User:Tie Koide

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Contact Info

Tie Koide (an artistic interpretation)

• Tie Koide
• Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto - Departamento de Bioquímica e Imunologia
• Avenida dos Bandeirantes, 3900
• Monte Alegre
• Ribeirão Preto - SP - BRASIL
• Email me through OpenWetWare

I work in the Laboratory of Systems Biology of Microorganisms at Universidade de São Paulo. I learned about OpenWetWare from From synthetic biology pages from MIT and Ricardo Vencio, from Universidade de São Paulo, who hosts his lab page at openwet ware, and I've joined because I would like to create my lab home page in OpenWetWare. I am starting my carreer as a Professor and starting a lab.

Education

• 2006, PhD,Department of Biochemistry - Instituto de Química - USP
• 2001, BS, Curso de Ciências Moleculares - USP

Research interests

1. Systems Biology
2. Microbiology
3. Molecular Biology

Publications

1. Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, and Baliga NS. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol. 2009;5:285. DOI:10.1038/msb.2009.42 |
2. Schmid AK, Reiss DJ, Pan M, Koide T, and Baliga NS. A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol. 2009;5:282. DOI:10.1038/msb.2009.40 |
3. Koide T, Pang WL, and Baliga NS. The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol. 2009 Apr;7(4):297-305. DOI:10.1038/nrmicro2107 |
4. Salem-Izacc SM, Koide T, Vêncio RZ, and Gomes SL. Global gene expression analysis during germination in the chytridiomycete Blastocladiella emersonii. Eukaryot Cell. 2009 Feb;8(2):170-80. DOI:10.1128/EC.00330-08 |
5. Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, and Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res. 2008 Sep;7(9):3755-64. DOI:10.1021/pr800031f |
6. da Silva Neto JF, Koide T, Abe CM, Gomes SL, and Marques MV. Role of sigma54 in the regulation of genes involved in type I and type IV pili biogenesis in Xylella fastidiosa. Arch Microbiol. 2008 Mar;189(3):249-61. DOI:10.1007/s00203-007-0314-x |
7. da Silva Neto JF, Koide T, Gomes SL, and Marques MV. The single extracytoplasmic-function sigma factor of Xylella fastidiosa is involved in the heat shock response and presents an unusual regulatory mechanism. J Bacteriol. 2007 Jan;189(2):551-60. DOI:10.1128/JB.00986-06 |
8. Koide T, Vêncio RZ, and Gomes SL. Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa. J Bacteriol. 2006 Aug;188(16):5821-30. DOI:10.1128/JB.00182-06 |
9. Koide T, Salem-Izacc SM, Gomes SL, and Vêncio RZ. SpotWhatR: a user-friendly microarray data analysis system. Genet Mol Res. 2006 Mar 31;5(1):93-107.
10. Vêncio RZ, Koide T, Gomes SL, and Pereira CA. BayGO: Bayesian analysis of ontology term enrichment in microarray data. BMC Bioinformatics. 2006 Feb 23;7:86. DOI:10.1186/1471-2105-7-86 |
11. Vêncio RZ and Koide T. HTself: self-self based statistical test for low replication microarray studies. DNA Res. 2005;12(3):211-4. DOI:10.1093/dnares/dsi007 |
12. Koide T, Zaini PA, Moreira LM, Vêncio RZ, Matsukuma AY, Durham AM, Teixeira DC, El-Dorry H, Monteiro PB, da Silva AC, Verjovski-Almeida S, da Silva AM, and Gomes SL. DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence. J Bacteriol. 2004 Aug;186(16):5442-9. DOI:10.1128/JB.186.16.5442-5449.2004 |
13. Koide T, da Silva Neto JF, Gomes SL, and Marques MV. Insertional transposon mutagenesis in the Xylella fastidiosa Citrus Variegated Chlorosis strain with transposome. Curr Microbiol. 2004 Apr;48(4):247-50. DOI:10.1007/s00284-003-4189-z |
14. da Silva Neto JF, Koide T, Gomes SL, and Marques MV. Site-directed gene disruption in Xylella fastidiosa. FEMS Microbiol Lett. 2002 Apr 23;210(1):105-10. DOI:10.1111/j.1574-6968.2002.tb11167.x |

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