Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching

Autor: Joris J. R. Louwen, Marnix H. Medema, Justin J. J. van der Hooft

Publikováno v: Microbiome, Vol 11, Iss 1, Pp 1-12 (2023)

Abstract Background It is well-known that the microbiome produces a myriad of specialised metabolites with diverse functions. To better characterise their structures and identify their producers in complex samples, integrative genome and metabolome m

Externí odkaz: https://doaj.org/article/64adb32a491840738686867bbd496ca0

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

Autor: Barbara R Terlouw, Kai Blin, Jorge C Navarro-Muñoz, Nicole E Avalon, Marc G Chevrette, Susan Egbert, Sanghoon Lee, David Meijer, Michael J J Recchia, Zachary L Reitz, Jeffrey A van Santen, Nelly Selem-Mojica, Thomas Tørring, Liana Zaroubi, Mohammad Alanjary, Gajender Aleti, César Aguilar, Suhad A 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, Victor 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 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 J U Pronk, Adriana Rego, Devasahayam Arokia Balaya Rex, Serina Robinson, L Rodrigo Rosas-Becerra, Eve T Roxborough, Michelle A Schorn, Darren J Scobie, Kumar Saurabh Singh, Nika Sokolova, Xiaoyu Tang, Daniel 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

Publikováno v: Nucleic Acids Research, 51(D1), D603-D610. Oxford University Press
Terlouw, B R, Blin, K, Navarro-Muñoz, J C, Avalon, N E, Chevrette, M G, Egbert, S, Lee, S, Meijer, D, Recchia, M J J, Reitz, ZL, van Santen, JA, Selem-Mojica, N, Tørring, T, Zaroubi, L, Alanjary, M, Aleti, G, Aguilar, C, Al-Salihi, S A A, Augustijn, HE, Avelar-Rivas, JA, Avitia-Domínguez, LA, Barona-Gómez, F, Bernaldo-Agüero, J, Bielinski, V A, Biermann, F, Booth, TJ, Carrion Bravo, VJ, Castelo-Branco, R, Chagas, FO, Cruz-Morales, P, Du, C, Duncan, KR, Gavriilidou, A, Gayrard, D, Gutiérrez-García, K, Haslinger, K, Helfrich, E J N, van der Hooft, J J J, Jati, AP, Kalkreuter, E, Kalyvas, N, Kang, KB, Kautsar, S, Kim, W, Kunjapur, AM, Li, Y-X, Lin, G-M, Loureiro, C, Louwen, J J R, Louwen, N L L, Lund, G, Parra, J, Philmus, B, Pourmohsenin, B, Pronk, L J U, Rego, A, Rex, DAB, Robinson, S, Rosas-Becerra, LR, Roxborough, ET, Schorn, MA, Scobie, DJ, Singh, KS, Sokolova, N, Tang, X, Udwary, D, Vigneshwari, A, Vind, K, Vromans, S P J M, Waschulin, V, Williams, SE, Winter, JM, Witte, TE, Xie, H, Yang, D, Yu, J, Zdouc, M, Zhong, Z, Collemare, J, Linington, RG, Weber, T & Medema, MH 2023, ' MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters ', Nucleic Acids Research, vol. 51, no. D1, gkac1049, pp. D603-D610 . https://doi.org/10.1093/nar/gkac1049
Terlouw, B R, Blin, K, Navarro-Muñoz, J C, Avalon, N E, Chevrette, M G, Egbert, S, Lee, S, Meijer, D, Recchia, M J J, Reitz, Z L, van Santen, J A, Selem-Mojica, N, Tørring, T, Zaroubi, L, Alanjary, M, Aleti, G, Aguilar, C, Al-Salihi, S A A, Augustijn, H E, Avelar-Rivas, J A, Avitia-Domínguez, L A, Barona-Gómez, F, Bernaldo-Agüero, J, Bielinski, V A, Biermann, F, Booth, T J, Carrion Bravo, V J, Castelo-Branco, R, Chagas, F O, Cruz-Morales, P, Du, C, Duncan, K R, Gavriilidou, A, Gayrard, D, Gutiérrez-García, K, Haslinger, K, Helfrich, E