Search Results - "Saraiva, Joao Pedro"

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes by Corrêa, Felipe Borim, Saraiva, João Pedro, Stadler, Peter F, da Rocha, Ulisses Nunes

“…Abstract Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the…”
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Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition by Tláskal, Vojtěch, Brabcová, Vendula, Větrovský, Tomáš, Jomura, Mayuko, López-Mondéjar, Rubén, Oliveira Monteiro, Lummy Maria, Saraiva, João Pedro, Human, Zander Rainier, Cajthaml, Tomáš, Nunes da Rocha, Ulisses, Baldrian, Petr

“…Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to…”
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Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood by Tláskal, Vojtěch, Brabcová, Vendula, Větrovský, Tomáš, López-Mondéjar, Rubén, Monteiro, Lummy Maria Oliveira, Saraiva, João Pedro, da Rocha, Ulisses Nunes, Baldrian, Petr

“…Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms –…”
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Fungal biomarker discovery by integration of classifiers by Saraiva, João Pedro, Oswald, Marcus, Biering, Antje, Röll, Daniela, Assmann, Cora, Klassert, Tilman, Blaess, Markus, Czakai, Kristin, Claus, Ralf, Löffler, Jürgen, Slevogt, Hortense, König, Rainer

“…The human immune system is responsible for protecting the host from infection. However, in immunocompromised individuals the risk of infection increases…”
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PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning by Oliveira Monteiro, Lummy Maria, Saraiva, João Pedro, Brizola Toscan, Rodolfo, Stadler, Peter F, Silva-Rocha, Rafael, Nunes da Rocha, Ulisses

“…Transcription factors (TFs) are proteins controlling the flow of genetic information by regulating cellular gene expression. A better understanding of TFs in a…”
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MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes by Nata'ala, Muhammad Kabiru, Avila Santos, Anderson P, Coelho Kasmanas, Jonas, Bartholomäus, Alexander, Saraiva, João Pedro, Godinho Silva, Sandra, Keller-Costa, Tina, Costa, Rodrigo, Gomes, Newton C. M, Ponce de Leon Ferreira de Carvalho, André Carlos, Stadler, Peter F, Sipoli Sanches, Danilo, Nunes da Rocha, Ulisses

“…Background Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major…”
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The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes by Avila Santos, Anderson Paulo, Kabiru Nata’ala, Muhammad, Kasmanas, Jonas Coelho, Bartholomäus, Alexander, Keller-Costa, Tina, Jurburg, Stephanie D., Tal, Tamara, Camarinha-Silva, Amélia, Saraiva, João Pedro, Ponce de Leon Ferreira de Carvalho, André Carlos, Stadler, Peter F., Sipoli Sanches, Danilo, Rocha, Ulisses

“…BACKGROUNDMetagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the…”
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Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes by Saraiva, Joao Pedro, Bartholomäus, Alexander, Toscan, Rodolfo Brizola, Baldrian, Petr, Nunes da Rocha, Ulisses

“…As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although…”
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Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns by Le, Anh Vu, Větrovský, Tomáš, Barucic, Denis, Saraiva, Joao Pedro, Dobbler, Priscila Thiago, Kohout, Petr, Pospíšek, Martin, da Rocha, Ulisses Nunes, Kléma, Jiří, Baldrian, Petr

“…Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA:…”
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Biotransformation of hexachlorocyclohexanes contaminated biomass for energetic utilization demonstrated in continuous anaerobic digestion system by Lian, Shujuan, Nikolausz, Marcell, Nijenhuis, Ivonne, da Rocha, Ulisses Nunes, Liu, Bin, Corrêa, Felipe Borim, Saraiva, João Pedro, Richnow, Hans Hermann

“…•A pollution clean-up strategy combines phytoremediation and anaerobic digestion.•Hexachlorocyclohexane (HCH) contaminated plant was used as substrate for…”
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Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa by Magnúsdóttir, Stefanía, Saraiva, Joao Pedro, Bartholomäus, Alexander, Soheili, Majid, Toscan, Rodolfo Brizola, Zhang, Junya, Nunes da Rocha, Ulisses

