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Items: 1 to 50 of 67

1.

Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model.

Camargo AP, Nakahara TS, Firmino LER, Netto PHM, do Nascimento JBP, Donnard ER, Galante PAF, Carazzolle MF, Malnic B, Papes F.

DNA Res. 2019 Jul 18. pii: dsz015. doi: 10.1093/dnares/dsz015. [Epub ahead of print]

PMID:
31321403
2.

Positive Selection Evidence in Xylose-Related Genes Suggests Methylglyoxal Reductase as a Target for the Improvement of Yeasts' Fermentation in Industry.

Borelli G, Fiamenghi MB, Dos Santos LV, Carazzolle MF, Pereira GAG, José J.

Genome Biol Evol. 2019 Jul 1;11(7):1923-1938. doi: 10.1093/gbe/evz036.

PMID:
31070742
3.

Lignocellulolytic characterization and comparative secretome analysis of a Trichoderma erinaceum strain isolated from decaying sugarcane straw.

da Silva DS, Dantzger M, Assis MA, Gallardo JCM, Teixeira GS, Missawa SK, Domingues RR, Carazzolle MF, Lunardi I, Leme AFP, Pereira GAG, Parreiras LS.

Fungal Biol. 2019 Apr;123(4):330-340. doi: 10.1016/j.funbio.2019.01.007. Epub 2019 Jan 31.

PMID:
30928041
4.

Genome Assembly of a Highly Aldehyde-Resistant Saccharomyces cerevisiae SA1-Derived Industrial Strain.

Nagamatsu ST, Teixeira GS, de Mello FDSB, Tizei PAG, Nakagawa BTG, de Carvalho LM, Pereira GAG, Carazzolle MF.

Microbiol Resour Announc. 2019 Mar 28;8(13). pii: e00071-19. doi: 10.1128/MRA.00071-19.

5.

Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler.

Nascimento LC, Yanagui K, Jose J, Camargo ELO, Grassi MCB, Cunha CP, Bressiani JA, Carvalho GMA, Carvalho CR, Prado PF, Mieczkowski P, Pereira GAG, Carazzolle MF.

DNA Res. 2019 Jun 1;26(3):205-216. doi: 10.1093/dnares/dsz001.

6.

Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species.

Bazzo BR, de Carvalho LM, Carazzolle MF, Pereira GAG, Colombo CA.

BMC Plant Biol. 2018 Nov 12;18(1):276. doi: 10.1186/s12870-018-1509-9.

7.

Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30.

Borin GP, Carazzolle MF, Dos Santos RAC, Riaño-Pachón DM, Oliveira JVC.

Front Bioeng Biotechnol. 2018 Oct 22;6:151. doi: 10.3389/fbioe.2018.00151. eCollection 2018.

8.

Synthesis and testing of novel alternative oxidase (AOX) inhibitors with antifungal activity against Moniliophthora perniciosa (Stahel), the causal agent of witches' broom disease of cocoa, and other phytopathogens.

Barsottini MR, Pires BA, Vieira ML, Pereira JG, Costa PC, Sanitá J, Coradini A, Mello F, Marschalk C, Silva EM, Paschoal D, Figueira A, Rodrigues FH, Cordeiro AT, Miranda PC, Oliveira PS, Sforça ML, Carazzolle MF, Rocco SA, Pereira GA.

Pest Manag Sci. 2019 May;75(5):1295-1303. doi: 10.1002/ps.5243. Epub 2018 Dec 3.

PMID:
30350447
9.

New insights into Phakopsora pachyrhizi infection based on transcriptome analysis in planta.

Rincão MP, Carvalho MCDCG, Nascimento LC, Lopes-Caitar VS, Carvalho K, Darben LM, Yokoyama A, Carazzolle MF, Abdelnoor RV, Marcelino-Guimarães FC.

Genet Mol Biol. 2018 Jul/Sept.;41(3):671-691. doi: 10.1590/1678-4685-GMB-2017-0161.

10.

Effect of Feeding Bacillus subtilis Spores to Broilers Challenged with Salmonella enterica serovar Heidelberg Brazilian Strain UFPR1 on Performance, Immune Response, and Gut Health.

Hayashi RM, Lourenço MC, Kraieski AL, Araujo RB, Gonzalez-Esquerra R, Leonardecz E, da Cunha AF, Carazzolle MF, Monzani PS, Santin E.

Front Vet Sci. 2018 Feb 13;5:13. doi: 10.3389/fvets.2018.00013. eCollection 2018.

11.

Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC).

