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Items: 1 to 50 of 92

1.

Molecular adaptations of bacterial mercuric reductase to the hypersaline Kebrit Deep in the Red Sea.

Ramadan E, Maged M, El Hosseiny A, Chambergo FS, Setubal JC, El Dorry H.

Appl Environ Microbiol. 2018 Nov 30. pii: AEM.01431-18. doi: 10.1128/AEM.01431-18. [Epub ahead of print]

PMID:
30504211
2.

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 noncoding RNA metabolism.

Pereira ASA, Amaral MS, Vasconcelos EJR, Pires DS, Asif H, daSilva LF, Morales-Vicente DA, Carneiro VC, Angeli CB, Palmisano G, Fantappie MR, Pierce RJ, Setubal JC, Verjovski-Almeida S.

PLoS Negl Trop Dis. 2018 Oct 26;12(10):e0006873. doi: 10.1371/journal.pntd.0006873. eCollection 2018 Oct.

3.

Machine learning meets genome assembly.

Padovani de Souza K, Setubal JC, Ponce de Leon F de Carvalho AC, Oliveira G, Chateau A, Alves R.

Brief Bioinform. 2018 Aug 17. doi: 10.1093/bib/bby072. [Epub ahead of print]

PMID:
30137230
4.

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

Amgarten D, Braga LPP, da Silva AM, Setubal JC.

Front Genet. 2018 Aug 7;9:304. doi: 10.3389/fgene.2018.00304. eCollection 2018.

5.

A Tropical Composting Operation Unit at São Paulo Zoo as a Source of Bacterial Proteolytic Enzymes.

Ramos PL, Kondo MY, Santos SMB, de Vasconcellos SP, Rocha RCS, da Cruz JB, Eugenio PFM, Cabral H, Juliano MA, Juliano L, Setubal JC, da Silva AM, Cappelini LTD.

Appl Biochem Biotechnol. 2018 Jun 23. doi: 10.1007/s12010-018-2810-7. [Epub ahead of print]

PMID:
29936594
6.

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

daSilva LF, Beckedorff FC, Ayupe AC, Amaral MS, Mesel V, Videira A, Reis EM, Setubal JC, Verjovski-Almeida S.

Front Genet. 2018 Apr 25;9:132. doi: 10.3389/fgene.2018.00132. eCollection 2018.

7.

Comparative Metagenomics.

Maltez Thomas A, Prata Lima F, Maria Silva Moura L, Maria da Silva A, Dias-Neto E, Setubal JC.

Methods Mol Biol. 2018;1704:243-260. doi: 10.1007/978-1-4939-7463-4_8.

PMID:
29277868
8.

Phylogenomics.

Patané JSL, Martins J Jr, Setubal JC.

Methods Mol Biol. 2018;1704:103-187. doi: 10.1007/978-1-4939-7463-4_5. Review.

PMID:
29277865
9.

Comparative Genomics for Prokaryotes.

Setubal JC, Almeida NF, Wattam AR.

Methods Mol Biol. 2018;1704:55-78. doi: 10.1007/978-1-4939-7463-4_3. Review.

PMID:
29277863
10.

Gene Phylogenies and Orthologous Groups.

Setubal JC, Stadler PF.

Methods Mol Biol. 2018;1704:1-28. doi: 10.1007/978-1-4939-7463-4_1.

PMID:
29277861
11.

Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae.

Assis RAB, Polloni LC, Patané JSL, Thakur S, Felestrino ÉB, Diaz-Caballero J, Digiampietri LA, Goulart LR, Almeida NF, Nascimento R, Dandekar AM, Zaini PA, Setubal JC, Guttman DS, Moreira LM.

Sci Rep. 2017 Nov 23;7(1):16133. doi: 10.1038/s41598-017-16325-1.

12.

Plasmid-mediated mcr-1 in carbapenem-susceptible Escherichia coli ST156 causing a blood infection: an unnoticeable spread of colistin resistance in Brazil?

Rossi F, Girardello R, Morais C, Cury AP, Martins LF, da Silva AM, Abdala E, Setubal JC, da Silva Duarte AJ.

Clinics (Sao Paulo). 2017 Oct;72(10):642-644. doi: 10.6061/clinics/2017(10)09.

