CV Lattes
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Universidade de São Paulo (USP). Faculdade de Medicina de Ribeirão Preto (FMRP) (Institutional affiliation from 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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Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e. ribonucleases which implement the cleavages) was generally more studied than the RNA perspective (i.e. processing sites). In the present in silico work,…
Antisense RNAs are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSS) and inferred the probable 3' ends of these transcripts. We analyzed the resulting asRNA…
The pervasive transcription hypothesis states that all DNA of an organism is associated with at least one transcript and it has been strenghtened by the acquisison of massive transcriptomic data. An important question that arises in this context is the functionality and regulation of theses transcripts in a global gene regulatory network, specially of transcripts located antisense to anno…
(Only some records are available in English at this moment)
Mapping transcription start sites (TSS) of genes provides a more detailed understanding of gene regulation, allowing the location of promoter regions and the identification of transcript isoforms. The dRNAseq (differential RNA sequencing) technique has been used in prokaryotes for global TSS mapping, revealing a variety of transcript isoforms. One underexplored class of transcripts is the…
Circular RNAs (circRNAs) are closed RNA molecules with their 5' and 3' ends covalently ligated. They were first discovered in viruses and viroids and then in eukaryotes. CircRNAs are progressively being understood as functional molecules and not as mere splicing by-products: their functions range from acting as genetic regulators to being translated. Next generation sequencing experiment…
Halobacterium salinarum NRC-1 is an extremophile halophile, and as an archaeon organism has characteristics shared by eukaryotes and bacteria. Since it is easy to manipulate H. salinarum in the laboratory, it has become a model for genetic studies, most of which characterized its genome as highly unstable due to the high frequency of spontaneous mutations. Our research group study differe…
Insertion sequences (IS) are ubiquitous mobile genetic elements in prokaryotes that promote great impact on host genomes. They can provide fitness to organisms by enhancing the genetic diversity and also by modulating gene expression. On the other hand, mobilization events that damage the host are also common, specially when an essential gene is disrupted and compromises the organism viab…
A plethora of circular RNAs (circRNAs) has been recently reported in organisms from all domains of life, indicating its importance in gene regulatory networks. In the Archaea domain, Halobacterium salinarum has been established as a model organism since it is easy to grow in the laboratory and amenable to genetic manipulations. These properties also allowed the acquisition of abundant dat…
(Only some records are available in English at this moment)
Circular RNAs (circRNAs) are RNA molecules with 5' and 3' ends covalently ligated. Their functions range from acting as genetic regulators to producing proteins, and they are often expressed in a tissue and condition-specific manner. Next-generation sequencing with prior RNA treatment with RNase R (Circ-Seq) has been widely used to identify circRNAs, mainly in model eukaryotes. However, w…
Our main project has the purpose of identifying the components of insertion sequence regulation in Halobacterium salinarum, primarily those acting on the post-transcriptional level. We successfully identified several transposase-encoding mRNAs binding to the LSm protein, which can repress or induce translation by changing the way ribosome couple with transcripts. We evaluated insertion se…