REGEN: Ancestral Genome Reconstruction for Bacteria

by João C. Setubal, Kuan Yang, Lenwood S. Heath
Published 2012-07-01

Editorial: Computational Methods for Microbiome Analysis

by João C. Setubal, Jens Stoye, Bas E. Dutilh
Published 2020-12-01

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins

by Deyvid Amgarten, Lucas P. P. Braga, Lucas P. P. Braga, Aline M. da Silva, João C. Setubal, João C. Setubal
Published 2018-08-01

Genetic resources for methane production from biomass described with gene ontology

by Endang ePurwantini, Trudy eTorto-Alalibo, Jane eLomax, João C. Setubal, João C. Setubal, Brett M. Tyler, Brett M. Tyler, Biswarup eMukhopadhyay, Biswarup eMukhopadhyay
Published 2014-12-01

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

by Lucas P. P. Braga, Aymé Spor, Witold Kot, Marie-Christine Breuil, Lars H. Hansen, João C. Setubal, Laurent Philippot
Published 2020-04-01

Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs

by Lucas F. daSilva, Lucas F. daSilva, Felipe C. Beckedorff, Felipe C. Beckedorff, Ana C. Ayupe, Murilo S. Amaral, Murilo S. Amaral, Vinícius Mesel, Alexandre Videira, Alexandre Videira, Eduardo M. Reis, João C. Setubal, João C. Setubal, Sergio Verjovski-Almeida, Sergio Verjovski-Almeida
Published 2018-04-01

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

by Lucas P. P. Braga, Lucas P. P. Braga, Shannon M. Soucy, Deyvid E. Amgarten, Aline M. da Silva, João C. Setubal
Published 2018-01-01

Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis.

by Emmanuel Dias-Neto, Diana N Nunes, Ricardo J Giordano, Jessica Sun, Gregory H Botz, Kuan Yang, João C Setubal, Renata Pasqualini, Wadih Arap
Published 2009-12-01

An anomalous type IV secretion system in Rickettsia is evolutionarily conserved.

by Joseph J Gillespie, Nicole C Ammerman, Sheila M Dreher-Lesnick, M Sayeedur Rahman, Micah J Worley, Joao C Setubal, Bruno S Sobral, Abdu F Azad
Published 2009-01-01

Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity

by Allison R Schwartz, Neha ePotnis, Sujan eTimilsina, Mark eWilson, José ePatane, Joaquim eMartins, Gerald V Minsavage, Douglas eDahlbeck, Alina eAkhunova, Nalvo eAlmeida, Gary E Vallad, Jeri D Barak, Frank F White, Sally A Miller, David eRitchie, Erica eGoss, Rebecca S Bart, João C Setubal, João C Setubal, Jeffrey B Jones, Brian J Staskawicz
Published 2015-06-01

Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq.

by Letícia Anderson, Murilo S Amaral, Felipe Beckedorff, Lucas F Silva, Bianca Dazzani, Katia C Oliveira, Giulliana T Almeida, Monete R Gomes, David S Pires, João C Setubal, Ricardo DeMarco, Sergio Verjovski-Almeida
Published 2015-12-01

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival.

by Rodrigo Guarischi-Sousa, Jhonatas S Monteiro, Lilian C Alecrim, Jussara S Michaloski, Laura B Cardeal, Elisa N Ferreira, Dirce M Carraro, Diana N Nunes, Emmanuel Dias-Neto, Jüri Reimand, Paul C Boutros, João C Setubal, Ricardo J Giordano
Published 2019-12-01

Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

by José S. L. Patané, Joaquim Martins, Luiz Thiberio Rangel, José Belasque, Luciano A. Digiampietri, Agda Paula Facincani, Rafael Marini Ferreira, Fabrício José Jaciani, Yunzeng Zhang, Alessandro M. Varani, Nalvo F. Almeida, Nian Wang, Jesus A. Ferro, Leandro M. Moreira, João C. Setubal
Published 2019-09-01

Inhibition of histone methyltransferase EZH2 in Schistosoma mansoni in vitro by GSK343 reduces egg laying and decreases the expression of genes implicated in DNA replication and no...

by Adriana S A Pereira, Murilo S Amaral, Elton J R Vasconcelos, David S Pires, Huma Asif, Lucas F daSilva, David A Morales-Vicente, Vitor C Carneiro, Claudia B Angeli, Giuseppe Palmisano, Marcelo R Fantappie, Raymond J Pierce, João C Setubal, Sergio Verjovski-Almeida
Published 2018-10-01

Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection

by Leandro M. Moreira, Márcia R. Soares, Agda P. Facincani, Cristiano B. Ferreira, Rafael M. Ferreira, Maria I. T. Ferro, Fábio C. Gozzo, Érica B. Felestrino, Renata A. B. Assis, Camila Carrião M. Garcia, João C. Setubal, Jesus A. Ferro, Julio C.F. de Oliveira
Published 2017-07-01

Maternal supplementation with a synbiotic has distinct outcomes on offspring gut microbiota formation in A/J and C57BL/6 mice, differentially affecting airway inflammatory cell inf...

by Claudio Fukumori, Mateus B. Casaro, Andrew M. Thomas, Eduardo Mendes, Willian R. Ribeiro, Amanda R. Crisma, Gilson M. Murata, Bruna Bizzarro, Emmanuel Dias-Neto, Joao C. Setubal, Maria A. Oliveira, Wothan Tavares-de-Lima, Rui Curi, Silvana Bordin, Patricia Sartorelli, Caroline M. Ferreira
Published 2019-10-01

Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.

by Joseph J Gillespie, Kelly Williams, Maulik Shukla, Eric E Snyder, Eric K Nordberg, Shane M Ceraul, Chitti Dharmanolla, Daphne Rainey, Jeetendra Soneja, Joshua M Shallom, Nataraj Dongre Vishnubhat, Rebecca Wattam, Anjan Purkayastha, Michael Czar, Oswald Crasta, Joao C Setubal, Abdu F Azad, Bruno S Sobral
Published 2008-01-01

The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity.

by Rongman Cai, James Lewis, Shuangchun Yan, Haijie Liu, Christopher R Clarke, Francesco Campanile, Nalvo F Almeida, David J Studholme, Magdalen Lindeberg, David Schneider, Massimo Zaccardelli, Joao C Setubal, Nadia P Morales-Lizcano, Adriana Bernal, Gitta Coaker, Christy Baker, Carol L Bender, Scotland Leman, Boris A Vinatzer
Published 2011-08-01

Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR

by Natasha P. Fonseca, Érica B. Felestrino, Washington L. Caneschi, Angélica B. Sanchez, Isabella F. Cordeiro, Camila G.C. Lemes, Renata A.B. Assis, Flávia M.S. Carvalho, Jesus A. Ferro, Alessandro M. Varani, José Belasque, Joao C. Setubal, Guilherme P. Telles, Deiviston S. Aguena, Nalvo F. Almeida, Leandro M. Moreira
Published 2019-10-01

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

by Ari J S Ferreira, Rania Siam, João C Setubal, Ahmed Moustafa, Ahmed Sayed, Felipe S Chambergo, Adam S Dawe, Mohamed A Ghazy, Hazem Sharaf, Amged Ouf, Intikhab Alam, Alyaa M Abdel-Haleem, Heikki Lehvaslaiho, Eman Ramadan, André Antunes, Ulrich Stingl, John A C Archer, Boris R Jankovic, Mitchell Sogin, Vladimir B Bajic, Hamza El-Dorry
Published 2014-01-01