Molano EPL, Cabrera OG, Jose J, do Nascimento LC, Carazzolle MF, Teixeira PJPL, Alvarez JC, Tiburcio RA, Tokimatu Filho PM, de Lima GMA, Guido RVC, Corrêa TLR, Leme AFP, Mieczkowski P, Pereira GAG.

BMC Genomics. 2018 Jan 17;19(1):58. doi: 10.1186/s12864-018-4440-4.

12.

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species.

Nascimento LC, Salazar MM, Lepikson-Neto J, Camargo ELO, Parreiras LS, Pereira GAG, Carazzolle MF.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax079.

13.

Phenotypic and Genotypic Features of a Salmonella Heidelberg Strain Isolated in Broilers in Brazil and Their Possible Association to Antibiotics and Short-Chain Organic Acids Resistance and Susceptibility.

Santin E, Hayashi RM, Wammes JC, Gonzalez-Esquerra R, Carazzolle MF, Freire CCM, Monzani PS, da Cunha AF.

Front Vet Sci. 2017 Nov 1;4:184. doi: 10.3389/fvets.2017.00184. eCollection 2017.

14.

Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer.

Quintero M, Adamoski D, Reis LMD, Ascenção CFR, Oliveira KRS, Gonçalves KA, Dias MM, Carazzolle MF, Dias SMG.

BMC Cancer. 2017 Nov 7;17(1):727. doi: 10.1186/s12885-017-3726-2.

15.

High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection.

Florez JC, Mofatto LS, do Livramento Freitas-Lopes R, Ferreira SS, Zambolim EM, Carazzolle MF, Zambolim L, Caixeta ET.

Plant Mol Biol. 2017 Dec;95(6):607-623. doi: 10.1007/s11103-017-0676-7. Epub 2017 Nov 1.

PMID:
29094279
16.

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components.

Heberle H, Carazzolle MF, Telles GP, Meirelles GV, Minghim R.

BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):395. doi: 10.1186/s12859-017-1787-5.

17.

Conversion of an inactive xylose isomerase into a functional enzyme by co-expression of GroEL-GroES chaperonins in Saccharomyces cerevisiae.

Temer B, Dos Santos LV, Negri VA, Galhardo JP, Magalhães PHM, José J, Marschalk C, Corrêa TLR, Carazzolle MF, Pereira GAG.

BMC Biotechnol. 2017 Sep 9;17(1):71. doi: 10.1186/s12896-017-0389-7.

18.

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis.

Ivamoto ST, Reis O Júnior, Domingues DS, Dos Santos TB, de Oliveira FF, Pot D, Leroy T, Vieira LG, Carazzolle MF, Pereira GA, Pereira LF.

PLoS One. 2017 Jan 9;12(1):e0169595. doi: 10.1371/journal.pone.0169595. eCollection 2017.

19.

Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains.

Dos Santos LV, Carazzolle MF, Nagamatsu ST, Sampaio NM, Almeida LD, Pirolla RA, Borelli G, Corrêa TL, Argueso JL, Pereira GA.

Sci Rep. 2016 Dec 21;6:38676. doi: 10.1038/srep38676.

20.

Expanding the Knowledge on Lignocellulolytic and Redox Enzymes of Worker and Soldier Castes from the Lower Termite Coptotermes gestroi.

Franco Cairo JP, Carazzolle MF, Leonardo FC, Mofatto LS, Brenelli LB, Gonçalves TA, Uchima CA, Domingues RR, Alvarez TM, Tramontina R, Vidal RO, Costa FF, Costa-Leonardo AM, Paes Leme AF, Pereira GA, Squina FM.

Front Microbiol. 2016 Oct 13;7:1518. eCollection 2016.

21.

Low-level laser therapy induces an upregulation of collagen gene expression during the initial process of bone healing: a microarray analysis.

Tim CR, Bossini PS, Kido HW, Malavazi I, von Zeska Kress MR, Carazzolle MF, Rennó AC, Parizotto NA.

J Biomed Opt. 2016 Aug 1;21(8):88001. doi: 10.1117/1.JBO.21.8.088001.

PMID:
27548776
22.

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;16:94. doi: 10.1186/s12870-016-0777-5.

23.

Prediction of the in planta Phakopsora pachyrhizi secretome and potential effector families.

de Carvalho MC, Costa Nascimento L, Darben LM, Polizel-Podanosqui AM, Lopes-Caitar VS, Qi M, Rocha CS, Carazzolle MF, Kuwahara MK, Pereira GA, Abdelnoor RV, Whitham SA, Marcelino-Guimarães FC.