13.

TabPath: interactive tables for metabolic pathway analysis.

Moraes LÂG, Felestrino ÉB, Assis RAB, Matos D, Lima JC, Lima LA, Almeida NF, Setubal JC, Garcia CCM, Moreira LM.

Bioinformatics. 2018 Mar 15;34(6):1040-1042. doi: 10.1093/bioinformatics/btx714.

PMID:
29112698
14.

Prophylactic Supplementation of Bifidobacterium longum 51A Protects Mice from Ovariectomy-Induced Exacerbated Allergic Airway Inflammation and Airway Hyperresponsiveness.

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.

Front Microbiol. 2017 Sep 11;8:1732. doi: 10.3389/fmicb.2017.01732. eCollection 2017.

15.

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

Moreira LM, Soares MR, Facincani AP, Ferreira CB, Ferreira RM, Ferro MIT, Gozzo FC, Felestrino ÉB, Assis RAB, Garcia CCM, Setubal JC, Ferro JA, de Oliveira JCF.

BMC Microbiol. 2017 Jul 11;17(1):155. doi: 10.1186/s12866-017-1063-x.

16.

The Candidatus Liberibacter-Host Interface: Insights into Pathogenesis Mechanisms and Disease Control.

Wang N, Pierson EA, Setubal JC, Xu J, Levy JG, Zhang Y, Li J, Rangel LT, Martins J Jr.

Annu Rev Phytopathol. 2017 Aug 4;55:451-482. doi: 10.1146/annurev-phyto-080516-035513. Epub 2017 Jun 21. Review.

PMID:
28637377
17.

Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages.

Amgarten D, Martins LF, Lombardi KC, Antunes LP, de Souza APS, Nicastro GG, Kitajima EW, Quaggio RB, Upton C, Setubal JC, da Silva AM.

BMC Genomics. 2017 May 4;18(1):346. doi: 10.1186/s12864-017-3729-z.

18.

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting.

Lemos LN, Pereira RV, Quaggio RB, Martins LF, Moura LMS, da Silva AR, Antunes LP, da Silva AM, Setubal JC.

Front Microbiol. 2017 Apr 19;8:644. doi: 10.3389/fmicb.2017.00644. eCollection 2017.

19.

Comparative Analysis of Ralstonia solanacearum Methylomes.

Erill I, Puigvert M, Legrand L, Guarischi-Sousa R, Vandecasteele C, Setubal JC, Genin S, Guidot A, Valls M.

Front Plant Sci. 2017 Apr 13;8:504. doi: 10.3389/fpls.2017.00504. eCollection 2017.

20.

Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii.

Puigvert M, Guarischi-Sousa R, Zuluaga P, Coll NS, Macho AP, Setubal JC, Valls M.

Front Plant Sci. 2017 Mar 20;8:370. doi: 10.3389/fpls.2017.00370. eCollection 2017.

21.

Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses.

Patané JS, Martins J, Beatriz Castelão A, Nishibe C, Montera L, Bigi F, Zumárraga MJ, Cataldi AA, Fonseca Junior A, Roxo E, Luiza A, Osório AR, Jorge Ufms KS, Thacker TC, Almeida NF, Araújo FR, Setubal JC.

Genome Biol Evol. 2017 Feb 13. doi: 10.1093/gbe/evx022. [Epub ahead of print] No abstract available.

22.

Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling.

Thomas AM, Jesus EC, Lopes A, Aguiar S Jr, Begnami MD, Rocha RM, Carpinetti PA, Camargo AA, Hoffmann C, Freitas HC, Silva IT, Nunes DN, Setubal JC, Dias-Neto E.

Front Cell Infect Microbiol. 2016 Dec 9;6:179. doi: 10.3389/fcimb.2016.00179. eCollection 2016.

23.

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics.

Antunes LP, Martins LF, Pereira RV, Thomas AM, Barbosa D, Lemos LN, Silva GM, Moura LM, Epamino GW, Digiampietri LA, Lombardi KC, Ramos PL, Quaggio RB, de Oliveira JC, Pascon RC, Cruz JB, da Silva AM, Setubal JC.

Sci Rep. 2016 Dec 12;6:38915. doi: 10.1038/srep38915.

