochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.

Published in:

BMC Genomics, 2010, v. 11, p. 299, doi. 10.1186/1471-2164-11-299

By:

Medema, Marnix H.;
Miaomiao Zhou;
van Hijum, Sacha A. F. T.;
Gloerich, Jolein;
Wessels, Hans J. C. T.;
Siezen, Roland J.;
Strous, Marc

Publication type:

Article

CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05311-2

By:

van den Belt, Matthias;
Gilchrist, Cameron;
Booth, Thomas J.;
Chooi, Yit-Heng;
Medema, Marnix H.;
Alanjary, Mohammad

Publication type:

Article

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters.

Published in:

Communications Biology, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42003-019-0333-6

By:

Del Carratore, Francesco;
Zych, Konrad;
Cummings, Matthew;
Takano, Eriko;
Medema, Marnix H.;
Breitling, Rainer

Publication type:

Article

Harnessing regulatory networks in Actinobacteria for natural product discovery.

Published in:

Journal of Industrial Microbiology & Biotechnology, 2024, v. 51, p. 1, doi. 10.1093/jimb/kuae011

By:

Augustijn, Hannah E;
Roseboom, Anna M;
Medema, Marnix H;
Wezel, Gilles P van

Publication type:

Article

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30849-9

By:

Oyserman, Ben O.;
Flores, Stalin Sarango;
Griffioen, Thom;
Pan, Xinya;
van der Wijk, Elmar;
Pronk, Lotte;
Lokhorst, Wouter;
Nurfikari, Azkia;
Paulson, Joseph N.;
Movassagh, Mercedeh;
Stopnisek, Nejc;
Kupczok, Anne;
Cordovez, Viviane;
Carrión, Víctor J.;
Ligterink, Wilco;
Snoek, Basten L.;
Medema, Marnix H.;
Raaijmakers, Jos M.

Publication type:

Article

MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models.

Published in:

PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0051511

By:

Zakrzewski, Piotr;
Medema, Marnix H.;
Gevorgyan, Albert;
Kierzek, Andrzej M.;
Breitling, Rainer;
Takano, Eriko

Publication type:

Article

Breaking into nature's secret medicine cabinet: lichens – a biochemical goldmine ready for discovery.

Published in:

New Phytologist, 2025, v. 246, n. 2, p. 437, doi. 10.1111/nph.70003

By:

Singh, Garima;
Dal Grande, Francesco;
Martin, Francis M.;
Medema, Marnix H.

Publication type:

Article

The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol.

Published in:

New Phytologist, 2022, v. 235, n. 5, p. 1884, doi. 10.1111/nph.18272

By:

Wang, Yanting;
Durairaj, Janani;
Suárez Duran, Hernando G.;
van Velzen, Robin;
Flokova, Kristyna;
Liao, Che‐Yang;
Chojnacka, Aleksandra;
MacFarlane, Stuart;
Schranz, M. Eric;
Medema, Marnix H.;
van Dijk, Aalt D. J.;
Dong, Lemeng;
Bouwmeester, Harro J.

Publication type:

Article

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

Published in:

Frontiers in Plant Science, 2019, p. 1, doi. 10.3389/fpls.2019.00846

By:

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

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.574053

By:

Oyserman, Ben O.;
Cordovez, Viviane;
Flores, Stalin Sarango;
Leite, Marcio F. A.;
Nijveen, Harm;
Medema, Marnix H.;
Raaijmakers, Jos M.

Publication type:

Article

Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.

Published in:

Environmental Microbiology, 2017, v. 19, n. 11, p. 4638, doi. 10.1111/1462-2920.13927

By:

Cheng, Xu;
Etalo, Desalegn W.;
van de Mortel, Judith E.;
Dekkers, Ester;
Nguyen, Linh;
Medema, Marnix H.;
Raaijmakers, Jos M.

Publication type:

Article

Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea.

Published in:

Environmental Microbiology, 2008, v. 10, n. 11, p. 3164, doi. 10.1111/j.1462-2920.2008.01724.x

By:

Ettwig, Katharina F.;
Shima, Seigo;
van de Pas-Schoonen, Katinka T.;
Kahnt, Jörg;
Medema, Marnix H.;
op den Camp, Huub J. M.;
Jetten, Mike S. M.;
Strous, Marc

Publication type:

Article

Comprehensive Genome Analysis of Halolamina pelagica CDK2: Insights into Abiotic Stress Tolerance Genes.

Published in:

Journal of Pure & Applied Microbiology, 2022, v. 16, n. 1, p. 460, doi. 10.22207/JPAM.16.1.44

By:

Gaba, Sonam;
Naitam, Mayur G.;
Kumari, Abha;
Medema, Marnix H.;
Kaushik, Rajeev

Publication type:

Article

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2018, v. 12, n. 9, p. 2307, doi. 10.1038/s41396-018-0186-x

By:

Carrión, Víctor J.;
Cordovez, Viviane;
Tyc, Olaf;
Etalo, Desalegn W.;
de Bruijn, Irene;
de Jager, Victor C. L.;
Medema, Marnix H.;
Eberl, Leo;
Raaijmakers, Jos M.

