Yasmmin Martins

Motivation Currently, the Polygenic Score Catalog (PGS) curates over 400 publications on over 500 traits corresponding to over 3,000 polygenic risk scores (PRS). To assess the feasibility of privately calculating the underlying multivariate relative risk for individuals with consumer genomics data, we developed an in-browserPRS calculator for genom...

Background There is an availability of omics and often multi-omics cancer datasets on public databases such as Gene Expression Omnibus (GEO), International Cancer Genome Consortium and The Cancer Genome Atlas Program. Most of these databases provide at least the gene expression data for the samples contained in the project. Multi-omics has been an...

Background The covid-19 pandemic brought negative impacts in almost every country in the world. These impacts were observed mainly in the public health sphere, with a rapid raise and spread of the disease and failed attempts to restrain it while there was no treatment. However, in developing countries, the impacts were severe in other aspects such...

Motivation The identification of the most important mutations, that lead to a structural and functional change in a highly transmissible virus variants, is essential to understand the impacts and the possible chances of vaccine and antibody escape. Strategies to rapidly associate mutations to functional and conformational properties are needed to r...

Protein-protein interactions (PPIs) can be used for a plenty of applications like inferring protein functions or even helping the drug discovery process. For human specie, there is a lot of validated information and functional annotations for the proteins in its interactome. In other species, the known interactome is much smaller compared with huma...

Semantic web standards have shown importance in the last 20 years in promoting data formalization and interlinking between the existing knowledge graphs. In this context, several ontologies and data integration initiatives have emerged in recent years for the biological area, such as the broadly used Gene Ontology that contains metadata to annotate...

Background Technological advances involving RNA-Seq and Bioinformatics allow quantifying the transcriptional levels of genes in cells, tissues, and cell lines, permitting the identification of Differentially Expressed Genes (DEGs). DESeq2 and edgeR are well-established computational tools used for this purpose and they are based upon generalized li...

Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expr...

Introduction Staphylococcus aureus is one of the most prevalent and relevant pathogens responsible for a wide spectrum of hospital-associated or community-acquired infections. In addition, methicillin-resistant Staphylococcus aureus may display multidrug resistance profiles that complicate treatment and increase the mortality rate. The ability to p...

Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression alleli...

In this study, we report the first case of intra-host SARS-CoV-2 recombination during a coinfection by the variants of concern (VOC) AY.33 (Delta) and P.1 (Gamma) supported by sequencing reads harboring a mosaic of lineage-defining mutations. By using next-generation sequencing reads intersecting regions that simultaneously overlap lineage-defining...

In this study, we report the first case of intra-host SARS-CoV-2 recombination during a coinfection by the variants of concern (VOC) AY.33 (Delta) and P.1 (Gamma) supported by sequencing reads harboring a mosaic of lineage-defining mutations. By using next-generation sequencing reads intersecting regions that simultaneously overlap lineage-defining...

Since the first reports of patients coinfected by two genetically-distinct lineages of SARS-CoV-2, the scientific community raised concerns about the recombination of intra-host viral RNA sequences as a possible mechanism underlying the emergence of novel variants. Indeed, this phenomenon occurs at a relatively high frequency among betacoronaviruse...

The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by imm...

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pand...

Predicting the physical or functional associations through protein-protein interactions (PPIs) represents an integral approach for inferring novel protein functions and discovering new drug targets during repositioning analysis. Recent advances in high-throughput data generation and multi-omics techniques have enabled large-scale PPI predictions, t...

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAD and sequenced more 1,927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the...

The Linking Open Data (LOD) cloud is a global data space for publishing and linking structured data on the Web. The idea is to facilitate the integration, exchange, and processing of data. The LOD cloud already includes a lot of datasets that are related to the biological area. Nevertheless, most of the datasets about protein interactions do not us...

Despite being developed from one zygote, heterokaryotypic monozygotic (MZ) co-twins exhibit discordant karyotypes. Epigenomic studies in biological samples from heterokaryotypic MZ co-twins are of the most significant value for assessing the effects on gene- and allele-specific expression of an extranumerary chromosomal copy or structural chromosom...

Considerable efforts have been made to build the Web of Data. One of the main challenges has to do with how to identify the most related datasets to connect to. Another challenge is to publish a local dataset into the Web of Data, following the Linked Data principles. The present work is based on the idea that a set of activities should guide the u...

This paper describes a method to encrypt informations using concepts of genetic strands. This method involves procedures that transform the plaintext and uses substitution cipher to compose the base sequence of ciphertext, ready to be synthesized, together with it key, molding a symmetric cipher system. Resumo. Este artigo descreve um método de cri...

This is a case study of text cues of affect and interaction in students’ postings in a virtual learning environment designed to support and expand face-to-face classes of English for Specific Purposes at university level. These categories of text analysis are indicators of the learner’s social presence in online activities. Methodology in this stud...