Mol Plant Pathol. 2017 Apr;18(3):363-377. doi: 10.1111/mpp.12405. Epub 2016 Jun 9.

PMID:
27010366
24.

Effects of low level laser therapy on inflammatory and angiogenic gene expression during the process of bone healing: A microarray analysis.

Tim CR, Bossini PS, Kido HW, Malavazi I, von Zeska Kress MR, Carazzolle MF, Parizotto NA, Rennó AC.

J Photochem Photobiol B. 2016 Jan;154:8-15. doi: 10.1016/j.jphotobiol.2015.10.028. Epub 2015 Oct 31.

PMID:
26599085
25.

Effects of low-level laser therapy on the expression of osteogenic genes during the initial stages of bone healing in rats: a microarray analysis.

Tim CR, Bossini PS, Kido HW, Malavazi I, von Zeska Kress MR, Carazzolle MF, Parizotto NA, Rennó AC.

Lasers Med Sci. 2015 Dec;30(9):2325-33. doi: 10.1007/s10103-015-1807-5. Epub 2015 Sep 28.

PMID:
26415929
26.

Genomic analyses and expression evaluation of thaumatin-like gene family in the cacao fungal pathogen Moniliophthora perniciosa.

Franco Sde F, Baroni RM, Carazzolle MF, Teixeira PJ, Reis O, Pereira GA, Mondego JM.

Biochem Biophys Res Commun. 2015 Oct 30;466(4):629-36. doi: 10.1016/j.bbrc.2015.09.054. Epub 2015 Sep 11.

PMID:
26367180
27.

Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits.

Yuyama PM, Reis Júnior O, Ivamoto ST, Domingues DS, Carazzolle MF, Pereira GA, Charmetant P, Leroy T, Pereira LF.

Mol Genet Genomics. 2016 Feb;291(1):323-36. doi: 10.1007/s00438-015-1111-x. Epub 2015 Sep 3.

PMID:
26334613
28.

Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production.

Carvalho-Netto OV, Carazzolle MF, Mofatto LS, Teixeira PJ, Noronha MF, Calderón LA, Mieczkowski PA, Argueso JL, Pereira GA.

Microb Cell Fact. 2015 Jan 30;14:13. doi: 10.1186/s12934-015-0196-6.

29.

MpSaci is a widespread gypsy-Ty3 retrotransposon highly represented by non-autonomous copies in the Moniliophthora perniciosa genome.

Pereira JF, Araújo EF, Brommonschenkel SH, Queiroz CB, Costa GG, Carazzolle MF, Pereira GA, Queiroz MV.

Curr Genet. 2015 May;61(2):185-202. doi: 10.1007/s00294-014-0469-3. Epub 2015 Jan 23.

PMID:
25614078
30.

Analysis of the ergosterol biosynthesis pathway cloning, molecular characterization and phylogeny of lanosterol 14 α-demethylase (ERG11) gene of Moniliophthora perniciosa.

de Oliveira Ceita G, Vilas-Boas LA, Castilho MS, Carazzolle MF, Pirovani CP, Selbach-Schnadelbach A, Gramacho KP, Ramos PI, Barbosa LV, Pereira GA, Góes-Neto A.

Genet Mol Biol. 2014 Oct;37(4):683-93. doi: 10.1590/S1415-47572014005000017. Epub 2014 Nov 3.

31.

Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus.

Camargo EL, Nascimento LC, Soler M, Salazar MM, Lepikson-Neto J, Marques WL, Alves A, Teixeira PJ, Mieczkowski P, Carazzolle MF, Martinez Y, Deckmann AC, Rodrigues JC, Grima-Pettenati J, Pereira GA.

BMC Plant Biol. 2014 Sep 28;14:256. doi: 10.1186/s12870-014-0256-9.

32.

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.

33.

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.

34.

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

Meinhardt LW, Costa GG, Thomazella DP, Teixeira PJ, Carazzolle MF, Schuster SC, Carlson JE, Guiltinan MJ, Mieczkowski P, Farmer A, Ramaraj T, Crozier J, Davis RE, Shao J, Melnick RL, Pereira GA, Bailey BA.

BMC Genomics. 2014 Feb 27;15:164. doi: 10.1186/1471-2164-15-164.

35.

Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response.

Pereira AL, Carazzolle MF, Abe VY, de Oliveira ML, Domingues MN, Silva JC, Cernadas RA, Benedetti CE.

