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Comparative Analysis of .

Frontiers in plant science

Erill I, Puigvert M, Legrand L, Guarischi-Sousa R, Vandecasteele C, Setubal JC, Genin S, Guidot A, Valls M.
PMID: 28450872
Front Plant Sci. 2017 Apr 13;8:504. doi: 10.3389/fpls.2017.00504. eCollection 2017.

No abstract available.

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Erill I, Puigvert M, Legrand L, et al. Comparative Analysis of . Front Plant Sci. 2017;8:504doi: 10.3389/fpls.2017.00504.
Erill, I., Puigvert, M., Legrand, L., Guarischi-Sousa, R., Vandecasteele, C., Setubal, J. C., Genin, S., Guidot, A., & Valls, M. (2017). Comparative Analysis of . Frontiers in plant science, 8504. https://doi.org/10.3389/fpls.2017.00504
Erill, Ivan, et al. "Comparative Analysis of ." Frontiers in plant science vol. 8 (2017): 504. doi: https://doi.org/10.3389/fpls.2017.00504
Erill I, Puigvert M, Legrand L, Guarischi-Sousa R, Vandecasteele C, Setubal JC, Genin S, Guidot A, Valls M. Comparative Analysis of . Front Plant Sci. 2017 Apr 13;8:504. doi: 10.3389/fpls.2017.00504. eCollection 2017. PMID: 28450872; PMCID: PMC5390034.
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Genetic resources for methane production from biomass described with the Gene Ontology.

Frontiers in microbiology

Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B.
PMID: 25520705
Front Microbiol. 2014 Dec 03;5:634. doi: 10.3389/fmicb.2014.00634. eCollection 2014.

Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of...

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Purwantini E, Torto-Alalibo T, Lomax J, et al. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol. 2014;5:634doi: 10.3389/fmicb.2014.00634.
Purwantini, E., Torto-Alalibo, T., Lomax, J., Setubal, J. C., Tyler, B. M., & Mukhopadhyay, B. (2014). Genetic resources for methane production from biomass described with the Gene Ontology. Frontiers in microbiology, 5634. https://doi.org/10.3389/fmicb.2014.00634
Purwantini, Endang, et al. "Genetic resources for methane production from biomass described with the Gene Ontology." Frontiers in microbiology vol. 5 (2014): 634. doi: https://doi.org/10.3389/fmicb.2014.00634
Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol. 2014 Dec 03;5:634. doi: 10.3389/fmicb.2014.00634. eCollection 2014. PMID: 25520705; PMCID: PMC4253957.
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Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.

Genome announcements

Raiol T, De-Souza MT, Oliveira JV, Silva HS, Orem JC, Cavalcante DA, Almeida NF, Telles GP, Setubal JC, Brigido MM, Torres FA, Stadler PS, Walter ME, Moraes LM.
PMID: 25301660
Genome Announc. 2014 Oct 09;2(5). doi: 10.1128/genomeA.01027-14.

A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had its entire genome sequenced.

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Raiol T, De-Souza MT, Oliveira JV, et al. Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring. Genome Announc. 2014;2(5)doi: 10.1128/genomeA.01027-14.
Raiol, T., De-Souza, M. T., Oliveira, J. V., Silva, H. S., Orem, J. C., Cavalcante, D. A., Almeida, N. F., Telles, G. P., Setubal, J. C., Brigido, M. M., Torres, F. A., Stadler, P. S., Walter, M. E., & Moraes, L. M. (2014). Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring. Genome announcements, 2(5), . https://doi.org/10.1128/genomeA.01027-14
Raiol, Tainá, et al. "Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring." Genome announcements vol. 2,5 (2014). doi: https://doi.org/10.1128/genomeA.01027-14
Raiol T, De-Souza MT, Oliveira JV, Silva HS, Orem JC, Cavalcante DA, Almeida NF, Telles GP, Setubal JC, Brigido MM, Torres FA, Stadler PS, Walter ME, Moraes LM. Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring. Genome Announc. 2014 Oct 09;2(5). doi: 10.1128/genomeA.01027-14. PMID: 25301660; PMCID: PMC4192392.
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Prophylactic Supplementation of .

Frontiers in microbiology

Mendes E, Acetturi BG, Thomas AM, Martins FDS, Crisma AR, Murata G, Braga TT, Camâra NOS, Franco ALDS, Setubal JC, Ribeiro WR, Valduga CJ, Curi R, Dias-Neto E, Tavares-de-Lima W, Ferreira CM.
PMID: 28959241
Front Microbiol. 2017 Sep 11;8:1732. doi: 10.3389/fmicb.2017.01732. eCollection 2017.

Asthma is a chronic inflammatory disease that affects more females than males after puberty, and its symptoms and severity in women change during menstruation and menopause. Recently, evidence has demonstrated that interactions among the microbiota, female sex hormones, and...

