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Marnix H. Medema
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2020 – today
- 2024
- [j27]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): 58 (2024) - 2023
- [j26]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): 181 (2023) - [j25]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): 603-610 (2023) - [j24]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): 46-50 (2023) - [j23]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) - 2022
- [j22]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): 34 (2022) - 2021
- [j21]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): 64 (2021) - [j20]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): D490-D497 (2021) - [j19]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): D639-D643 (2021) - [j18]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): 29-35 (2021) - [j17]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): 263-270 (2021) - 2020
- [j16]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): 4846-4853 (2020) - [j15]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): D454-D458 (2020) - [j14]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): W546-W552 (2020)
2010 – 2019
- 2019
- [j13]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): 1103-1113 (2019) - [j12]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): D625-D630 (2019) - [j11]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): W81-W87 (2019) - 2017
- [j10]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): 3202-3210 (2017) - [j9]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): D555-D559 (2017) - [j8]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): W36-W41 (2017) - [j7]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): W55-W63 (2017) - 2015
- [j6]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): W237-W243 (2015) - 2014
- [j5]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) - [j4]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) - 2013
- [j3]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): 204-212 (2013) - 2011
- [j2]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): 339-346 (2011) - [j1]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): 362-367 (2011)
Coauthor Index
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last updated on 2024-08-05 20:25 CEST by the dblp team
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