BMC Genomics. 2014 Feb 25;15:157. doi: 10.1186/1471-2164-15-157.

36.

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.

37.

Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.

Lopes FR, Jjingo D, da Silva CR, Andrade AC, Marraccini P, Teixeira JB, Carazzolle MF, Pereira GA, Pereira LF, Vanzela AL, Wang L, Jordan IK, Carareto CM.

PLoS One. 2013 Nov 11;8(11):e78931. doi: 10.1371/journal.pone.0078931. eCollection 2013.

38.

Identification of target genes using gene expression profile of granulocytes from patients with chronic myeloid leukemia treated with tyrosine kinase inhibitors.

Mascarenhas Cdo C, Ferreira da Cunha A, Brugnerotto AF, Gambero S, de Almeida MH, Carazzolle MF, Pagnano KB, Traina F, Costa FF, de Souza CA.

Leuk Lymphoma. 2014 Aug;55(8):1861-9. doi: 10.3109/10428194.2013.855311. Epub 2014 Feb 4.

PMID:
24144310
39.

A simple and effective set of PCR-based molecular markers for the monitoring of the Saccharomyces cerevisiae cell population during bioethanol fermentation.

Carvalho-Netto OV, Carazzolle MF, Rodrigues A, Bragança WO, Costa GG, Argueso JL, Pereira GA.

J Biotechnol. 2013 Dec;168(4):701-9. doi: 10.1016/j.jbiotec.2013.08.025. Epub 2013 Aug 29.

PMID:
23994268
40.

Gene expression analysis of the Brazilian type of hereditary persistence of fetal hemoglobin: identification of genes that could be related to γ-globin activation.

Roversi FM, da Cunha AF, Brugnerotto AF, Carazzolle MF, de Albuquerque DM, Lanaro C, Machado-Neto JA, Olalla Saad ST, da Costa FF.

Hemoglobin. 2013;37(6):516-35. doi: 10.3109/03630269.2013.818016. Epub 2013 Aug 19.

PMID:
23952144
41.

Deciphering the synergism of endogenous glycoside hydrolase families 1 and 9 from Coptotermes gestroi.

Cairo JP, Oliveira LC, Uchima CA, Alvarez TM, Citadini AP, Cota J, Leonardo FC, Costa-Leonardo AM, Carazzolle MF, Costa FF, Pereira GA, Squina FM.

Insect Biochem Mol Biol. 2013 Oct;43(10):970-81. doi: 10.1016/j.ibmb.2013.07.007. Epub 2013 Aug 2.

PMID:
23917163
42.

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.

43.

Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species.

Salazar MM, Nascimento LC, Camargo EL, Gonçalves DC, Lepikson Neto J, Marques WL, Teixeira PJ, Mieczkowski P, Mondego JM, Carazzolle MF, Deckmann AC, Pereira GA.

BMC Genomics. 2013 Mar 22;14:201. doi: 10.1186/1471-2164-14-201.

44.

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.

45.

A new set of reference genes for RT-qPCR assays in the yeast Dekkera bruxellensis.

de Barros Pita W, Leite FC, de Souza Liberal AT, Pereira LF, Carazzolle MF, Pereira GA, de Morais MA Jr.

Can J Microbiol. 2012 Dec;58(12):1362-7. doi: 10.1139/cjm-2012-0457. Epub 2012 Nov 25.

PMID:
23210993
46.

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.

47.

The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential.

Parizzi LP, Grassi MC, Llerena LA, Carazzolle MF, Queiroz VL, Lunardi I, Zeidler AF, Teixeira PJ, Mieczkowski P, Rincones J, Pereira GA.

BMC Genomics. 2012 Oct 19;13:562. doi: 10.1186/1471-2164-13-562.

48.

The yeast Dekkera bruxellensis genome contains two orthologs of the ARO10 gene encoding for phenylpyruvate decarboxylase.

de Souza Liberal AT, Carazzolle MF, Pereira GA, Simões DA, de Morais MA Jr.

World J Microbiol Biotechnol. 2012 Jul;28(7):2473-8. doi: 10.1007/s11274-012-1054-x. Epub 2012 Apr 22.

PMID:
22806152
49.

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.

50.

Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit.

Rodrigues FA, Marcolino-Gomes J, de Fátima Corrêa Carvalho J, do Nascimento LC, Neumaier N, Farias JR, Carazzolle MF, Marcelino FC, Nepomuceno AL.

Genet Mol Biol. 2012 Jun;35(1 (suppl)):304-14. doi: 10.1590/S1415-47572012000200011.

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