MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
Nucleic Acids Research, vol. 51, pp. D603–D610
Abstract
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.
Authors 80
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Novo Nordisk Foundation · Technical University of Denmark
Affiliation as printed
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Kgs. Lyngby, Denmark
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Westerdijk Fungal Biodiversity Institute · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
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Scripps Institution of Oceanography · University of California San Diego
Affiliation as printed
Scripps Institution of Oceanography, University of California San Diego , 9500 Gilman Drive, La Jolla , CA 92093-0212 , USA
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Affiliation as printed
Department of Microbiology and Cell Science, University of Florida , Gainesville , FL 32611, USA
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Affiliation as printed
Department of Chemistry, University of Manitoba , 66 Chancellors Cir, Winnipeg , MB R3T 2N2 , Canada
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Affiliation as printed
Department of Chemistry, Simon Fraser University, 8888 University Drive , Burnaby, British Columbia V5A 1S6 , Canada
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Affiliation as printed
Department of Chemistry, Simon Fraser University, 8888 University Drive , Burnaby, British Columbia V5A 1S6 , Canada
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Affiliation as printed
Department of Chemistry, Simon Fraser University, 8888 University Drive , Burnaby, British Columbia V5A 1S6 , Canada
Unnatural Products , 2161 Delaware Ave. Suite A, Santa Cruz , CA 95060 , USA
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Centro de Ciencias Matemáticas · Universidad Nacional Autónoma de México
Affiliation as printed
Centro de Ciencias Matemáticas UNAM , Morelia , México
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Affiliation as printed
Department of Biological and Chemical Engineering, Aarhus University , Denmark
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Affiliation as printed
Department of Chemistry, Simon Fraser University, 8888 University Drive , Burnaby, British Columbia V5A 1S6 , Canada
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Affiliation as printed
Food and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University , Nashville , TN 37209, USA
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Purdue University West Lafayette
Affiliation as printed
Department of Chemistry, Purdue University , West Lafayette , IN , USA
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University of Technology - Iraq
Affiliation as printed
Department of Applied Sciences, University of Technology , Iraq
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Leiden University · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden, The Netherlands
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Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Affiliation as printed
Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada , Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato , Gto., México
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Leiden University · Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Affiliation as printed
Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden, The Netherlands
Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada , Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato , Gto., México
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Leiden University · Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Affiliation as printed
Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden, The Netherlands
Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada , Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato , Gto., México
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Universidad Nacional Autónoma de México
Affiliation as printed
Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca , Morelos , México
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Affiliation as printed
Synthetic Biology and Bioenergy Group, J. Craig Venter Institute , La Jolla , CA 92037 , USA
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Goethe University Frankfurt · LOEWE Centre for Translational Biodiversity Genomics · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
Institute of Molecular Bio Science, Goethe-University Frankfurt , D-60438 Frankfurt am Main, Germany
LOEWE Center for Translational Biodiversity Genomics (TBG) , Senckenberganlage 25, 60325 Frankfurt am Main, Germany
LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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The University of Western Australia · Novo Nordisk Foundation · Technical University of Denmark
Affiliation as printed
School of Molecular Sciences, University of Western Australia , Perth , Australia
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Kgs. Lyngby, Denmark
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Universidade do Porto · Centro Interdisciplinar de Investigação Marinha e Ambiental
Affiliation as printed
Faculty of Sciences, University of Porto , 4150 -179 Porto , Portugal
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto , Portugal
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Universidade Federal do Rio de Janeiro
Affiliation as printed
Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , 21941-599, Brazil
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Novo Nordisk Foundation · Technical University of Denmark
Affiliation as printed
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Kgs. Lyngby, Denmark
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Affiliation as printed
Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden, The Netherlands
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Affiliation as printed
University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences , 141 Cathedral Street, Glasgow , G4 ORE UK
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Affiliation as printed
Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen , Tübingen , Germany
Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen , Tübingen, Germany
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John Innes Centre · Norwich Research Park
Affiliation as printed
Department of Molecular Microbiology , John Innes Centre, Norwich Research Park, Norwich , NR4 7UH, UK
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Carnegie Institution for Science · Department of Embryology
Affiliation as printed
Department of Embryology, Carnegie Institution for Science , 3520 San Martin Drive, Baltimore , MD 21218, USA
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Affiliation as printed
Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Goethe University Frankfurt · LOEWE Centre for Translational Biodiversity Genomics
Affiliation as printed
Institute of Molecular Bio Science, Goethe-University Frankfurt , D-60438 Frankfurt am Main, Germany
LOEWE Center for Translational Biodiversity Genomics (TBG) , Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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University of Johannesburg · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
