Taxometer: Improving taxonomic classification of metagenomics contigs

Autor: Svetlana Kutuzova, Mads Nielsen, Pau Piera, Jakob Nybo Nissen, Simon Rasmussen

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-9 (2024)

Abstract For taxonomy based classification of metagenomics assembled contigs, current methods use sequence similarity to identify their most likely taxonomy. However, in the related field of metagenomic binning, contigs are routinely clustered using

Externí odkaz: https://doaj.org/article/a2e85bf5648d470399ac3f8d5f6821ef

Genome binning of viral entities from bulk metagenomics data

Autor: Joachim Johansen, Damian R. Plichta, Jakob Nybo Nissen, Marie Louise Jespersen, Shiraz A. Shah, Ling Deng, Jakob Stokholm, Hans Bisgaard, Dennis Sandris Nielsen, Søren J. Sørensen, Simon Rasmussen

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-12 (2022)

Here, Johansen et al. develop an approach, Phages from Metagenomics Binning (PHAMB), that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate t

Externí odkaz: https://doaj.org/article/2c44accba90c47bbab7eeacd53765ca3

Critical Assessment of Metagenome Interpretation - the second round of challenges

Autor: Zho. Wang, Ariane Khaledi, Alice C. McHardy, Anton Korobeynikov, A. Cristian, Gherman Uritskiy, Huijue Jia, Philip Thomas Lanken Conradsen Clausen, Till Strowig, Denis Bertrand, N. Smit, Niranjan Nagarajan, Enrico Seiler, Adam G. Thomas, David Koslicki, Piotr Wojtek Dabrowski, Vitor C. Piro, Andreas Bremges, L. Oliker, Petra Gastmeier, Steven Hofmeyr, Zhe Wang, Jason C. Kwan, Alessio Milanese, Tue Sparholt Jørgensen, Mohammed Alser, J. S. Porter, Alexander Sczyrba, Georg Zeller, Bernhard Y. Renard, Chenhao Li, Riccardo Vicedomini, Chengxuan Tong, Andrew S. Warren, Jaqueline J. Brito, Alexey Gurevich, Axel Kola, C.T. Brown, Julien Tremblay, Shinichi Sunagawa, F. Maechler, G. Robertson, Jakob Nybo Nissen, Ruben Garrido-Oter, Rob Egan, Simon Rasmussen, Katherine Yelick, Fernando Meyer, Zhengqiao Zhao, Daniel R Mende, Shanfeng Zhu, Lizhen Shi, F. Malcher-Miranda, Fengzhu Sun, Zi. Wang, Lars Hestbjerg Hansen, J. Buchmann, S. D. Kieser, Jie Zhu, E. M. Robertsen, Fantin Mesny, Sergey Nurk, Pierre Marijon, Dmitry Meleshko, Gail L. Rosen, Nicola Segata, Nathan LaPierre, Eugene Goltsman, Varuni Sarwal, Mirko Trajkovski, Dmitry Antipov, P. Huang, Vanesa R. Marcelino, Francesco Beghini, Antoine Limasset, Rayan Chikhi, Eleazar Eskin, M. A. Gray, Camille Marchet, Lucas Paoli, Adrian Fritz, Evangelos Georganas, Zhi-Luo Deng, T. Klemetsen, Hans-Joachim Ruscheweyh, Evan R. Rees, S. Häußler, Simona Radutoiu, Stéphane Hacquard, Paul Schulze-Lefert, Mikhail Kolmogorov, N. P. Willassen, Pierre Peterlongo, Knut Reinert, Claire Lemaitre, Ronghui You, Søren J. Sørensen, Aydin Buluc, Luiz Irber, Serghei Mangul, B. Chen, Aaron E. Darling

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to asses

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::30f2c611599ba0fd5421c09bf5485486
https://doi.org/10.1101/2021.07.12.451567

Improved metagenome binning and assembly using deep variational autoencoders

Autor: Henrik Nielsen, Rosa Lundbye Allesøe, Simon Rasmussen, Ole Winther, Jakob Nybo Nissen, Jose Juan Almagro Armenteros, Thomas Nordahl Petersen, Casper Kaae Sønderby, Joachim Johansen, Lars Juhl Jensen, Christopher Heje Grønbech

Publikováno v: Nissen, J N, Johansen, J, Allesøe, R L, Sønderby, C K, Armenteros, J J A, Grønbech, C H, Jensen, L J, Nielsen, H B, Petersen, T N, Winther, O & Rasmussen, S 2021, ' Improved metagenome binning and assembly using deep variational autoencoders ', Nature Biotechnology, vol. 39, pp. 555–560 . https://doi.org/10.1038/s41587-020-00777-4
Nissen, J N, Johansen, J, Allesoe, R L, Sonderby, C K, Armenteros, J J A, Gronbech, C H, Jensen, L J, Nielsen, H B, Petersen, T N, Winther, O & Rasmussen, S 2021, ' Improved metagenome binning and assembly using deep variational autoencoders ', Nature Biotechnology, vol. 39, pp. 555-560 . https://doi.org/10.1038/s41587-020-00777-4

Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ea882c6a29925f82f93f66ca2c1649eb
https://orbit.dtu.dk/en/publications/b3877c32-c445-4074-ab33-a45602985a09

Two residues determine the product profile of the class II diterpene synthases TPS14 and TPS21 of Tripterygium wilfordii

Autor: Jakob Nybo Nissen, Nikolaj Lervad Hansen, Björn Hamberger

Publikováno v: Phytochemistry. 138

The medicinal plant Tripterygium wilfordii (Celastraceae) contains a pair of class II diterpene synthases (diTPS) of specialized labdane-type metabolism that, despite remarkably close homology, form strikingly different products. TwTPS21 catalyzes bi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e68d8156c900b6115c19491e24f087c9
https://pubmed.ncbi.nlm.nih.gov/28279524