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Mendes E, Acetturi BG, Thomas AM, et al. Prophylactic Supplementation of . Front Microbiol. 2017;8:1732doi: 10.3389/fmicb.2017.01732.
Mendes, E., Acetturi, B. G., Thomas, A. M., Martins, F. D. S., Crisma, A. R., Murata, G., Braga, T. T., Camâra, N. O. S., Franco, A. L. D. S., Setubal, J. C., Ribeiro, W. R., Valduga, C. J., Curi, R., Dias-Neto, E., Tavares-de-Lima, W., & Ferreira, C. M. (2017). Prophylactic Supplementation of . Frontiers in microbiology, 81732. https://doi.org/10.3389/fmicb.2017.01732
Mendes, Eduardo, et al. "Prophylactic Supplementation of ." Frontiers in microbiology vol. 8 (2017): 1732. doi: https://doi.org/10.3389/fmicb.2017.01732
Mendes E, Acetturi BG, Thomas AM, Martins FDS, Crisma AR, Murata G, Braga TT, Camâra NOS, Franco ALDS, Setubal JC, Ribeiro WR, Valduga CJ, Curi R, Dias-Neto E, Tavares-de-Lima W, Ferreira CM. Prophylactic Supplementation of . Front Microbiol. 2017 Sep 11;8:1732. doi: 10.3389/fmicb.2017.01732. eCollection 2017. PMID: 28959241; PMCID: PMC5604069.
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Consent insufficient for data release-Response.

Science (New York, N.Y.)

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.
PMID: 31048484
Science. 2019 May 03;364(6439):446. doi: 10.1126/science.aax7509.

No abstract available.

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Amann RI, Baichoo S, Blencowe BJ, et al. Consent insufficient for data release-Response. Science. 2019;364(6439):446doi: 10.1126/science.aax7509.
Amann, R. I., Baichoo, S., Blencowe, B. J., Bork, P., Borodovsky, M., Brooksbank, C., Chain, P. S. G., Colwell, R. R., Daffonchio, D. G., Danchin, A., de Lorenzo, V., Dorrestein, P. C., Finn, R. D., Fraser, C. M., Gilbert, J. A., Hallam, S. J., Hugenholtz, P., Ioannidis, J. P. A., Jansson, J. K., Kim, J. F., Klenk, H. P., Klotz, M. G., Knight, R., Konstantinidis, K. T., Kyrpides, N. C., Mason, C. E., McHardy, A. C., Meyer, F., Ouzounis, C. A., Patrinos, A. A. N., Podar, M., Pollard, K. S., Ravel, J., Muñoz, A. R., Roberts, R. J., Rosselló-Móra, R., Sansone, S. A., Schloss, P. D., Schriml, L. M., Setubal, J. C., Sorek, R., Stevens, R. L., Tiedje, J. M., Turjanski, A., Tyson, G. W., Ussery, D. W., Weinstock, G. M., White, O., Whitman, W. B., & Xenarios, I. (2019). Consent insufficient for data release-Response. Science (New York, N.Y.), 364(6439), 446. https://doi.org/10.1126/science.aax7509
Amann, Rudolf I, et al. "Consent insufficient for data release-Response." Science (New York, N.Y.) vol. 364,6439 (2019): 446. doi: https://doi.org/10.1126/science.aax7509
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Consent insufficient for data release-Response. Science. 2019 May 03;364(6439):446. doi: 10.1126/science.aax7509. PMID: 31048484.
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Genomic Characterization of .

Frontiers in microbiology

Girardello R, Piroupo CM, Martins J, Maffucci MH, Cury AP, Franco MRG, Malta FM, Rocha NC, Pinho JRR, Rossi F, Duarte AJDS, Setubal JC.
PMID: 34177843
Front Microbiol. 2021 Jun 09;12:663414. doi: 10.3389/fmicb.2021.663414. eCollection 2021.

Polymyxins are one of most important antibiotics available for multidrug-resistant Gram-negative infections. Diverse chromosomal resistance mechanisms have been described, but the polymyxin resistance phenotype is not yet completely understood. The objective of this study was to characterize colistin resistant

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Girardello R, Piroupo CM, Martins J, et al. Genomic Characterization of . Front Microbiol. 2021;12:663414doi: 10.3389/fmicb.2021.663414.
Girardello, R., Piroupo, C. M., Martins, J., Maffucci, M. H., Cury, A. P., Franco, M. R. G., Malta, F. M., Rocha, N. C., Pinho, J. R. R., Rossi, F., Duarte, A. J. D. S., & Setubal, J. C. (2021). Genomic Characterization of . Frontiers in microbiology, 12663414. https://doi.org/10.3389/fmicb.2021.663414
Girardello, Raquel, et al. "Genomic Characterization of ." Frontiers in microbiology vol. 12 (2021): 663414. doi: https://doi.org/10.3389/fmicb.2021.663414
Girardello R, Piroupo CM, Martins J, Maffucci MH, Cury AP, Franco MRG, Malta FM, Rocha NC, Pinho JRR, Rossi F, Duarte AJDS, Setubal JC. Genomic Characterization of . Front Microbiol. 2021 Jun 09;12:663414. doi: 10.3389/fmicb.2021.663414. eCollection 2021. PMID: 34177843; PMCID: PMC8221240.
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Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis.

