Search Results - "SETUBAL, Joao C"

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes by Dos Santos, Patricia C, Fang, Zhong, Mason, Steven W, Setubal, João C, Dixon, Ray

“…The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of…”
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Metagenome-assembled genomes: concepts, analogies, and challenges by Setubal, João C.

“…Metagenome-assembled genomes (MAGs) are microbial genomes reconstructed from metagenome data. In the last few years, many thousands of MAGs have been reported…”
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Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios by Braga, Lucas P P, Spor, Aymé, Kot, Witold, Breuil, Marie-Christine, Hansen, Lars H, Setubal, João C, Philippot, Laurent

“…Bacteriophages, the viruses infecting bacteria, are biological entities that can control their host populations. The ecological relevance of phages for…”
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MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins by Amgarten, Deyvid, Braga, Lucas P P, da Silva, Aline M, Setubal, João C

“…Here we present MARVEL, a tool for prediction of double-stranded DNA bacteriophage sequences in metagenomic bins. MARVEL uses a random forest machine learning…”
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Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq by Anderson, Letícia, Amaral, Murilo S, Beckedorff, Felipe, Silva, Lucas F, Dazzani, Bianca, Oliveira, Katia C, Almeida, Giulliana T, Gomes, Monete R, Pires, David S, Setubal, João C, DeMarco, Ricardo, Verjovski-Almeida, Sergio

“…Schistosomiasis is one of the most prevalent parasitic diseases worldwide and is a public health problem. Schistosoma mansoni is the most widespread species…”
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Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses by Patané, José S L, Martins, Jr, Joaquim, Rangel, Luiz Thiberio, Belasque, José, Digiampietri, Luciano A, Facincani, Agda Paula, Ferreira, Rafael Marini, Jaciani, Fabrício José, Zhang, Yunzeng, Varani, Alessandro M, Almeida, Nalvo F, Wang, Nian, Ferro, Jesus A, Moreira, Leandro M, Setubal, João C

“…Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a…”
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Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology by Tseng, Tsai-Tien, Tyler, Brett M, Setubal, João C

“…Protein secretion plays a central role in modulating the interactions of bacteria with their environments. This is particularly the case when symbiotic…”
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The complete genome sequence of 'Candidatus Liberibacter americanus', associated with Citrus huanglongbing by Wulff, Nelson A, Zhang, Shujian, Setubal, João C, Almeida, Nalvo F, Martins, Elaine C, Harakava, Ricardo, Kumar, Dibyendu, Rangel, Luiz Thiberio, Foissac, Xavier, Bové, Joseph M, Gabriel, Dean W

“…Liberibacter spp. form a Rhizobiaceae clade of phloem-limited pathogens of limited host range. Two obligately parasitic species have been sequenced:…”
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Transcriptional Profiling of Nitrogen Fixation in Azotobacter vinelandii by HAMILTON, Trinity L, LUDWIG, Marcus, DIXON, Ray, BOYD, Eric S, DOS SANTOS, Patricia C, SETUBAL, Joao C, BRYANT, Donald A, DEAN, Dennis R, PETERS, John W

“…Article Usage Stats Services JB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses by Paez-Espino, David, Chen, I-Min A, Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Szeto, Ernest, Pillay, Manoj, Huang, Jinghua, Markowitz, Victor M, Nielsen, Torben, Huntemann, Marcel, K Reddy, T B, Pavlopoulos, Georgios A, Sullivan, Matthew B, Campbell, Barbara J, Chen, Feng, McMahon, Katherine, Hallam, Steve J, Denef, Vincent, Cavicchioli, Ricardo, Caffrey, Sean M, Streit, Wolfgang R, Webster, John, Handley, Kim M, Salekdeh, Ghasem H, Tsesmetzis, Nicolas, Setubal, Joao C, Pope, Phillip B, Liu, Wen-Tso, Rivers, Adam R, Ivanova, Natalia N, Kyrpides, Nikos C

