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Tie Koide

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Universidade de São Paulo (USP). Faculdade de Medicina de Ribeirão Preto (FMRP)  (Institutional affiliation for the last research proposal)
Birthplace: Brazil

Graduate at Curso de Ciências Moleculares from Pró-reitoria de graduação (2001), PhD. in Biochemistry from Universidade de São Paulo (2006) and post-doctoral fellow at the Institute for Systems Biology, Seattle -USA (2008). I've been working in the fields of Microbiology, Biochemistry and Molecular Biology with emphasis in Systems Biology, analyzing genome-scale expression data and helping in the development of bioinformatics tools. Fields of Interest: gene expression, microbiology, environmental stress response, integrative data analysis, predictive models, non-coding RNAs, archaea, bioinformatics. (Source: Lattes Curriculum)

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Scientific publications resulting from Research Grants and Scholarships under the grantee's responsibility (17)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

Publications16
Citations140
Cit./Article8.8
Data from Web of Science

ZARAMELA, LIVIA S.; VENCIO, RICARDO Z. N.; TEN-CATEN, FELIPE; BALIGA, NITIN S.; KOIDE, TIE. Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life. PLoS One, v. 9, n. 9, . Web of Science Citations: 8. (09/09532-0, 11/07487-7, 11/14455-4)

GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL; WARD, RICHARD JOHN. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. MICROBIAL BIOTECHNOLOGY, v. 8, n. 1, p. 52-64, . Web of Science Citations: 22. (10/18850-2, 13/04125-2)

SILVA-ROCHA, RAFAEL; CASTRO, LILIAN DOS SANTOS; CAMPOS ANTONIERO, AMANDA CRISTINA; GUAZZARONI, MARIA-EUGENIA; PERSINOTI, GABRIELA FELIX; SILVA, ROBERTO NASCIMENTO. Deciphering the Cis-Regulatory Elements for XYR1 and CRE1 Regulators in Trichoderma reesei. PLoS One, v. 9, n. 6, . Web of Science Citations: 19. (13/04125-2)

SILVA-ROCHA, RAFAEL; DE LORENZO, VICTOR. The pWW0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in Pseudomonas putida. FEMS Microbiology Letters, v. 356, n. 2, SI, p. 176-183, . Web of Science Citations: 4. (13/04125-2)

PEREIRA DE ALMEIDA, JOAO PAULO; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN P. R.; TEN-CATEN, FELIPE; GOMES-FILHO, JOSE VICENTE; KOIDE, TIE. The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1. GENES, v. 10, n. 4, . Web of Science Citations: 0. (15/12012-9, 15/21038-1, 13/21522-5, 17/03052-2, 11/14455-4)

SILVA, LARISSA G.; LORENZETTI, ALAN P. R.; RIBEIRO, RODOLFO A.; ALVES, INGRID R.; LEADEN, LAURA; GALHARDO, RODRIGO S.; KOIDE, TIE; MARQUES, MARILIS V.. OxyR and the hydrogen peroxide stress response in Caulobacter crescentus. Gene, v. 700, p. 70-84, . Web of Science Citations: 0. (15/07386-7, 16/06378-3, 15/21038-1, 14/04046-8, 17/03052-2)

COELHO, PRISCILA DE O.; GUARNIER, FLAVIA A.; FIGUEIREDO, LEONARDO BRUNO; ZARAMELA, LIVIA S.; PACINI, ENIO S. A.; GODINHO, ROSELY O.; GOMES, MARCELO D.. Identification of potential target genes associated with the reversion of androgen-dependent skeletal muscle atrophy. Archives of Biochemistry and Biophysics, v. 663, p. 173-182, . Web of Science Citations: 0. (15/07019-4, 14/10898-7, 11/07487-7)