Environmental microbiology reports

Braga LPP, Coutinho FH, Amgarten DE, Kot W, Hansen L, Setubal JC, Philippot L.
PMID: 34018688
Environ Microbiol Rep. 2021 Jun;13(3):348-354. doi: 10.1111/1758-2229.12939.

Viruses are now recognized as important players in microbial dynamics and biogeochemical cycles in the oceans. Yet, compared with aquatic ecosystems, virus discovery in terrestrial ecosystems has been challenging partly due to the inherent complexity of soils. To expand...

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Braga LPP, Coutinho FH, Amgarten DE, et al. Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis. Environ Microbiol Rep. 2021;13(3):348-354doi: 10.1111/1758-2229.12939.
Braga, L. P. P., Coutinho, F. H., Amgarten, D. E., Kot, W., Hansen, L., Setubal, J. C., & Philippot, L. (2021). Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis. Environmental microbiology reports, 13(3), 348-354. https://doi.org/10.1111/1758-2229.12939
Braga, Lucas P P, et al. "Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis." Environmental microbiology reports vol. 13,3 (2021): 348-354. doi: https://doi.org/10.1111/1758-2229.12939
Braga LPP, Coutinho FH, Amgarten DE, Kot W, Hansen L, Setubal JC, Philippot L. Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis. Environ Microbiol Rep. 2021 Jun;13(3):348-354. doi: 10.1111/1758-2229.12939. PMID: 34018688.
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Global Distribution and Evolution of .

Frontiers in microbiology

Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-Pereira TT, Camargo NCS, de Souza Filho AF, Ikuta CY, Neto JSF, Setubal JC, Heinemann MB, Guimaraes AMS.
PMID: 32477295
Front Microbiol. 2020 May 07;11:843. doi: 10.3389/fmicb.2020.00843. eCollection 2020.

No abstract available.

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Zimpel CK, Patané JSL, Guedes ACP, et al. Global Distribution and Evolution of . Front Microbiol. 2020;11:843doi: 10.3389/fmicb.2020.00843.
Zimpel, C. K., Patané, J. S. L., Guedes, A. C. P., de Souza, R. F., Silva-Pereira, T. T., Camargo, N. C. S., de Souza Filho, A. F., Ikuta, C. Y., Neto, J. S. F., Setubal, J. C., Heinemann, M. B., & Guimaraes, A. M. S. (2020). Global Distribution and Evolution of . Frontiers in microbiology, 11843. https://doi.org/10.3389/fmicb.2020.00843
Zimpel, Cristina Kraemer, et al. "Global Distribution and Evolution of ." Frontiers in microbiology vol. 11 (2020): 843. doi: https://doi.org/10.3389/fmicb.2020.00843
Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-Pereira TT, Camargo NCS, de Souza Filho AF, Ikuta CY, Neto JSF, Setubal JC, Heinemann MB, Guimaraes AMS. Global Distribution and Evolution of . Front Microbiol. 2020 May 07;11:843. doi: 10.3389/fmicb.2020.00843. eCollection 2020. PMID: 32477295; PMCID: PMC7232559.
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An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.

Genome biology and evolution

Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP.
PMID: 34390574
Genome Biol Evol. 2021 Sep 01;13(9). doi: 10.1093/gbe/evab187.

Assessing the compatibility between gene family phylogenies is a crucial and often computationally demanding step in many phylogenomic analyses. Here, we describe the Evolutionary Similarity Index (IES), a means to assess shared evolution between gene families using a weighted...

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Rangel LT, Soucy SM, Setubal JC, et al. An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets. Genome Biol Evol. 2021;13(9)doi: 10.1093/gbe/evab187.
Rangel, L. T., Soucy, S. M., Setubal, J. C., Gogarten, J. P., & Fournier, G. P. (2021). An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets. Genome biology and evolution, 13(9), . https://doi.org/10.1093/gbe/evab187
Rangel, Luiz Thibério, et al. "An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets." Genome biology and evolution vol. 13,9 (2021). doi: https://doi.org/10.1093/gbe/evab187
Rangel LT, Soucy SM, Setubal JC, Gogarten JP, Fournier GP. An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets. Genome Biol Evol. 2021 Sep 01;13(9). doi: 10.1093/gbe/evab187. PMID: 34390574; PMCID: PMC8483891.
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Detection and identification of .