“…Every year, millions of deaths are associated with the increased spread of antimicrobial resistance genes (ARGs) in bacteria. With the increasing urbanization…”
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MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy by Rocha, Ulisses, Coelho Kasmanas, Jonas, Kallies, René, Saraiva, Joao Pedro, Toscan, Rodolfo Brizola, Štefanič, Polonca, Bicalho, Marcos Fleming, Borim Correa, Felipe, Baştürk, Merve Nida, Fousekis, Efthymios, Viana Barbosa, Luiz Miguel, Plewka, Julia, Probst, Alexander J., Baldrian, Petr, Stadler, Peter F., Bartholomäus, Alexander, Rosado, Alexandre Soares, Fiore‐Donno, Ana‐Maria, Leon Ferreira de Carvalho, André Carlos Ponce, Gubry‐Rangin, Cecile, Machado, Daniel, Sanches, Danilo S., Wagner, Dirk, Berg, Gabriele, Mulec, Ines Mundic, Muehe, Marie, Bonkowski, Michael, Gomes, Newton, Peixoto, Raquel, Costa, Rodrigo, Kleinsteuber, Sabine, Gribaldo, Simonetta, Costa, Tina Keller, Pellizari, Vivian

“…Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for…”
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Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater by Abdulkadir, Nafi'u, Saraiva, Joao Pedro, Zhang, Junya, Stolte, Stefan, Gillor, Osnat, Harms, Hauke, Rocha, Ulisses

“…Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements…”
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Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge by Abdulkadir, Nafi'u, Saraiva, Joao Pedro, Schattenberg, Florian, Toscan, Rodolfo Brizola, Borim Correa, Felipe, Harms, Hauke, Müller, Susann, da Rocha, Ulisses Nunes

“…The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even…”
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Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data by Saraiva, Joao Pedro, Worrich, Anja, Karakoç, Canan, Kallies, Rene, Chatzinotas, Antonis, Centler, Florian, Nunes da Rocha, Ulisses

“…Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data…”
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OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes by Saraiva, João Pedro, Bartholomäus, Alexandre, Kallies, René, Gomes, Marta, Bicalho, Marcos, Coelho Kasmanas, Jonas, Vogt, Carsten, Chatzinotas, Antonis, Stadler, Peter, Dias, Oscar, Nunes da Rocha, Ulisses

“…The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present…”
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The Influence of the Type of Surgical Thread and Suture in the Open Carpal Tunnel Syndrome Surgery by Magalhães, Marcelo José Silva, Cruz, Beatriz Xavier, Santos, Fabrício Conceição dos, Oliveira, Isabella Mendes de, Sousa, João Pedro Saraiva, Guimarães, Thaís de Oliveira, Lopes, Thiago Antunes, Hoffmann, Ernesto José

“…Carpal tunnel syndrome (CTS) is the result of compression and/or traction of the median nerve in the carpal tunnel. It is the most frequent compressive…”
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Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery by Rocha, Ulisses, Kasmanas, Jonas Coelho, Toscan, Rodolfo, Sanches, Danilo S, Magnusdottir, Stefania, Saraiva, Joao Pedro

“…We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To…”
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Competitive inhibition and mutualistic growth in co-infections: deciphering Staphylococcus aureus-Acinetobacter baumannii interaction dynamics by Timme, Sandra, Wendler, Sindy, Klassert, Tilman E, Saraiva, Joao Pedro, da Rocha, Ulisses Nunes, Wittchen, Manuel, Schramm, Sareda, Ehricht, Ralf, Monecke, Stefan, Edel, Birgit, Rödel, Jürgen, Löffler, Bettina, Ramirez, Maria Soledad, Slevogt, Hortense, Figge, Marc Thilo, Tuchscherr, Lorena

“…and are frequently co-isolated from polymicrobial infections that are severe and refractory to therapy. Here, we apply a combination of wet-lab experiments and…”
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Automatic Text Summarization by Saraiva, João Pedro Abrantes

“…Writing text was one of the first ever methods used by humans to represent their knowledge. Text can be of different types and have different purposes.Due to…”
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