Koide:Tie Koide

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Contact Info

Tie Oct/2009

I am starting my career as a Professor at University of São Paulo, where I will coordinate the Laboratory of Systems Biology of Microorganisms. I learned about OpenWetWare from from Synthetic Biology web pages from MIT and from Prof. Vêncio, who hosts his lab page at OpenWetWare. I've joined to host the Laboratory of Systems Biology of Microorganisms home page at OpenWetWare.


Research interests

  1. Systems Biology
  2. Microbiology
  3. Molecular Biology
  4. Bioinformatics


  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 | PubMed ID:19536208 | HubMed [Paper1]
  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 | PubMed ID:19536205 | HubMed [Paper2]
  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 | PubMed ID:19252506 | HubMed [Paper3]
  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 | PubMed ID:19098129 | HubMed [Paper4]
  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 | PubMed ID:18652504 | HubMed [Paper5]
  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 | PubMed ID:17985115 | HubMed [Paper6]
  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 | PubMed ID:17098905 | HubMed [Paper7]
  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 | PubMed ID:16885450 | HubMed [Paper8]
  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. PubMed ID:16755501 | HubMed [Paper9]
  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 | PubMed ID:16504085 | HubMed [Paper10]
  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 | PubMed ID:16303752 | HubMed [Paper11]
  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 | PubMed ID:15292146 | HubMed [Paper12]
  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 | PubMed ID:15057448 | HubMed [Paper13]
  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 | PubMed ID:12023085 | HubMed [Paper14]
All Medline abstracts: PubMed | HubMed