Related papers: Robust Representation and Efficient Feature Select…
While many epidemiological models have being proposed to understand and handle COVID-19, too little has been invested to understand how the virus replicates in the human body and potential antiviral can be used to control the replication…
In this thesis, we propose several modelling strategies to tackle evolving data in different contexts. In the framework of static clustering, we start by introducing a soft kernel spectral clustering (SKSC) algorithm, which can better deal…
The unprecedented outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), or COVID-19, continues to be a significant worldwide problem. As a result, a surge of new COVID-19 related research has followed suit. The growing…
More infectious virus variants can arise from rapid mutations in their proteins, creating new infection waves. These variants can evade one's immune system and infect vaccinated individuals, lowering vaccine efficacy. Hence, to improve…
A possible explanation based on first principles for the appearance of the Omicron variant of the SARS-CoV-2 virus is proposed involving coinfection with HIV. The gist is that the resultant HIV-induced immunocompromise allows SARS-CoV-2…
SARS-CoV-2 is colloquially known as COVID-19 that had an initial outbreak in December 2019. The deadly virus has spread across the world, taking part in the global pandemic disease since March 2020. In addition, a recent variant of…
We examine a pair of graph generative models for the therapeutic design of novel drug candidates targeting SARS-CoV-2 viral proteins. Due to a sense of urgency, we chose well-validated models with unique strengths: an autoencoder that…
Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this…
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…
Suppressing SARS-CoV-2 will likely require the rapid identification and isolation of infected individuals, on an ongoing basis. RT-PCR (reverse transcription polymerase chain reaction) tests are accurate but costly, making regular testing…
A theory on the conformation transition for SARS-CoV-2 spike protein (S) is proposed. The conformation equilibrium between open (up) and closed (down) conformations of receptor binding domain (RBD) of the spike is studied from the…
The identification of the transmission parameters of a virus is fundamental to identify the optimal public health strategy. These parameters can present significant changes over time caused by genetic mutations or viral recombination,…
The COVID-19 outbreak resulted in multiple waves of infections that have been associated with different SARS-CoV-2 variants. Studies have reported differential impact of the variants on respiratory health of patients. We explore whether…
We extend the knockoffs method for selecting predictors to clustered data (cross-sectional or repeated measures). In the setting of clustered data, variable selection is complex because some predictors are measured at the observation level…
COVID-19 pandemic has reshaped our world in a timescale much shorter than what we can understand. Particularities of SARS-CoV-2, such as its persistence in surfaces and the lack of a curative treatment or vaccine against COVID-19, have…
Standard approaches to tackle high-dimensional supervised classification problem often include variable selection and dimension reduction procedures. The novel methodology proposed in this paper combines clustering of variables and feature…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
Computational models for the simulation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic evolution would be extremely useful to support authorities in designing healthcare policies and lockdown measures to…
At the end of 2020, policy responses to the SARS-CoV-2 outbreak have been shaken by the emergence of virus variants. The emergence of these more contagious, more severe, or even vaccine-resistant strains have challenged worldwide policy…
Clustering of proteins is of interest in cancer cell biology. This article proposes a hierarchical Bayesian model for protein (variable) clustering hinging on correlation structure. Starting from a multivariate normal likelihood, we enforce…