相关论文: Temporal epistasis inference from more than 3,500,…

Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to a deeper understanding of microbial pathogenesis. We have considered all complete SARS-CoV-2 genomes…

Direct Coupling Analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to…

The emergence of new variants of SARS-CoV-2 is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all…

In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such allosteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data.…

The COVID-19 pandemic has profoundly affected global health, driven by the remarkable transmissibility and mutational adaptability of the SARS-CoV-2 virus. Although five variants of concern, Alpha, Beta, Gamma, Delta, and Omicron, have been…

The genetic evolution of SARS-CoV-2 has caused recurring epidemic waves, understanding its global dispersal patterns is critical for effective surveillance. We developed the Site-based mutation dynamics - Equal Power Sampling (S-EPS)…

COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…

The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…

The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail unlike any virus before it.…

Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specific phenotype. However, a particular phenotype is…

Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods and data…

Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…

With the rapid spread of COVID-19 worldwide, viral genomic data is available in the order of millions of sequences on public databases such as GISAID. This Big Data creates a unique opportunity for analysis towards the research of effective…

SARS-CoV-2 is an upper respiratory system RNA virus that has caused over 3 million deaths and infecting over 150 million worldwide as of May 2021. With thousands of strains sequenced to date, SARS-CoV-2 mutations pose significant challenges…

In this work, we aim to study that the dynamics behavior for cumulative number of SARS-CoV-2 pandemic can provide information on the overall behavior of the spread over daily time.The cumulative data can be synthesized in an empirical form…

We compute the allele frequencies of the alpha (B.1.1.7), beta (B.1.351) and delta (B.167.2) variants of SARS-CoV-2 from almost two million genome sequences on the GISAID repository. We find that the frequencies of a majority of the…

SARS-CoV-2, like any other virus, continues to mutate as it spreads, according to an evolutionary process. Unlike any other virus, the number of currently available sequences of SARS-CoV-2 in public databases such as GISAID is already…

2 Diabetes is a leading worldwide public health concern, and its increasing prevalence has significant health and economic importance in all nations. The condition is a multifactorial disorder with a complex aetiology. The genetic…

The emergence of SARS-CoV-2 variants of concern endangers the long-term control of COVID-19, especially in countries with limited genomic surveillance. In this work, we explored genomic drivers of contagion in Chile. We sequenced 3443…

Understanding epistasis (genetic interaction) may shed some light on the genomic basis of common diseases, including disorders of maximum interest due to their high socioeconomic burden, like schizophrenia. Distance correlation is an…