PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning

Autor: Lummy Maria Oliveira Monteiro, João Pedro Saraiva, Rodolfo Brizola Toscan, Peter F. Stadler, Rafael Silva-Rocha, Ulisses Nunes da Rocha

Publikováno v: Environmental Microbiome, Vol 17, Iss 1, Pp 1-11 (2022)

Abstract Background Transcription factors (TFs) are proteins controlling the flow of genetic information by regulating cellular gene expression. A better understanding of TFs in a bacterial community context may open novel revenues for exploring gene

Externí odkaz: https://doaj.org/article/bc17ba1b7db740998c31980b20b20c56

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge

Autor: Nafi’u Abdulkadir, Joao Pedro Saraiva, Florian Schattenberg, Rodolfo Brizola Toscan, Felipe Borim Correa, Hauke Harms, Susann Müller, Ulisses Nunes da Rocha

Publikováno v: Microorganisms, Vol 11, Iss 1, p 175 (2023)

The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry ce

Externí odkaz: https://doaj.org/article/9038459221f54ad9990a26f857c605fe

Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes

Autor: Joao Pedro Saraiva, Alexander Bartholomäus, Rodolfo Brizola Toscan, Petr Baldrian, Ulisses Nunes da Rocha

Publikováno v: Molecular Ecology Resources

As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::272528ffceb826a0e78c040fba1faf9f
https://gfzpublic.gfz-potsdam.de/pubman/item/item_5015832_2/component/file_5019720/5015832.pdf

Draft Genome Sequences of Two Sphingobium Species Associated with Hexachlorocyclohexane (HCH) Degradation Isolated from an HCH-Contaminated Soil

Autor: Nelson Khan, Rodolfo Brizola Toscan, Accadius Lunayo, Benson Wamalwa, Edward Muge, Francis J. Mulaa, René Kallies, Hauke Harms, Lukas Y. Wick, Ulisses Nunes da Rocha

Publikováno v: Microbiology Resource Announcements. 11

The draft genome sequences of two Sphingobium strains that are hexachlorocyclohexane (HCH) degraders are presented. The strains were isolated from HCH-contaminated soil in Kitengela, Kenya. Both genomes possess the lin genes responsible for HCH degra

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a6fbca3f73e8cc58945416d8107a08f9
https://doi.org/10.1128/mra.00886-21

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Autor: U. Nunes da Rocha, Jorge M.S. Gonçalves, Cymon J. Cox, Rodolfo Brizola Toscan, Tina Keller-Costa, Asunción Lago-Lestón, Rodrigo Costa, Sandra Silva, Nikos C. Kyrpides, João Pedro Saraiva

Publikováno v: Microbiome, vol 9, iss 1
Microbiome
Microbiome, Vol 9, Iss 1, Pp 1-21 (2021)
Repositório Científico de Acesso Aberto de Portugal
Repositório Científico de Acesso Aberto de Portugal (RCAAP)
instacron:RCAAP

Background In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic fe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::52b0697f164b46bf9c1ca7863c60eca0
https://escholarship.org/uc/item/66b26744