Navegando por Autor "Stransky, Beatriz"

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An integrated approach to identify bimodal genes associated with prognosis in cancer
(FapUNIFESP (SciELO), 2021-07-08) Justino, Josivan Ribeiro; Reis, Clovis Ferreira dos; Fonseca, André Luiz; Souza, Sandro José de; Stransky, Beatriz
Bimodal gene expression (where a gene expression distribution has two maxima) is associated with phenotypic diversity in different biological systems. A critical issue, thus, is the integration of expression and phenotype data to identify genuine associations. Here, we developed tools that allow both: i) the identification of genes with bimodal gene expression and ii) their association with prognosis in cancer patients from The Cancer Genome Atlas (TCGA). Bimodality was observed for 554 genes in expression data from 25 tumor types. Furthermore, 96 of these genes presented different prognosis when patients belonging to the two expression peaks were compared. The software to execute the method and the corresponding documentation are available at the Data access section
A small interfering RNA (siRNA) database for SARS-CoV-2
(2021-04-23) Medeiros, Inácio Gomes; Khayat, André Salim; Stransky, Beatriz; Santos, Sidney; Assumpção, Paulo; Souza, Jorge Estefano Santana de
Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we presented a database of SARS-CoV-2 targets for small interference RNA (siRNA) based approaches, aiming to speed the design process by providing a broad set of possible targets and siRNA sequences. The siRNAs sequences are characterized and evaluated by more than 170 features, including thermodynamic information, base context, target genes and alignment information of sequences against the human genome, and diverse SARS-CoV-2 strains, to assess possible bindings to off-target sequences. This dataset is available as a set of four tables, available in a spreadsheet and CSV (Comma-Separated Values) formats, each one corresponding to sequences of 18, 19, 20, and 21 nucleotides length, aiming to meet the diversity of technology and expertise among laboratories around the world. A metadata table (Supplementary Table S1), which describes each feature, is also provided in the aforementioned formats. We hope that this database helps to speed up the development of new target antivirals for SARS-CoV-2, contributing to a possible strategy for a faster and effective response to the COVID-19 pandemic

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Navegando por Autor "Stransky, Beatriz"