24.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

25.

Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U.

Lima-Junior JD, Viana-Niero C, Conde Oliveira DV, Machado GE, Rabello MC, Martins-Junior J, Martins LF, Digiampietri LA, da Silva AM, Setubal JC, Russell DA, Jacobs-Sera D, Pope WH, Hatfull GF, Leão SC.

BMC Microbiol. 2016 Jun 17;16(1):111. doi: 10.1186/s12866-016-0734-3.

26.

Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031.

Guarischi-Sousa R, Puigvert M, Coll NS, Siri MI, Pianzzola MJ, Valls M, Setubal JC.

Stand Genomic Sci. 2016 Jan 15;11:7. doi: 10.1186/s40793-016-0131-4. eCollection 2016.

27.

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

Anderson L, Amaral MS, Beckedorff F, Silva LF, Dazzani B, Oliveira KC, Almeida GT, Gomes MR, Pires DS, Setubal JC, DeMarco R, Verjovski-Almeida S.

PLoS Negl Trop Dis. 2015 Dec 31;9(12):e0004334. doi: 10.1371/journal.pntd.0004334. eCollection 2015 Dec.

28.

TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013.

Setubal JC, Almeida N.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):499. No abstract available.

PMID:
26605385
29.

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

Schwartz AR, Potnis N, Timilsina S, Wilson M, Patané J, Martins J Jr, Minsavage GV, Dahlbeck D, Akhunova A, Almeida N, Vallad GE, Barak JD, White FF, Miller SA, Ritchie D, Goss E, Bart RS, Setubal JC, Jones JB, Staskawicz BJ.

Front Microbiol. 2015 Jun 3;6:535. doi: 10.3389/fmicb.2015.00535. eCollection 2015.

30.

Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas.

Zhang Y, Jalan N, Zhou X, Goss E, Jones JB, Setubal JC, Deng X, Wang N.

ISME J. 2015 Oct;9(10):2128-38. doi: 10.1038/ismej.2015.15. Epub 2015 Feb 17.

31.

Genetic resources for methane production from biomass described with the Gene Ontology.

Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B.

Front Microbiol. 2014 Dec 3;5:634. doi: 10.3389/fmicb.2014.00634. eCollection 2014.

32.

Genetic resources for advanced biofuel production described with the Gene Ontology.

Torto-Alalibo T, Purwantini E, Lomax J, Setubal JC, Mukhopadhyay B, Tyler BM.

Front Microbiol. 2014 Oct 10;5:528. doi: 10.3389/fmicb.2014.00528. eCollection 2014. Review.

33.

Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.

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.

Genome Announc. 2014 Oct 9;2(5). pii: e01027-14. doi: 10.1128/genomeA.01027-14.

34.

Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms.

Thomas AM, Gleber-Netto FO, Fernandes GR, Amorim M, Barbosa LF, Francisco AL, de Andrade AG, Setubal JC, Kowalski LP, Nunes DN, Dias-Neto E.

BMC Microbiol. 2014 Oct 3;14:250. doi: 10.1186/s12866-014-0250-2.

35.

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

Ferreira AJ, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, Dawe AS, Ghazy MA, Sharaf H, Ouf A, Alam I, Abdel-Haleem AM, Lehvaslaiho H, Ramadan E, Antunes A, Stingl U, Archer JA, Jankovic BR, Sogin M, Bajic VB, El-Dorry H.

PLoS One. 2014 Jun 12;9(6):e97338. doi: 10.1371/journal.pone.0097338. eCollection 2014.

36.

A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea.

Sayed A, Ghazy MA, Ferreira AJ, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JA, Bajic VB, Siam R, El-Dorry H.

J Biol Chem. 2014 Jan 17;289(3):1675-87. doi: 10.1074/jbc.M113.493429. Epub 2013 Nov 26.

37.

The complete genome sequence of 'Candidatus Liberibacter americanus', associated with Citrus huanglongbing.

Wulff NA, Zhang S, Setubal JC, Almeida NF, Martins EC, Harakava R, Kumar D, Rangel LT, Foissac X, Bové JM, Gabriel DW.

Mol Plant Microbe Interact. 2014 Feb;27(2):163-76. doi: 10.1094/MPMI-09-13-0292-R.

