Search | Virtual Health Library

1.

A widely distributed gene cluster compensates for uricase loss in hominids.

Liu, Yuanyuan; Jarman, J Bryce; Low, Yen S; Augustijn, Hannah E; Huang, Steven; Chen, Haoqing; DeFeo, Mary E; Sekiba, Kazuma; Hou, Bi-Huei; Meng, Xiandong; Weakley, Allison M; Cabrera, Ashley V; Zhou, Zhiwei; van Wezel, Gilles; Medema, Marnix H; Ganesan, Calyani; Pao, Alan C; Gombar, Saurabh; Dodd, Dylan.

Cell ; 186(16): 3400-3413.e20, 2023 08 03.

Article in English | MEDLINE | ID: mdl-37541197

2.

Freedom of expression: A synthetic route to metabolites.

Augustijn, Hannah E; Medema, Marnix H.

Cell ; 185(9): 1449-1451, 2022 04 28.

Article in English | MEDLINE | ID: mdl-35487188

3.

A widely distributed gene cluster compensates for uricase loss in hominids.

Liu, Yuanyuan; Jarman, J Bryce; Low, Yen S; Augustijn, Hannah E; Huang, Steven; Chen, Haoqing; DeFeo, Mary E; Sekiba, Kazuma; Hou, Bi-Huei; Meng, Xiandong; Weakley, Allison M; Cabrera, Ashley V; Zhou, Zhiwei; van Wezel, Gilles; Medema, Marnix H; Ganesan, Calyani; Pao, Alan C; Gombar, Saurabh; Dodd, Dylan.

Cell ; 186(20): 4472-4473, 2023 Sep 28.

Article in English | MEDLINE | ID: mdl-37774682

4.

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.

Cimermancic, Peter; Medema, Marnix H; Claesen, Jan; Kurita, Kenji; Wieland Brown, Laura C; Mavrommatis, Konstantinos; Pati, Amrita; Godfrey, Paul A; Koehrsen, Michael; Clardy, Jon; Birren, Bruce W; Takano, Eriko; Sali, Andrej; Linington, Roger G; Fischbach, Michael A.

Cell ; 158(2): 412-421, 2014 Jul 17.

Article in English | MEDLINE | ID: mdl-25036635

5.

Mining genomes to illuminate the specialized chemistry of life.

Medema, Marnix H; de Rond, Tristan; Moore, Bradley S.

Nat Rev Genet ; 22(9): 553-571, 2021 09.

Article in English | MEDLINE | ID: mdl-34083778

6.

Convergent evolution for antibiotic biosynthesis in bacteria and animals.

Papon, Nicolas; Courdavault, Vincent; Medema, Marnix H.

Trends Genet ; 39(4): 237-239, 2023 04.

Article in English | MEDLINE | ID: mdl-36822964

7.

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

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

Nucleic Acids Res ; 52(D1): D586-D589, 2024 Jan 05.

Article in English | MEDLINE | ID: mdl-37904617

8.

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

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.

Nucleic Acids Res ; 51(W1): W46-W50, 2023 07 05.

Article in English | MEDLINE | ID: mdl-37140036

9.

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

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.

Environ Microbiol ; 26(2): e16589, 2024 Feb.

Article in English | MEDLINE | ID: mdl-38356049

10.

An isotopic labeling approach linking natural products with biosynthetic gene clusters.

McCaughey, Catherine S; van Santen, Jeffrey A; van der Hooft, Justin J J; Medema, Marnix H; Linington, Roger G.

Nat Chem Biol ; 18(3): 295-304, 2022 03.

Article in English | MEDLINE | ID: mdl-34969972

11.

Discovery and biosynthesis of cyclic plant peptides via autocatalytic cyclases.

Chigumba, Desnor N; Mydy, Lisa S; de Waal, Floris; Li, Wenjie; Shafiq, Khadija; Wotring, Jesse W; Mohamed, Osama G; Mladenovic, Tim; Tripathi, Ashootosh; Sexton, Jonathan Z; Kautsar, Satria; Medema, Marnix H; Kersten, Roland D.

Nat Chem Biol ; 18(1): 18-28, 2022 01.

Article in English | MEDLINE | ID: mdl-34811516

12.

iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures.

Louwen, Joris J R; Kautsar, Satria A; van der Burg, Sven; Medema, Marnix H; van der Hooft, Justin J J.

PLoS Comput Biol ; 19(2): e1010462, 2023 02.

Article in English | MEDLINE | ID: mdl-36758069

13.

Structure and function of the global topsoil microbiome.

Bahram, Mohammad; Hildebrand, Falk; Forslund, Sofia K; Anderson, Jennifer L; Soudzilovskaia, Nadejda A; Bodegom, Peter M; Bengtsson-Palme, Johan; Anslan, Sten; Coelho, Luis Pedro; Harend, Helery; Huerta-Cepas, Jaime; Medema, Marnix H; Maltz, Mia R; Mundra, Sunil; Olsson, Pål Axel; Pent, Mari; Põlme, Sergei; Sunagawa, Shinichi; Ryberg, Martin; Tedersoo, Leho; Bork, Peer.

Nature ; 560(7717): 233-237, 2018 08.

Article in English | MEDLINE | ID: mdl-30069051

14.

Harnessing regulatory networks in Actinobacteria for natural product discovery.

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

J Ind Microbiol Biotechnol ; 512024 Jan 09.

Article in English | MEDLINE | ID: mdl-38569653

15.

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

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

BMC Bioinformatics ; 24(1): 181, 2023 May 03.

Article in English | MEDLINE | ID: mdl-37131131

16.

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

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.

PLoS Biol ; 18(12): e3001026, 2020 12.

Article in English | MEDLINE | ID: mdl-33351797

17.

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

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

Nucleic Acids Res ; 49(D1): D639-D643, 2021 01 08.

Article in English | MEDLINE | ID: mdl-33152079

18.

BiG-FAM: the biosynthetic gene cluster families database.

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

Nucleic Acids Res ; 49(D1): D490-D497, 2021 01 08.

Article in English | MEDLINE | ID: mdl-33010170

19.

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

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

Nucleic Acids Res ; 49(W1): W263-W270, 2021 07 02.

Article in English | MEDLINE | ID: mdl-34019648

20.

antiSMASH 6.0: improving cluster detection and comparison capabilities.

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

Nucleic Acids Res ; 49(W1): W29-W35, 2021 07 02.

Article in English | MEDLINE | ID: mdl-33978755

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A widely distributed gene cluster compensates for uricase loss in hominids.

Freedom of expression: A synthetic route to metabolites.

A widely distributed gene cluster compensates for uricase loss in hominids.

Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.

Mining genomes to illuminate the specialized chemistry of life.

Convergent evolution for antibiotic biosynthesis in bacteria and animals.

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

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

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

An isotopic labeling approach linking natural products with biosynthetic gene clusters.

Discovery and biosynthesis of cyclic plant peptides via autocatalytic cyclases.

iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures.

Structure and function of the global topsoil microbiome.

Harnessing regulatory networks in Actinobacteria for natural product discovery.

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

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

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

BiG-FAM: the biosynthetic gene cluster families database.

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

antiSMASH 6.0: improving cluster detection and comparison capabilities.