“…Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number…”
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The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity by Cai, Rongman, Lewis, James, Yan, Shuangchun, Liu, Haijie, Clarke, Christopher R, Campanile, Francesco, Almeida, Nalvo F, Studholme, David J, Lindeberg, Magdalen, Schneider, David, Zaccardelli, Massimo, Setubal, Joao C, Morales-Lizcano, Nadia P, Bernal, Adriana, Coaker, Gitta, Baker, Christy, Bender, Carol L, Leman, Scotland, Vinatzer, Boris A

“…Recently, genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and…”
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Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling by Thomas, Andrew M, Jesus, Eliane C, Lopes, Ademar, Aguiar, Jr, Samuel, Begnami, Maria D, Rocha, Rafael M, Carpinetti, Paola Avelar, Camargo, Anamaria A, Hoffmann, Christian, Freitas, Helano C, Silva, Israel T, Nunes, Diana N, Setubal, João C, Dias-Neto, Emmanuel

“…Sporadic and inflammatory forms of colorectal cancer (CRC) account for more than 80% of cases. Recent publications have shown mechanistic evidence for the…”
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Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range by Jalan, Neha, Kumar, Dibyendu, Andrade, Maxuel O, Yu, Fahong, Jones, Jeffrey B, Graham, James H, White, Frank F, Setubal, João C, Wang, Nian

“…Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of…”
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Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis by Dias-Neto, Emmanuel, Nunes, Diana N, Giordano, Ricardo J, Sun, Jessica, Botz, Gregory H, Yang, Kuan, Setubal, João C, Pasqualini, Renata, Arap, Wadih

“…Combinatorial phage display has been used in the last 20 years in the identification of protein-ligands and protein-protein interactions, uncovering relevant…”
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Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas by Zhang, Yunzeng, Jalan, Neha, Zhou, Xiaofeng, Goss, Erica, Jones, Jeffrey B, Setubal, João C, Deng, Xiaoling, Wang, Nian

“…Understanding the evolutionary history and potential of bacterial pathogens is critical to prevent the emergence of new infectious bacterial diseases…”
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Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii by Puigvert, Marina, Guarischi-Sousa, Rodrigo, Zuluaga, Paola, Coll, Núria S, Macho, Alberto P, Setubal, João C, Valls, Marc

“…Bacterial wilt of potatoes-also called brown rot-is a devastating disease caused by the vascular pathogen that leads to significant yield loss. As in other…”
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Role of Recombination in the Evolution of the Model Plant Pathogen Pseudomonas syringae pv. tomato DC3000, a Very Atypical Tomato Strain by Yan, Shuangchun, Liu, Haijie, Mohr, Toni J, Jenrette, Jenny, Chiodini, Rossella, Zaccardelli, Massimo, Setubal, João C, Vinatzer, Boris A

“…Pseudomonas syringae pv. tomato strain DC3000 (PtoDC3000) is one of the most intensively studied bacterial plant pathogens today. Here we report a thorough…”
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PAMDB, A Multilocus Sequence Typing and Analysis Database and Website for Plant-Associated Microbes by Almeida, Nalvo F, Yan, Shuangchun, Cai, Rongman, Clarke, Christopher R, Morris, Cindy E, Schaad, Norman W, Schuenzel, Erin L, Lacy, George H, Sun, Xiaoan, Jones, Jeffrey B, Castillo, Jose A, Bull, Carolee T, Leman, Scotland, Guttman, David S, Setubal, João C, Vinatzer, Boris A

“…Although there are adequate DNA sequence differences among plant-associated and plant-pathogenic bacteria to facilitate molecular approaches for their…”
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Editorial: Computational Methods for Microbiome Analysis by Setubal, João C, Stoye, Jens, Dutilh, Bas E

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New insights into plant natriuretic peptide evolution: From the lysogenic conversion in Xanthomonas to the lateral transfer to the whitefly Bemisia tabaci by Patané, José S.L., Moreira, Leandro M., de Melo Teixeira, Marcus, Martins Jr, Joaquim, Setubal, João C., Varani, Alessandro M.

“…•Parallel gains and duplications of plant natriuretic peptide (PNP) in many plant lineages.•Xanthomonas-phage coevolution in favor of bacterial virulence and…”
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