38.

Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range.

Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N.

BMC Genomics. 2013 Aug 14;14:551. doi: 10.1186/1471-2164-14-551.

39.

Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms.

Martins LF, Antunes LP, Pascon RC, de Oliveira JC, Digiampietri LA, Barbosa D, Peixoto BM, Vallim MA, Viana-Niero C, Ostroski EH, Telles GP, Dias Z, da Cruz JB, Juliano L, Verjovski-Almeida S, da Silva AM, Setubal JC.

PLoS One. 2013 Apr 24;8(4):e61928. doi: 10.1371/journal.pone.0061928. Print 2013. Erratum in: PLoS One. 2013;8(6). doi:10.1371/annotation/2cca811e-d45b-4854-a420-d0405309ef43.

40.

Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages.

Rajasekaran P, Alexander JC, Seleem MN, Jain N, Sriranganathan N, Wattam AR, Setubal JC, Boyle SM.

Int J Antimicrob Agents. 2013 Apr;41(4):358-62. doi: 10.1016/j.ijantimicag.2012.11.017. Epub 2013 Jan 8.

41.

Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium.

Slater S, Setubal JC, Goodner B, Houmiel K, Sun J, Kaul R, Goldman BS, Farrand SK, Almeida N Jr, Burr T, Nester E, Rhoads DM, Kadoi R, Ostheimer T, Pride N, Sabo A, Henry E, Telepak E, Cromes L, Harkleroad A, Oliphant L, Pratt-Szegila P, Welch R, Wood D.

Appl Environ Microbiol. 2013 Feb;79(4):1414-7. doi: 10.1128/AEM.03192-12. Epub 2012 Dec 14.

42.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Nov 6;3(5):e00246-11. doi: 10.1128/mBio.00388-12.

43.

Sequence verification of synthetic DNA by assembly of sequencing reads.

Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, Setubal JC, Tyler BM, Peccoud J.

Nucleic Acids Res. 2013 Jan 7;41(1):e25. doi: 10.1093/nar/gks908. Epub 2012 Oct 4.

44.

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway.

Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, De Castro C, Molinaro A, Boyle SM, De BK, Setubal JC.

MBio. 2012 Aug 28;3(5):e00246-12. doi: 10.1128/mBio.00246-12. Print 2012. Erratum in: MBio. 2012 Nov-Dec;3(6):e00388-12.

45.

SIS: a program to generate draft genome sequence scaffolds for prokaryotes.

Dias Z, Dias U, Setubal JC.

BMC Bioinformatics. 2012 May 14;13:96. doi: 10.1186/1471-2105-13-96.

46.

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes.

Dos Santos PC, Fang Z, Mason SW, Setubal JC, Dixon R.

BMC Genomics. 2012 May 3;13:162. doi: 10.1186/1471-2164-13-162.

47.

Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases.

Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simões ZL, Verjovski-Almeida S, Durham AM.

RNA Biol. 2012 Mar;9(3):274-82. doi: 10.4161/rna.19352. Epub 2012 Mar 1. Review.

PMID:
22336709
48.

REGEN: Ancestral Genome Reconstruction for Bacteria.

Yang K, Heath LS, Setubal JC.

Genes (Basel). 2012 Jul 18;3(3):423-43. doi: 10.3390/genes3030423.

49.

Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients.

Staquicini FI, Cardó-Vila M, Kolonin MG, Trepel M, Edwards JK, Nunes DN, Sergeeva A, Efstathiou E, Sun J, Almeida NF, Tu SM, Botz GH, Wallace MJ, O'Connell DJ, Krajewski S, Gershenwald JE, Molldrem JJ, Flamm AL, Koivunen E, Pentz RD, Dias-Neto E, Setubal JC, Cahill DJ, Troncoso P, Do KA, Logothetis CJ, Sidman RL, Pasqualini R, Arap W.

Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18637-42. doi: 10.1073/pnas.1114503108. Epub 2011 Nov 2.

50.

Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity.

Jalan N, Aritua V, Kumar D, Yu F, Jones JB, Graham JH, Setubal JC, Wang N.

J Bacteriol. 2011 Nov;193(22):6342-57. doi: 10.1128/JB.05777-11. Epub 2011 Sep 9.

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