A computational framework to interpret the chemical language of the microbiome

Informazioni relative al progetto

DECIPHER

ID dell’accordo di sovvenzione: 948770

DOI

10.3030/948770

Progetto chiuso

Data della firma CE 20 Ottobre 2020

Data di avvio 1 Dicembre 2020

Data di completamento 30 Novembre 2025

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 499 965,00

Contributo UE

€ 1 499 965,00

Coordinato da

WAGENINGEN UNIVERSITY
Netherlands

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (25)

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Autori: Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG, Egbert S, Lee S, Meijer D, Recchia MJJ, Reitz ZL, van Santen JA, Selem-Mojica N, Tørring T, Zaroubi L, Alanjary M, Aleti G, Aguilar C, Al-Salihi SAA, Augustijn HE, Avelar-Rivas JA, Avitia-Domínguez LA, Barona-Gómez F, Bernaldo-Agüero J, Bielinski VA, Biermann F, Booth TJ, Carrion Bravo VJ, Castelo-Branco R, Chagas FO, Cruz-Morales
Pubblicato in: Nucleic Acids Research, 2023, Pagina/e D603-D610, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkac1049

Harnessing regulatory networks in Actinobacteria for natural product discovery

Autori: Hannah E Augustijn, Anna M Roseboom, Marnix H Medema, Gilles P van Wezel
Pubblicato in: Journal of Industrial Microbiology and Biotechnology, Numero 51, 2025, ISSN 1367-5435
Editore: Springer Verlag
DOI: 10.1093/jimb/kuae011

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota

Autori: Victòria Pascal Andreu; Hannah E. Augustijn; Lianmin Chen; Alexandra Zhernakova; Jingyuan Fu; Michael A. Fischbach; Dylan Dodd; Marnix H. Medema
Pubblicato in: ISSN=10870156;TITLE=Nature Biotechnology, Numero 1, 2023, ISSN 1546-1696
Editore: Springer Nature
DOI: 10.1038/s41587-023-01675-1

gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota

Autori: Yijun Zhu, Hannah E. Augustijn, Victòria Pascal Andreu, Arjan Draisma, Gilles P. van Wezel, Dylan Dodd, Michael A. Fischbach, Marnix H. Medema
Pubblicato in: Journal of Molecular Biology, 2026, Pagina/e 169567, ISSN 0022-2836
Editore: Academic Press
DOI: 10.1016/j.jmb.2025.169567

CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer

Autori: David Meijer, Marnix H. Medema, Justin J. J. van der Hooft
Pubblicato in: Journal of Cheminformatics, Numero 16, 2024, Pagina/e 58, ISSN 1758-2946
Editore: Chemistry Central
DOI: 10.26434/chemrxiv-2024-bvxr2

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

Autori: Hannah E. Augustijn, Zachary L. Reitz, Le Zhang, Jeanine A. Boot, Somayah S. Elsayed, Gregory L. Challis, Marnix H. Medema, Gilles P. van Wezel
Pubblicato in: PLOS Biology, Numero 23, 2025, Pagina/e e3003183, ISSN 1545-7885
Editore: Public Library of Science (PLoS)
DOI: 10.1371/journal.pbio.3003183

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation

Autori: Kai Blin, Simon Shaw, Lisa Vader, Judit Szenei, Zachary L Reitz, Hannah E Augustijn, José D D Cediel-Becerra, Valérie de Crécy-Lagard, Robert A Koetsier, Sam E Williams, Pablo Cruz-Morales, Sopida Wongwas, Alejandro E Segurado Luchsinger, Friederike Biermann, Aleksandra Korenskaia, Mitja M Zdouc, David Meijer, Barbara R Terlouw, Justin J J van der Hooft, Nadine Ziemert, Eric J N H
Pubblicato in: Nucleic Acids Research, Numero 53, 2025, Pagina/e W32-W38, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaf334

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

Autori: Kai Blin; Simon Shaw; Marnix H Medema; Tilmann Weber
Pubblicato in: Crossref, Numero 2, 2023, Pagina/e 0305-1048, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad984

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

Autori: Zachary L. Reitz, Bita Pourmohsenin, Melanie Susman, Emil Thomsen, Daniel Roth, Alison Butler, Nadine Ziemert, Marnix H. Medema
Pubblicato in: eLife, 2026, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.1101/2025.07.29.667501

RAIChU: automating the visualisation of natural product biosynthesis

Autori: Barbara R. Terlouw, Friederike Biermann, Sophie P. J. M. Vromans, Elham Zamani, Eric J. N. Helfrich, Marnix H. Medema
Pubblicato in: Journal of Cheminformatics, Numero 16, 2024, ISSN 1758-2946
Editore: Chemistry Central
DOI: 10.1186/s13321-024-00898-x

LogoMotif: a comprehensive database of transcription factor binding site profiles in Actinobacteria

Autori: Hannah E. Augustijn, Dimitris Karapliafis, Kristy Joosten, Sébastien Rigali, Gilles P. van Wezel, Marnix H. Medema
Pubblicato in: Journal of Molecular Biology, Numero 436, 2024, Pagina/e 168558, ISSN 1089-8638
Editore: Elsevier
DOI: 10.1101/2024.02.28.582527

Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint

Autori: Lucina-May Nollen, David Meijer, Maria Sorokina, Justin J. J. van der Hooft
Pubblicato in: Journal of Cheminformatics, Numero 17, 2025, ISSN 1758-2946
Editore: Chemistry Central
DOI: 10.1186/s13321-025-01081-6

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

Autori: Victòria Pascal Andreu; Jorge Roel-Touris; Dylan Dodd; Michael A. Fischbach; Marnix H. Medema
Pubblicato in: urn:issn:03051048, Numero 1, 2021, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkab353

Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

Autori: Doris A. van Bergeijk, Hannah E. Augustijn, Somayah S. Elsayed, Joost Willemse, Victor J. Carrión, Mia Urem, Lena V. Grigoreva, Maksim Y. Cheprasov, Semyon Grigoriev, Bas Wintermans, Andries E. Budding, Herman P. Spaink, Marnix H. Medema, Gilles P. van Wezel
Pubblicato in: Environmental Microbiology, 2026, ISSN 1462-2920
Editore: Wiley
DOI: 10.1101/2022.12.22.521380

improving cluster detection and comparison capabilities

Autori: Kai Blin; Simon Shaw; Alexander M. Kloosterman; Zach Charlop-Powers; Gilles P. van Wezel; Marnix H. Medema; Marnix H. Medema; Tilmann Weber
Pubblicato in: TITLE=Nucleic Acids Research, Numero 1, 2021, Pagina/e W29-W35, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkab335

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Autori: Arjan Draisma, Catarina Loureiro, Nico L. L. Louwen, Satria A. Kautsar, Jorge C. Navarro-Muñoz, Drew T. Doering, Nigel J. Mouncey & Marnix H. Medema
Pubblicato in: Nature Communications, 2026, ISSN 2041-1723
Editore: Nature Publishing Group

Genome mining strategies for metallophore discovery.

Autori: Zachary L Reitz; Marnix H Medema
Pubblicato in: urn:issn:09581669, Numero 1, 2022, Pagina/e 102757, ISSN 1879-0429
Editore: Elsevier
DOI: 10.1016/j.copbio.2022.102757

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

Autori: Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T
Pubblicato in: Nucleic Acids Research, 2023, Pagina/e W46-W50, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkad344

MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis

Autori: Adriano Rutz, Daniel Probst, César Aguilar, Daniel Y Akiyama, Fabrizio Alberti, Hannah E Augustijn, Nicole E Avalon, Christine Beemelmanns, Hellen Bertoletti Barbieri, Friederike Biermann, Alan J Bridge, Esteban Charria Girón, Russell Cox, Max Crüsemann, Paul M D’Agostino, Marc Feuermann, Jennifer Gerke, Karina Gutiérrez García, Jonathan E Holme, Ji-Yeon Hwang, Riccardo Iacovelli, Júlio C
Pubblicato in: Nucleic Acids Research, Numero 54, 2026, Pagina/e D635-D642, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaf969

Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

Autori: Athina Gavriilidou; Satria A. Kautsar; Nestor Zaburannyi; Daniel Krug; Rolf Müller; Marnix H. Medema; Nadine Ziemert
Pubblicato in: ISSN: 2058-5276, Numero 1, 2022, ISSN 2058-5276
Editore: Springer Nature
DOI: 10.1038/s41564-022-01110-2

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

Autori: Floriane Odje, David Meijer, Elena von Coburg, Justin J. J. van der Hooft, Sebastian Dunst, Marnix H. Medema, Andrea Volkamer
Pubblicato in: Frontiers in Toxicology, Numero 6, 2024, ISSN 2673-3080
Editore: Frontiers Media SA
DOI: 10.3389/ftox.2024.1401036

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs

Autori: David Meijer, Mehdi A. Beniddir, Connor W. Coley, Yassine M. Mejri, Meltem Öztürk, Justin J. J. van der Hooft, Marnix H. Medema, Adam Skiredj
Pubblicato in: Natural Product Reports, Numero 42, 2025, Pagina/e 654-662, ISSN 0265-0568
Editore: Royal Society of Chemistry
DOI: 10.1039/d4np00008k

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

Autori: Matthias van den Belt; Cameron Gilchrist; Thomas J. Booth; Yit-Heng Chooi; Marnix H. Medema; Mohammad Alanjary
Pubblicato in: ISSN: 1471-2105, Numero 2, 2023, Pagina/e 181, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-023-05311-2

Taxonomic and metabolic diversity of <scp>Actinomycetota</scp> isolated from faeces of a 28,000‐year‐old mammoth

Autori: Doris A. van Bergeijk, Hannah E. Augustijn, Somayah S. Elsayed, Joost Willemse, Victor J. Carrión, Chao Du, Mia Urem, Lena V. Grigoreva, Maksim Y. Cheprasov, Semyon Grigoriev, Hans Jansen, Bas Wintermans, Andries E. Budding, Herman P. Spaink, Marnix H. Medema, Gilles P. van Wezel
Pubblicato in: Environmental Microbiology, Numero 26, 2024, ISSN 1462-2912
Editore: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.16589

Artificial intelligence for natural product drug discovery

Autori: Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kauts
Pubblicato in: Nature Reviews Drug Discovery, 2023, ISSN 1474-1776
Editore: Nature Publishing Group
DOI: 10.1038/s41573-023-00774-7

Other (2)

Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures

Autori: Reitz ZL, Butler A, Medema MH
Pubblicato in: BioRxiv, 2022
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.12.14.519525

PARAS: high-accuracy machine learning of substrate specificities in nonribosomal peptide synthetases

Autori: Barbara R. Terlouw, Chuan Huang, David Meijer, José D. D. Cediel-Becerra, Ruolin He, Marlene L. Rothe, Matthew Jenner, Shanshan Zhou, Yu Zhang, Christopher D. Fage, Yuta Tsun- ematsu, Gilles P. van Wezel, Serina L. Robinson, Fabrizio Alberti, Lona M. Alkhalaf, Marc G. Chevrette, Gregory L. Challis and Marnix H. Medema
Pubblicato in: 2025
Editore: BiorXiv, Cold Spring Harbor Laboratory