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Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.

Mofatto LS, Carneiro Fde A, Vieira NG, Duarte KE, Vidal RO, Alekcevetch JC, Cotta MG, Verdeil JL, Lapeyre-Montes F, Lartaud M, Leroy T, De Bellis F, Pot D, Rodrigues GC, Carazzolle MF, Pereira GA, Andrade AC, Marraccini P.

BMC Plant Biol. 2016 Apr 19;16(1):94. doi: 10.1186/s12870-016-0777-5.


DNA methylation changes in plasticity genes accompany the formation and maintenance of memory.

Halder R, Hennion M, Vidal RO, Shomroni O, Rahman RU, Rajput A, Centeno TP, van Bebber F, Capece V, Garcia Vizcaino JC, Schuetz AL, Burkhardt S, Benito E, Navarro Sala M, Javan SB, Haass C, Schmid B, Fischer A, Bonn S.

Nat Neurosci. 2016 Jan;19(1):102-10. doi: 10.1038/nn.4194. Epub 2015 Dec 14.


IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.

Carazzolle MF, de Carvalho LM, Slepicka HH, Vidal RO, Pereira GA, Kobarg J, Meirelles GV.

PLoS One. 2014 Jun 20;9(6):e100385. doi: 10.1371/journal.pone.0100385. eCollection 2014. Erratum in: PLoS One. 2014;9(9):e108101.


Transcription factors involved in prostate gland adaptation to androgen deprivation.

Rosa-Ribeiro R, Nishan U, Vidal RO, Barbosa GO, Reis LO, Cesar CL, Carvalho HF.

PLoS One. 2014 Jun 2;9(6):e97080. doi: 10.1371/journal.pone.0097080. eCollection 2014.


Integrated proteomics identified up-regulated focal adhesion-mediated proteins in human squamous cell carcinoma in an orthotopic murine model.

Granato DC, Zanetti MR, Kawahara R, Yokoo S, Domingues RR, Aragão AZ, Agostini M, Carazzolle MF, Vidal RO, Flores IL, Korvala J, Cervigne NK, Silva AR, Coletta RD, Graner E, Sherman NE, Paes Leme AF.

PLoS One. 2014 May 23;9(5):e98208. doi: 10.1371/journal.pone.0098208. eCollection 2014.


Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner-toward the identification of candidate genes for marker assisted-selection.

Cardoso DC, Martinati JC, Giachetto PF, Vidal RO, Carazzolle MF, Padilha L, Guerreiro-Filho O, Maluf MP.

BMC Genomics. 2014 Jan 24;15:66. doi: 10.1186/1471-2164-15-66.


The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models.

Real F, Vidal RO, Carazzolle MF, Mondego JM, Costa GG, Herai RH, Würtele M, de Carvalho LM, Carmona e Ferreira R, Mortara RA, Barbiéri CL, Mieczkowski P, da Silveira JF, Briones MR, Pereira GA, Bahia D.

DNA Res. 2013 Dec;20(6):567-81. doi: 10.1093/dnares/dst031. Epub 2013 Jul 15.


Increasing the density of markers around a major QTL controlling resistance to angular leaf spot in common bean.

Oblessuc PR, Cardoso Perseguini JM, Baroni RM, Chiorato AF, Carbonell SA, Mondego JM, Vidal RO, Camargo LE, Benchimol-Reis LL.

Theor Appl Genet. 2013 Oct;126(10):2451-65. doi: 10.1007/s00122-013-2146-1. Epub 2013 Jul 6.


Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome.

Ambrosio AB, do Nascimento LC, Oliveira BV, Teixeira PJ, Tiburcio RA, Toledo Thomazella DP, Leme AF, Carazzolle MF, Vidal RO, Mieczkowski P, Meinhardt LW, Pereira GA, Cabrera OG.

BMC Genomics. 2013 Feb 11;14:91. doi: 10.1186/1471-2164-14-91.


Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.

