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Real-time viral genome detection, taxonomic classification and phylogenetic analysis are critical for efficient tracking and control of viral pandemics such as Covid-19. However, the unprecedented and still growing amounts of viral genome…
Controlling the COVID-19 pandemic is an urgent global challenge. The rapid geographic spread of SARS-CoV-2 directly reflects the social structure. Before effective vaccines and treatments are widely available, we have to rely on…
We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions of proteins surfaces. This innovative and general procedure, based on the representation of the molecular…
Network theory-based approaches provide valuable insights into the variations in global structural connectivity between differing dynamical states of proteins. Our objective is to review network-based analyses to elucidate such variations,…
As the year 2020 draws to an end, several new strains have been reported for the SARS-CoV-2 coronavirus, the agent responsible for the COVID-19 pandemic that has afflicted us all this past year. However, it is difficult to comprehend the…
During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns…
The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biology. However, the molecular determinants underlying binding…
The deadly coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gone out of control globally. Despite much effort by scientists, medical experts, and society in general, the…
The devastating impact of the COVID-19 pandemic caused by SARS coronavirus 2 (SARS CoV 2) has raised important questions about viral origin, mechanisms of zoonotic transfer to humans, whether companion or commercial animals can act as…
Forecasting the change in the distribution of viral variants is crucial for therapeutic design and disease surveillance. This task poses significant modeling challenges due to the sharp differences in virus distributions across…
Machine learning (ML) models, such as SVM, for tasks like classification and clustering of sequences, require a definition of distance/similarity between pairs of sequences. Several methods have been proposed to compute the similarity…
We investigate connectivity properties of the SARS-CoV2 spike protein-human ACE2-receptor complex employing a protein side chain-based network method that allows us to span a range from atomic to global protein scales. We analyze network…
Rapid, sensitive detection of biomolecules is important for improved testing methods for viruses as well as biomarkers and environmental hormones. For example, testing for SARS-CoV-2 is essential in the fight against the COVID-19 pandemic.…
With the huge spike in the COVID-19 cases across the globe and reverse transcriptase-polymerase chain reaction (RT-PCR) test remains a key component for rapid and accurate detection of severe acute respiratory syndrome coronavirus 2…
Coronaviruses are membrane-enveloped, non-segmented positive-strand RNA viruses belonging to the Coronaviridae family. Various animal species, mainly mammalian and avian, are severely infected by various coronaviruses, causing serious…
A pipeline to evaluate the evolution of viral dynamics based on a new model-driven approach has been developed in the present study. The proposed methods exploit real data and the multiscale structure of the infection dynamics to provide…
Coronaviruses are a class of virus responsible of the recent outbreak of Human Severe Acute Respiratory Syndrome. The molecular machinery behind the viral entry and thus infectivity is based on the formation of the complex of virus spike…
The SARS-CoV2 virus has caused a lot of tribulation to the human population. Predictive modeling that can accurately determine whether a person is infected with COVID-19 is imperative. The study proposes a novel approach that utilizes deep…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
During 2020 and 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission has been increasing amongst the world's population at an alarming rate. Reducing the spread of SARS-CoV-2 and other diseases that are spread in…