Marnix H. Medema

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 22

Top Topics

Top Venues

Nucleic Acids Res.

J. Cheminformatics

PLoS Comput. Biol.

Publications

David Meijer, Marnix H. Medema, Justin J. J. van der Hooft
CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer. J. Cheminformatics 16 (1) (2024)
Kai Blin, Simon Shaw, Hannah E. Augustijn, Zachary L. Reitz, Friederike Biermann, Mohammad Alanjary, Artem Fetter, Barbara R. Terlouw, William W. Metcalf, Eric J. N. Helfrich, Gilles P. van Wezel, Marnix H. Medema, Tilmann Weber
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51 (W1) (2023)
Joris J. R. Louwen, Satria A. Kautsar, Sven van der Burg, Marnix H. Medema, Justin J. J. van der Hooft
iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures. PLoS Comput. Biol. 19 (2) (2023)
Barbara R. Terlouw, Kai Blin, Jorge C. Navarro-Muñoz, Nicole E. Avalon, Marc G. Chevrette, Susan Egbert, Sanghoon Lee, David Meijer, Michael J. Recchia, Zachary L. Reitz, Jeffrey A. van Santen, Nelly Selem Mojica, Thomas Tørring, Liana Zaroubi, Mohammad Alanjary, Gajender Aleti, César Aguilar, Suhad A. Al-Salihi, Hannah E. Augustijn, J. Abraham Avelar-Rivas, Luis A. Avitia-Domínguez, Francisco Barona-Gómez, Jordan Bernaldo-Agüero, Vincent A. Bielinski, Friederike Biermann, Thomas J. Booth, J. Carrion Bravo, Raquel Castelo-Branco, Fernanda O. Chagas, Pablo Cruz-Morales, Chao Du, Katherine R. Duncan, Athina Gavriilidou, Damien Gayrard, Karina Gutiérrez-García, Kristina Haslinger, Eric J. N. Helfrich, Justin J. J. van der Hooft, Afif P. Jati, Edward Kalkreuter, Nikolaos Kalyvas, Kyo Bin Kang, Satria A. Kautsar, Wonyong Kim, Aditya M. Kunjapur, Yong-Xin Li, Geng-Min Lin, Catarina Loureiro, Joris J. R. Louwen, Nico l L. Louwen, George Lund, Jonathan Parra, Benjamin Philmus, Bita Pourmohsenin, Lotte U. Pronk, Adriana Rego, Devasahayam Arokia Balaya Rex, Serina L. Robinson, L. Rodrigo Rosas-Becerra, Eve T. Roxborough, Michelle A. Schorn, Darren J. Scobie, Kumar Saurabh Singh, Nika Sokolova, Xiaoyu Tang, Daniel W. Udwary, Aruna Vigneshwari, Kristiina Vind, Sophie P. J. M. Vromans, Valentin Waschulin, Sam E. Williams, Jaclyn M. Winter, Thomas E. Witte, Huali Xie, Dong Yang, Jingwei Yu, Mitja Zdouc, Zheng Zhong, Jérôme Collemare, Roger G. Linington, Tilmann Weber, Marnix H. Medema
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res. 51 (D1) (2023)
Matthias van den Belt, Cameron L. M. Gilchrist, Thomas J. Booth, Yit-Heng Chooi, Marnix H. Medema, Mohammad Alanjary
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters. BMC Bioinform. 24 (1) (2023)
Barbara R. Terlouw, Sophie P. J. M. Vromans, Marnix H. Medema
PIKAChU: a Python-based informatics kit for analysing chemical units. J. Cheminformatics 14 (1) (2022)
Satria A. Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H. Medema
BiG-FAM: the biosynthetic gene cluster families database. Nucleic Acids Res. 49 (Database-Issue) (2021)
Kai Blin, Simon Shaw, Satria A. Kautsar, Marnix H. Medema, Tilmann Weber
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes. Nucleic Acids Res. 49 (Database-Issue) (2021)
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 F. 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
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J. Cheminformatics 13 (1) (2021)
Victòria Pascal Andreu, Jorge Roel-Touris, Dylan Dodd, Michael A. Fischbach, Marnix H. Medema
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Kai Blin, Simon Shaw, Alexander M. Kloosterman, Zachary Charlop-Powers, Gilles P. van Wezel, Marnix H. Medema, Tilmann Weber
antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Mehmet Direnç Mungan, Mohammad Alanjary, Kai Blin, Tilmann Weber, Marnix H. Medema, Nadine Ziemert
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Satria A. Kautsar, Kai Blin, Simon Shaw, Jorge C. Navarro-Muñoz, Barbara R. Terlouw, Justin J. J. van der Hooft, Jeffrey A. van Santen, Vittorio Tracanna, Hernando G. Suarez Duran, Victòria Pascal Andreu, Nelly Selem Mojica, Mohammad Alanjary, Serina L. Robinson, George Lund, Samuel C. Epstein, Ashley C. Sisto, Louise K. Charkoudian, Jérôme Collemare, Roger G. Linington, Tilmann Weber, Marnix H. Medema
MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. 48 (Database-Issue) (2020)
Yan Wang, Miguel Correa Marrero, Marnix H. Medema, Aalt D. J. van Dijk
Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines. Bioinform. 36 (19) (2020)
Kai Blin, Hyun Uk Kim, Marnix H. Medema, Tilmann Weber
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Briefings Bioinform. 20 (4) (2019)
Kai Blin, Victòria Pascal Andreu, Emmanuel L. C. de los Santos, Francesco Del Carratore, Sang Yup Lee, Marnix H. Medema, Tilmann Weber
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 47 (Database-Issue) (2019)
Kai Blin, Simon Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H. Medema, Tilmann Weber
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
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
antiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Satria A. Kautsar, Hernando G. Suarez Duran, Kai Blin, Anne Osbourn, Marnix H. Medema
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Marc G. Chevrette, Fabian Aicheler, Oliver Kohlbacher, Cameron R. Currie, Marnix H. Medema
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria. Bioinform. 33 (20) (2017)
Kai Blin, Marnix H. Medema, Renzo Kottmann, Sang Yup Lee, Tilmann Weber
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 45 (Database-Issue) (2017)
Tilmann Weber, Kai Blin, Srikanth Duddela, Daniel Krug, Hyun Uk Kim, Robert E. Bruccoleri, Sang Yup Lee, Michael A. Fischbach, Rolf Müller, Wolfgang Wohlleben, Rainer Breitling, Eriko Takano, Marnix H. Medema
antiSMASH 3.0 - a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Marnix H. Medema, Yared Paalvast, Don D. Nguyen, Alexey Melnik, Pieter C. Dorrestein, Eriko Takano, Rainer Breitling
Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products. PLoS Comput. Biol. 10 (9) (2014)
Marnix H. Medema, Peter Cimermancic, Andrej Sali, Eriko Takano, Michael A. Fischbach
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis. PLoS Comput. Biol. 10 (12) (2014)
Kai Blin, Marnix H. Medema, Daniyal Kazempour, Michael A. Fischbach, Rainer Breitling, Eriko Takano, Tilmann Weber
antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Eriko Takano, Rainer Breitling
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Marc Röttig, Marnix H. Medema, Kai Blin, Tilmann Weber, Christian Rausch, Oliver Kohlbacher
NRPSpredictor2 - a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)