LEADEN, LAURA; SILVA, LARISSA G.; RIBEIRO, RODOLFO A.; DOS SANTOS, NAARA M.; LORENZETTI, ALAN P. R.; ALEGRIA, THIAGO G. P.; SCHULZ, MARIANE L.; MEDEIROS, MARISA H. G.; KOIDE, TIE; MARQUES, V, MARILIS. Iron Deficiency Generates Oxidative Stress and Activation of the SOS Response in Caulobacter crescentus. FRONTIERS IN MICROBIOLOGY, v. 9, . Web of Science Citations: 5. (17/02127-9, 14/04046-8, 15/21038-1, 17/03052-2, 16/06378-3, 15/07386-7)

NIKEL, PABLO IVAN; SILVA-ROCHA, RAFAEL; BENEDETTI, ILARIA; DE LORENZO, VICTOR. The private life of environmental bacteria: pollutant biodegradation at the single cell level. ENVIRONMENTAL MICROBIOLOGY, v. 16, n. 3, p. 628-642, . Web of Science Citations: 34. (13/04125-2)

CAMPOS ANTONIETO, AMANDA CRISTINA; CASTRO, LILIAN DOS SANTOS; SILVA-ROCHA, RAFAEL; PERSINOTI, GABRIELA FELIX; SILVA, ROBERTO NASCIMENTO. Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis. Fungal Genetics and Biology, v. 73, p. 93-103, . Web of Science Citations: 26. (10/15683-8, 13/04125-2)

ZARAMELA, LIVIA S.; VENCIO, RICARDO Z. N.; TEN-CATEN, FELIPE; BALIGA, NITIN S.; KOIDE, TIE. Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life. PLoS One, v. 9, n. 9, . Web of Science Citations: 8. (11/07487-7, 11/14455-4, 09/09532-0)

GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL; WARD, RICHARD JOHN. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. MICROBIAL BIOTECHNOLOGY, v. 8, n. 1, p. 52-64, . Web of Science Citations: 22. (13/04125-2, 10/18850-2)

DE ARAUJO, HUGO L.; MARTINS, BIANCA P.; VICENTE, ALEXANDRE M.; LORENZETTI, ALAN P. R.; KOIDE, TIE; MARQUES, V, MARILIS. Cold Regulation of Genes Encoding Ion Transport Systems in the Oligotrophic Bacterium Caulobacter crescentus. MICROBIOLOGY SPECTRUM, v. 9, n. 1, . Web of Science Citations: 0. (19/08514-0, 18/17309-8, 19/13440-5, 14/13552-4, 17/03052-2)

GOMES-FILHO, JOSE VICENTE; ZARAMELA, LIVIA SOARES; DA SILVA ITALIANI, VALERIA CRISTINA; BALIGA, NITIN S.; VENCIO, RICARDO Z. N.; KOIDE, TIE. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA BIOLOGY, v. 12, n. 5, p. 490-500, . Web of Science Citations: 7. (13/21522-5, 11/07487-7, 09/09532-0, 10/10195-5)

FERNANDES PEDRO, DANIEL LONGHI; RODRIGUES LORENZETTI, ALAN PERICLES; DOMINGUES, DOUGLAS SILVA; PASCHOAL, ALEXANDRE ROSSI. PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, . Web of Science Citations: 1. (17/03052-2)

TEN-CATEN, FELIPE; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN PERICLES R.; ZARAMELA, LIVIA SOARES; SANTANA, ANA CAROLINA; KOIDE, TIE. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA BIOLOGY, v. 15, n. 8, p. 1119-1132, . Web of Science Citations: 4. (11/07487-7, 15/12012-9, 11/14455-4, 17/03052-2, 15/21038-1)

IBRAHIM, AMR GALAL ABD EL-RAHEEM; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN P. R.; KOIDE, TIE. Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites. GENES, v. 12, n. 7, . Web of Science Citations: 0. (15/21038-1, 17/03052-2)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

FILHO, José Vicente Gomes. RNAs não-codificantes associados a IS200/605: identificação e caracterização funcional na archaea Halobacterium salinarum NRC-1. Tese (Doutorado) -  Faculdade de Medicina de Ribeirão Preto.  Universidade de São Paulo (USP).  Ribeirão Preto.  (13/21522-5

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