Department of Biochemistry, University of Johannesburg , Auckland Park, Johannesburg 2006 , South Africa
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Affiliation as printed
Indonesian Society of Bioinformatics And Biodiversity , Indonesia
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Affiliation as printed
Department of Chemistry, University of Florida Scripps Biomedical Research , 110 Scripps Way, Jupiter , FL 33458, USA
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Westerdijk Fungal Biodiversity Institute
Affiliation as printed
Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
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College of Pharmacy, Sookmyung Women's University , Seoul , South Korea
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Department of Chemistry, University of Florida Scripps Biomedical Research , 110 Scripps Way, Jupiter , FL 33458, USA
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Korean Lichen Research Institute, Sunchon National Universtiy , Suncheon , South Korea
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Department of Chemical & Biomolecular Engineering, University of Delaware , Newark , DE 19716 , USA
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Department of Chemistry, The University of Hong Kong , Pokfulam Road, Hong Kong , P.R. China
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Massachusetts Institute of Technology
Affiliation as printed
Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge , MA , USA
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Wageningen University & Research
Affiliation as printed
Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708WE, Wageningen , The Netherlands
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Universidad de Costa Rica · Consejo Nacional de Rectores
Affiliation as printed
Centro Nacional de Innovaciones Biotecnológicas (CENIBiot) , CeNAT-CONARE, 1174-1200, San José , Costa Rica
Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica , San José , 11501-2060 , Costa Rica
Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica , San José , 11501-2060 , Costa Rica
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Affiliation as printed
Department of Pharmaceutical Sciences, Oregon State University , USA
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Affiliation as printed
Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen , Tübingen , Germany
Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen , Tübingen, Germany
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Universidade do Porto · Centro Interdisciplinar de Investigação Marinha e Ambiental · Instituto de Ciências Biomédicas Albel Salazar
Affiliation as printed
Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto , Portugal
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto , Portugal
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Affiliation as printed
Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University) , Mangalore 575018 , India
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Swiss Federal Institute of Aquatic Science and Technology
Affiliation as printed
Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology , Überlandstrasse 133, CH-8600 Dübendorf , Switzerland
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Leiden University · Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Affiliation as printed
Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden, The Netherlands
Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada , Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato , Gto., México
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Affiliation as printed
School of Chemistry, University of Nottingham, University Park , Nottingham NG7 2RD, UK
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Wageningen University & Research
Affiliation as printed
Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708WE, Wageningen , The Netherlands
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Affiliation as printed
University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences , 141 Cathedral Street, Glasgow , G4 ORE UK
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Affiliation as printed
Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Affiliation as printed
Institute of Chemical Biology, Shenzhen Bay Laboratory , Shenzhen 518132 , China
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
DOE Joint Genome Institute , Lawrence Berkeley National Lab, Berkeley, CA, USA
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Affiliation as printed
Department of Microbiology, University of Szeged , Hungary
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Wageningen University & Research
Affiliation as printed
Host-Microbe Interactomics Group, Wageningen University , 6708 WD Wageningen, The Netherlands
NAICONS Srl , 20139 Milan , Italy
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Affiliation as printed
School of Life Sciences, The University of Warwick , Coventry CV4 7AL, UK
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School of Biochemistry, University of Bristol, University Walk , Bristol BS8 1TD, UK
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Department of Medicinal Chemistry, University of Utah , Salt Lake City , UT 84112 , USA
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Affiliation as printed
Department of Chemistry and Biomolecular Sciences, University of Ottawa , Ottawa , Canada
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Chinese Academy of Agricultural Sciences · Oil Crops Research Institute · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
Key laboratory of Detection for Biotoxins, Ministry of Agriculture and Rural Affairs and Oil Crops Research Institute, Chinese Academy of Agricultural Sciences , Wuhan 430061 , China
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Affiliation as printed
Department of Chemistry and Natural Products Discovery Center, UF Scripps Biomedical Research, University of Florida , Jupiter , FL 33458 , USA
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Southern University of Science and Technology
Affiliation as printed
SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology , Shenzhen , Guangdong 518055 , China
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
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Wageningen University & Research
Affiliation as printed
Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708WE, Wageningen , The Netherlands
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Westerdijk Fungal Biodiversity Institute
Affiliation as printed
Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
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Affiliation as printed
Department of Chemistry, Simon Fraser University, 8888 University Drive , Burnaby, British Columbia V5A 1S6 , Canada
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Tilmann Weber corresponding
Novo Nordisk Foundation · Technical University of Denmark
Affiliation as printed
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Kgs. Lyngby, Denmark
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Leiden University · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands
Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden, The Netherlands
Cited by 445 stored of 447
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