Related papers: Virus2Vec: Viral Sequence Classification Using Mac…
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…
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an…
Given the existing COVID-19 pandemic worldwide, it is critical to systematically study the interactions between hosts and coronaviruses including SARS-Cov, MERS-Cov, and SARS-CoV-2 (cause of COVID-19). We first created four host-pathogen…
Motivation: As viruses that mainly infect bacteria, phages are key players across a wide range of ecosystems. Analyzing phage proteins is indispensable for understanding phages' functions and roles in microbiomes. High-throughput sequencing…
The importance of understanding SARS-CoV-2 evolution cannot be overemphasized. Recent studies confirm that natural selection is the dominating mechanism of SARS-CoV-2 evolution, which favors mutations that strengthen viral infectivity. We…
The phylogenetic tree of SARS-CoV-2 (nCov-19) viruses is reconstructed according to the similarity of genome sequences. The tree topology of Betacoronavirus is remarkably consistent with biologist's systematics. Because the tree…
Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein…
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…
Novel Coronavirus disease (COVID-19) is an extremely contagious and quickly spreading Coronavirus infestation. Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), which outbreak in 2002 and 2011, and the…
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…
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 distribution of amino acid along the protein sequences plays an imperative role in facilitating different biological functions. Currently, there is insufficient scientific data, which represents the arrangement of amino acid in the…
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…
The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of…
Audio Word2Vec offers vector representations of fixed dimensionality for variable-length audio segments using Sequence-to-sequence Autoencoder (SA). These vector representations are shown to describe the sequential phonetic structures of…
Motivation: PCR is more economical and quicker than Next Generation Sequencing for detecting target organisms, with primer design being a critical step. In epidemiology with rapidly mutating viruses, designing effective primers is…
Rapid digitalisation spurred by the Covid-19 pandemic has resulted in more cyber crime. Malware-as-a-service is now a booming business for cyber criminals. With the surge in malware activities, it is vital for cyber defenders to understand…
Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they…
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection which precedes structural rearrangements by…
Virtual screening (VS) is an essential technique for understanding biomolecular interactions, particularly, drug design and discovery. The best-performing VS models depend vitally on three-dimensional (3D) structures, which are not…