J N, van der Hooft, J J J, Jati, A P, Kalkreuter, E, Kalyvas, N, Kang, K B, Kautsar, S, Kim, W, Kunjapur, A M, Li, Y-X, Lin, G-M, Loureiro, C, Louwen, J J R, Louwen, N L L, Lund, G, Parra, J, Philmus, B, Pourmohsenin, B, Pronk, L J U, Rego, A, Rex, D A B, Robinson, S, Rosas-Becerra, L R, Roxborough, E T, Schorn, M A, Scobie, D J, Singh, K S, Sokolova, N, Tang, X, Udwary, D, Vigneshwari, A, Vind, K, Vromans, S P J M, Waschulin, V, Williams, S E, Winter, J M, Witte, T E, Xie, H, Yang, D, Yu, J, Zdouc, M, Zhong, Z, Collemare, J, Linington, R G, Weber, T & Medema, M H 2023, ' MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters ', Nucleic Acids Research, vol. 51, no. D1, pp. D603–D610 . https://doi.org/10.1093/nar/gkac1049
Terlouw, B R, Blin, K, Navarro-Muñoz, J C, Avalon, N E, Chevrette, M G, Egbert, S, Lee, S, Meijer, D, Recchia, M J J, Reitz, Z L, van Santen, J A, Selem-Mojica, N, Tørring, T, Zaroubi, L, Alanjary, M, Aleti, G, Aguilar, C, Al-Salihi, S A A, Augustijn, H E, Avelar-Rivas, J A, Avitia-Domínguez, L A, Barona-Gómez, F, Bernaldo-Agüero, J, Bielinski, V A, Biermann, F, Booth, T J, Carrion Bravo, V J, Castelo-Branco, R, Chagas, F O, Cruz-Morales, P, Du, C, Duncan, K R, Gavriilidou, A, Gayrard, D, Gutiérrez-García, K, Haslinger, K, Helfrich, E J N, van der Hooft, J J J, Jati, A P, Kalkreuter, E, Kalyvas, N, Kang, K B, Kautsar, S, Kim, W, Kunjapur, A M, Li, Y-X, Lin, G-M, Loureiro, C, Louwen, J J R, Louwen, N L L, Lund, G, Parra, J, Philmus, B, Pourmohsenin, B, Pronk, L J U, Rego, A, Rex, D A B, Robinson, S, Rosas-Becerra, L R, Roxborough, E T, Schorn, M A, Scobie, D J, Singh, K S, Sokolova, N, Tang, X, Udwary, D, Vigneshwari, A, Vind, K, Vromans, S P J M, Waschulin, V, Williams, S E, Winter, J M, Witte, T E, Xie, H, Yang, D, Yu, J, Zdouc, M, Zhong, Z, Collemare, J, Linington, R G, Weber, T & Medema, M H 2023, ' MIBiG 3.0 : a community-driven effort to annotate experimentally validated biosynthetic gene clusters ', Nucleic Acids Research, vol. 51, no. D1, pp. D603–D610 . https://doi.org/10.1093/nar/gkac1049
Nucleic acids research, 51(D1), D603-D610
Nucleic acids research 51 (2023) D1

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

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5e557bd5c3d2ddd7d6574fc9d08027c2
https://pure.knaw.nl/portal/en/publications/4e99309a-6840-4150-801f-070cfa20d40c

NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

Autor: Tiago F Leão, Mingxun Wang, Ricardo da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender P Gomes, Asker Brejnrod, Evgenia Glukhov, Allegra T Aron, Joris J R Louwen, Hyun Woo Kim, Raphael Reher, Marli F Fiore, Justin J J van der Hooft, Lena Gerwick, William H Gerwick, Nuno Bandeira, Pieter C Dorrestein

Publikováno v: PNAS Nexus 1 (2022) 5
PNAS nexus, vol 1, iss 5
PNAS Nexus, 1(5)

Microbial specialized metabolites are an important source of and inspiration for many pharmaceutical, biotechnological products and play key roles in ecological processes. However, most bioactivity-guided isolation and identification methods widely e

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::61845ae73ee905ab31d4af2ebe6e0c87
https://doi.org/10.1093/pnasnexus/pgac257