PeerJ

Fonseca NP, Felestrino ÉB, Caneschi WL, Sanchez AB, Cordeiro IF, Lemes CGC, Assis RAB, Carvalho FMS, Ferro JA, Varani AM, Belasque J, Setubal JC, Telles GP, Aguena DS, Almeida NF, Moreira LM.
PMID: 31592342
PeerJ. 2019 Oct 01;7:e7676. doi: 10.7717/peerj.7676. eCollection 2019.

BACKGROUND: In RESULTS: Using comparative genomics approaches, primers were synthesized for the identification of the four causative agents of citrus diseases. These primers were validated for their specificity to their target DNA by both conventional and multiplex PCR. Upon...

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Fonseca NP, Felestrino ÉB, Caneschi WL, et al. Detection and identification of . PeerJ. 2019;7:e7676doi: 10.7717/peerj.7676.
Fonseca, N. P., Felestrino, �. �. B., Caneschi, W. L., Sanchez, A. B., Cordeiro, I. F., Lemes, C. G. C., Assis, R. A. B., Carvalho, F. M. S., Ferro, J. A., Varani, A. M., Belasque, J., Setubal, J. C., Telles, G. P., Aguena, D. S., Almeida, N. F., & Moreira, L. M. (2019). Detection and identification of . PeerJ, 7e7676. https://doi.org/10.7717/peerj.7676
Fonseca, Natasha P, et al. "Detection and identification of ." PeerJ vol. 7 (2019): e7676. doi: https://doi.org/10.7717/peerj.7676
Fonseca NP, Felestrino ÉB, Caneschi WL, Sanchez AB, Cordeiro IF, Lemes CGC, Assis RAB, Carvalho FMS, Ferro JA, Varani AM, Belasque J, Setubal JC, Telles GP, Aguena DS, Almeida NF, Moreira LM. Detection and identification of . PeerJ. 2019 Oct 01;7:e7676. doi: 10.7717/peerj.7676. eCollection 2019. PMID: 31592342; PMCID: PMC6777491.
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Transcriptomes of .

Frontiers in plant science

Puigvert M, Guarischi-Sousa R, Zuluaga P, Coll NS, Macho AP, Setubal JC, Valls M.
PMID: 28373879
Front Plant Sci. 2017 Mar 20;8:370. doi: 10.3389/fpls.2017.00370. eCollection 2017.

Bacterial wilt of potatoes-also called brown rot-is a devastating disease caused by the vascular pathogen

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Puigvert M, Guarischi-Sousa R, Zuluaga P, et al. Transcriptomes of . Front Plant Sci. 2017;8:370doi: 10.3389/fpls.2017.00370.
Puigvert, M., Guarischi-Sousa, R., Zuluaga, P., Coll, N. S., Macho, A. P., Setubal, J. C., & Valls, M. (2017). Transcriptomes of . Frontiers in plant science, 8370. https://doi.org/10.3389/fpls.2017.00370
Puigvert, Marina, et al. "Transcriptomes of ." Frontiers in plant science vol. 8 (2017): 370. doi: https://doi.org/10.3389/fpls.2017.00370
Puigvert M, Guarischi-Sousa R, Zuluaga P, Coll NS, Macho AP, Setubal JC, Valls M. Transcriptomes of . Front Plant Sci. 2017 Mar 20;8:370. doi: 10.3389/fpls.2017.00370. eCollection 2017. PMID: 28373879; PMCID: PMC5357869.
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MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins.

Frontiers in genetics

Amgarten D, Braga LPP, da Silva AM, Setubal JC.
PMID: 30131825
Front Genet. 2018 Aug 07;9:304. doi: 10.3389/fgene.2018.00304. eCollection 2018.

Here we present MARVEL, a tool for prediction of double-stranded DNA bacteriophage sequences in metagenomic bins. MARVEL uses a random forest machine learning approach. We trained the program on a dataset with 1,247 phage and 1,029 bacterial genomes, and...

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Amgarten D, Braga LPP, da Silva AM, et al. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. Front Genet. 2018;9:304doi: 10.3389/fgene.2018.00304.
Amgarten, D., Braga, L. P. P., da Silva, A. M., & Setubal, J. C. (2018). MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. Frontiers in genetics, 9304. https://doi.org/10.3389/fgene.2018.00304
Amgarten, Deyvid, et al. "MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins." Frontiers in genetics vol. 9 (2018): 304. doi: https://doi.org/10.3389/fgene.2018.00304
Amgarten D, Braga LPP, da Silva AM, Setubal JC. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. Front Genet. 2018 Aug 07;9:304. doi: 10.3389/fgene.2018.00304. eCollection 2018. PMID: 30131825; PMCID: PMC6090037.
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