Lacape JM, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J, Dereeper A, Huguet S, Giband M, Lanaud C.

PLoS One. 2012;7(11):e48855. doi: 10.1371/journal.pone.0048855. Epub 2012 Nov 15.


The fungal pathogen Moniliophthora perniciosa has genes similar to plant PR-1 that are highly expressed during its interaction with cacao.

Teixeira PJ, Thomazella DP, Vidal RO, do Prado PF, Reis O, Baroni RM, Franco SF, Mieczkowski P, Pereira GA, Mondego JM.

PLoS One. 2012;7(9):e45929. doi: 10.1371/journal.pone.0045929. Epub 2012 Sep 20.


Molecular cloning and insecticidal effect of Inga laurina trypsin inhibitor on Diatraea saccharalis and Heliothis virescens.

Ramos Vda S, Cabrera OG, Camargo EL, Ambrósio AB, Vidal RO, da Silva DS, Guimarães LC, Marangoni S, Parra JR, Pereira GA, Macedo ML.

Comp Biochem Physiol C Toxicol Pharmacol. 2012 Nov;156(3-4):148-58. doi: 10.1016/j.cbpc.2012.07.007. Epub 2012 Aug 2.


Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance.

Vidal RO, do Nascimento LC, Mondego JM, Pereira GA, Carazzolle MF.

Genet Mol Biol. 2012 Jun;35(1 (suppl)):331-4. doi: 10.1590/S1415-47572012000200014.


Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system.

Silva CC, Hayden H, Sawbridge T, Mele P, Kruger RH, Rodrigues MV, Costa GG, Vidal RO, Sousa MP, Torres AP, Santiago VM, Oliveira VM.

AMB Express. 2012 Mar 27;2(1):18. doi: 10.1186/2191-0855-2-18.


A simple boiling-based DNA extraction for RAPD profiling of landfarm soil to provide representative metagenomic content.

Amorim JH, Vidal RO, Lacerda-Junior GV, Dias JC, Brendel M, Rezende RP, Cascardo JC.

Genet Mol Res. 2012 Jan 27;11(1):182-9. doi: 10.4238/2012.January.27.5.


An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora.

Mondego JM, Vidal RO, Carazzolle MF, Tokuda EK, Parizzi LP, Costa GG, Pereira LF, Andrade AC, Colombo CA, Vieira LG, Pereira GA; Brazilian Coffee Genome Project Consortium.

BMC Plant Biol. 2011 Feb 8;11:30. doi: 10.1186/1471-2229-11-30.


A transcriptomic analysis of gene expression in the venom gland of the snake Bothrops alternatus (urutu).

Cardoso KC, Da Silva MJ, Costa GG, Torres TT, Del Bem LE, Vidal RO, Menossi M, Hyslop S.

BMC Genomics. 2010 Oct 26;11:605. doi: 10.1186/1471-2164-11-605.


A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica.

Vidal RO, Mondego JM, Pot D, Ambrósio AB, Andrade AC, Pereira LF, Colombo CA, Vieira LG, Carazzolle MF, Pereira GA.

Plant Physiol. 2010 Nov;154(3):1053-66. doi: 10.1104/pp.110.162438. Epub 2010 Sep 23.


Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production.

Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F, Costa GG, Vidal RO, Noronha MF, Dominska M, Andrietta MG, Andrietta SR, Cunha AF, Gomes LH, Tavares FC, Alcarde AR, Dietrich FS, McCusker JH, Petes TD, Pereira GA.

Genome Res. 2009 Dec;19(12):2258-70. doi: 10.1101/gr.091777.109. Epub 2009 Oct 7.


Simple DNA extraction protocol for a 16S rDNA study of bacterial diversity in tropical landfarm soil used for bioremediation of oil waste.

Maciel BM, Santos AC, Dias JC, Vidal RO, Dias RJ, Gross E, Cascardo JC, Rezende RP.

Genet Mol Res. 2009 Mar 31;8(1):375-88.

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