Publication type:

Article

Unleashing the potential of cell painting assays for compound activities and hazards prediction.

Published in:

Frontiers in Toxicology, 2024, p. 1, doi. 10.3389/ftox.2024.1401036

By:

Odje, Floriane;
Meijer, David;
von Coburg, Elena;
van der Hooft, Justin J. J.;
Dunst, Sebastian;
Medema, Marnix H.;
Volkamer, Andrea

Publication type:

Article

cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters.

Published in:

Bioinformatics Advances, 2021, v. 1, n. 1, p. 1, doi. 10.1093/bioadv/vbab016

By:

Gilchrist, Cameron L. M.;
Booth, Thomas J.;
Wersch, Bram van;
Grieken, Liana van;
Medema, Marnix H.;
Yit-Heng Chooi

Publication type:

Article

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters.

Published in:

Briefings in Bioinformatics, 2019, p. 1103, doi. 10.1093/bib/bbx146

By:

Blin, Kai;
Kim, Hyun Uk;
Medema, Marnix H;
Weber, Tilmann

Publication type:

Article

Microbial assimilatory sulfate reduction-mediated H<sub>2</sub>S: an overlooked role in Crohn's disease development.

Published in:

Microbiome, 2024, v. 12, n. 1, p. 1, doi. 10.1186/s40168-024-01873-2

By:

Luo, Wanrong;
Zhao, Min;
Dwidar, Mohammed;
Gao, Yang;
Xiang, Liyuan;
Wu, Xueting;
Medema, Marnix H.;
Xu, Shu;
Li, Xiaozhi;
Schäfer, Hendrik;
Chen, Minhu;
Feng, Rui;
Zhu, Yijun

Publication type:

Article

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching.

Published in:

Microbiome, 2023, v. 11, n. 1, p. 1, doi. 10.1186/s40168-022-01444-3

By:

Louwen, Joris J. R.;
Medema, Marnix H.;
van der Hooft, Justin J. J.

Publication type:

Article

Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae.

Published in:

New Phytologist, 2020, v. 227, n. 4, p. 1109, doi. 10.1111/nph.16338

By:

Liu, Zhenhua;
Suarez Duran, Hernando G.;
Harnvanichvech, Yosapol;
Stephenson, Michael J.;
Schranz, M. Eric;
Nelson, David;
Medema, Marnix H.;
Osbourn, Anne

Publication type:

Article

Evolution of combinatorial diversity in transacyltransferase polyketide synthase assembly lines across bacteria.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21163-x

By:

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

Publication type:

Article

Genome-wide gene expression changes in an industrial clavulanic acid overproduction strain of Streptomyces clavuligerus.

Published in:

Microbial Biotechnology, 2011, v. 4, n. 2, p. 300, doi. 10.1111/j.1751-7915.2010.00226.x

By:

Medema, Marnix H.;
Alam, Mohammad T.;
Heijne, Wilbert H. M.;
van den Berg, Marco A.;
Müller, Ulrike;
Trefzer, Axel;
Bovenberg, Roel A. L.;
Breitling, Rainer;
Takano, Eriko

Publication type:

Article

Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2154-4

By:

Salo, Oleksandr V.;
Ries, Marco;
Medema, Marnix H.;
Lankhorst, Peter P.;
Vreeken, Rob J.;
Bovenberg, Roel A. L.;
Driessen, Arnold J. M.

Publication type:

Article

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1004016

By:

Medema, Marnix H.;
Cimermancic, Peter;
Sali, Andrej;
Takano, Eriko;
Fischbach, Michael A.

Publication type:

Article

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 9, p. 1, doi. 10.1371/journal.pcbi.1003822

By:

Medema, Marnix H.;
Paalvast, Yared;
Nguyen, Don D.;
Melnik, Alexey;
Dorrestein, Pieter C.;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

Metabolomics methods for the synthetic biology of secondary metabolism.

Published in:

FEBS Letters, 2012, v. 586, n. 15, p. 2177, doi. 10.1016/j.febslet.2012.02.008

By:

Nguyen, Quoc-Thai;
Merlo, Maria E.;
Medema, Marnix H.;
Jankevics, Andris;
Breitling, Rainer;
Takano, Eriko

Publication type:

Article

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

Published in:

FEBS Letters, 2011, v. 585, n. 14, p. 2389, doi. 10.1016/j.febslet.2011.06.014

By:

Alam, Mohammad Tauqeer;
Medema, Marnix H.;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

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

Published in:

PLoS Biology, 2020, v. 18, n. 12, p. 1, doi. 10.1371/journal.pbio.3001026

By:

Kloosterman, Alexander M.;
Cimermancic, Peter;
Elsayed, Somayah S.;
Du, Chao;
Hadjithomas, Michalis;
Donia, Mohamed S.;
Fischbach, Michael A.;
van Wezel, Gilles P.;
Medema, Marnix H.

Publication type:

Article

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

Published in:

Standards in Genomic Sciences, 2018, v. 13, n. 1, p. N.PAG, doi. 10.1186/s40793-018-0318-y

By:

Epstein, Samuel C.;
Charkoudian, Louise K.;
Medema, Marnix H.

