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The coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS-CoV-2, has caused 60 millions of infections and 1.38 millions of fatalities. Genomic analysis of SARS-CoV-2 can provide insights on drug design and vaccine…

SARS-CoV-2 coronavirus infection is mediated by the binding of its spike protein to the angiotensin-converting enzyme 2 (ACE2), which plays a pivotal role in the renin-angiotensin system (RAS). The study of RAS dysregulation due to…

The SARS-CoV-2 pandemic has emphasised the importance of developing a universal vaccine that can protect against current and future variants of the virus. The present study proposes a novel conditional protein Language Model architecture,…

This paper presents a federated learning (FL) approach to train an AI model for SARS-Cov-2 variant classification. We analyze the SARS-CoV-2 spike sequences in a distributed way, without data sharing, to detect different variants of this…

Nowcasting and forecasting of infectious diseases have become increasingly important since the SARS-CoV-2 pandemic. In particular, methods for modeling the composition of circulating variants at a given time have seen more use in part due…

Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has…

Accurate in-silico prediction of conformational B-cell epitopes would lead to major improvements in disease diagnostics, drug design and vaccine development. A variety of computational methods, mainly based on machine learning approaches,…

During their evolution, proteins explore sequence space via an interplay between random mutations and phenotypic selection. Here we build upon recent progress in reconstructing data-driven fitness landscapes for families of homologous…

The COVID-19 pandemic has severely impacted health systems and economies worldwide. Significant global efforts are therefore ongoing to improve vaccine efficacies, optimize vaccine deployment, and develop new antiviral therapies to combat…

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing pandemic infecting 219 million people as of 10/19/21, with a 3.6% mortality rate. Natural selection can generate favorable mutations with improved fitness…

The spike protein (SP) of SARS-CoV-2 is the major molecular target for making diagnostic tests, vaccines, and therapeutic development. We used a combination of transmission electron microscopy (TEM) and surface enhanced Raman microscopy…

Background: Global viral threats underscore the need for effective genomic surveillance, but high costs and uneven resource distribution hamper its implementation. Targeting surveillance to international travelers in major travel hubs may…

Recent outbreaks of infectious diseases have been monitored closely from an epidemiological and microbiological perspective. Extracting from this wealth of data the information that is relevant for the evolution of the pathogen and predict…

Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute…

The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…

We propose two stochastic models for the Coronavirus pandemic. The statistical properties of the models, in particular the correlation functions and the probability density function, have duly been computed. Our models, which generalises a…

Despite the progress in medical care, combined population-wide interventions (such as physical distancing, testing and contact tracing) are still crucial to manage the SARS-CoV-2 pandemic, aggravated by the emergence of new highly…

The outbreak of COVID-19 caused millions of deaths worldwide, and the number of total infections is still rising. It is necessary to identify some potentially effective drugs that can be used to prevent the development of severe symptoms or…

The COVID-19 pandemic has been a great catastrophe that upended human lives and caused millions of deaths all over the world. The rapid spread of the virus, with its early-stage exponential growth and subsequent 'waves', caught many medical…

This paper presents a critical analysis of the literature and perspective research ideas for modeling the epidemics caused by the SARS-CoV-2 virus. It goes beyond deterministic population dynamics to consider several key complexity features…