Publication type:

Article

Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium.

Published in:

Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2018.01158

By:

Hoogendoorn, Koen;
Barra, Lena;
Waalwijk, Cees;
Dickschat, Jeroen S.;
van der Lee, Theo A. J.;
Medema, Marnix H.

Publication type:

Article

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D618, doi. 10.1093/nar/gkae953

By:

Bağcı, Caner;
Nuhamunada, Matin;
Goyat, Hemant;
Ladanyi, Casimir;
Sehnal, Ludek;
Blin, Kai;
Kautsar, Satria A;
Tagirdzhanov, Azat;
Gurevich, Alexey;
Mantri, Shrikant;
von Mering, Christian;
Udwary, Daniel;
Medema, Marnix H;
Weber, Tilmann;
Ziemert, Nadine

Publication type:

Article

The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more.

Published in:

Nucleic Acids Research, 2024, v. 52, n. D1, p. D586, doi. 10.1093/nar/gkad984

By:

Blin, Kai;
Shaw, Simon;
Medema, Marnix H;
Weber, Tilmann

Publication type:

Article

antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation.

Published in:

Nucleic Acids Research, 2023, v. 51, n. W1, p. W46, doi. 10.1093/nar/gkad344

By:

Blin, Kai;
Shaw, Simon;
Augustijn, Hannah E;
Reitz, Zachary L;
Biermann, Friederike;
Alanjary, Mohammad;
Fetter, Artem;
Terlouw, Barbara R;
Metcalf, William W;
Helfrich, Eric J N;
van Wezel, Gilles P;
Medema, Marnix H;
Weber, Tilmann

Publication type:

Article

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota.

Published in:

Nucleic Acids Research, 2021, v. 49, n. W1, p. W263, doi. 10.1093/nar/gkab353

By:

Pascal Andreu, Victòria;
Roel-Touris, Jorge;
Dodd, Dylan;
Fischbach, Michael A;
Medema, Marnix H

Publication type:

Article

antiSMASH 6.0: improving cluster detection and comparison capabilities.

Published in:

Nucleic Acids Research, 2021, v. 49, n. W1, p. W29, doi. 10.1093/nar/gkab335

By:

Blin, Kai;
Shaw, Simon;
Kloosterman, Alexander M;
Charlop-Powers, Zach;
van Wezel, Gilles P;
Medema, Marnix H;
Weber, Tilmann

Publication type:

Article

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes.

Published in:

Nucleic Acids Research, 2021, v. 49, n. D1, p. D639, doi. 10.1093/nar/gkaa978

By:

Blin, Kai;
Shaw, Simon;
Kautsar, Satria A;
Medema, Marnix H;
Weber, Tilmann

Publication type:

Article

BiG-FAM: the biosynthetic gene cluster families database.

Published in:

Nucleic Acids Research, 2021, v. 49, n. D1, p. D490, doi. 10.1093/nar/gkaa812

By:

Kautsar, Satria A;
Blin, Kai;
Shaw, Simon;
Weber, Tilmann;
Medema, Marnix H

Publication type:

Article

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining.

Published in:

Nucleic Acids Research, 2020, v. 48, n. W1, p. W546, doi. 10.1093/nar/gkaa374

By:

Mungan, Mehmet Direnç;
Alanjary, Mohammad;
Blin, Kai;
Weber, Tilmann;
Medema, Marnix H;
Ziemert, Nadine

Publication type:

Article

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.

Published in:

Nucleic Acids Research, 2019, v. 47, n. W1, p. W81, doi. 10.1093/nar/gkz310

By:

Blin, Kai;
Shaw, Simon;
Steinke, Katharina;
Villebro, Rasmus;
Ziemert, Nadine;
Lee, Sang Yup;
Medema, Marnix H;
Weber, Tilmann

Publication type:

Article

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D625, doi. 10.1093/nar/gky1060

By:

Blin, Kai;
Pascal Andreu, Victòria;
de los Santos, Emmanuel L C;
Del Carratore, Francesco;
Lee, Sang Yup;
Medema, Marnix H;
Weber, Tilmann

Publication type:

Article

Computational approaches to natural product discovery.

Published in:

Nature Chemical Biology, 2015, v. 11, n. 9, p. 639, doi. 10.1038/nchembio.1884

By:

Medema, Marnix H;
Fischbach, Michael A

Publication type:

Article

Minimum Information about a Biosynthetic Gene cluster.

Published in:

Nature Chemical Biology, 2015, v. 11, n. 9, p. 625, doi. 10.1038/nchembio.1890

By:

Medema, Marnix H;
Kottmann, Renzo;
Yilmaz, Pelin;
Cummings, Matthew;
Biggins, John B;
Blin, Kai;
de Bruijn, Irene;
Chooi, Yit Heng;
Claesen, Jan;
Coates, R Cameron;
Cruz-Morales, Pablo;
Duddela, Srikanth;
Düsterhus, Stephanie;
Edwards, Daniel J;
Fewer, David P;
Garg, Neha;
Geiger, Christoph;
Gomez-Escribano, Juan Pablo;
Greule, Anja;
Hadjithomas, Michalis

Publication type:

Article