The TargetID pipeline enables rapid identification and characterization of binding sites in SARS-CoV-2 proteins as well as the core chemical components with which these sites interact.

Code used together with its results for the paper as part of my Bachelor's Thesis project. The research consists of optimizing the kallisto algorithm for predicting the abundances of SARS-CoV-2 variants in wastewater samples. Specifically, I look at how only sequencing ...

SpikePro algorithm predicts the fitness of a SARS-CoV-2 strain from the sequence of its spike protein. Given the target sequence in fasta format, the algorithm aligns it to the reference SARS-CoV-2 spike protein, list all mutations with respect to the reference and comp...

InterARTIC is an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses.

Background: Machine learning (ML) based risk stratification models of Electronic Health records (EHR) data may help to optimize treatment of COVID-19 patients, but are often limited by their lack of clinical interpretability and cost of laboratory tests. We develop a ML...

Here we have developed a pipeline for the fast evaluation of viral emerging risks (FEVER) that generates primer and probe sets for genetically diverse viruses. The goal of probe design is to produce a short nucleotide sequence (called a K-mer, as it is of length K) that...

I am submitting an umbrella/blanket disclosure because I am working on several inter-related projects in a fast-moving research area. The general theme is statistical analysis and visualization of SARS-CoV-2 viral genetic sequence data in order to learn about epidemiolo...

The package covid19census provides functions to extract COVID-19 cases, deaths, hospitalizations and test of U.S. and Italy at the county and regional level, respectively, and then combines them with other population metrics (age, sex, prevalence of chronic conditions, ...

COVID-19-CT-CXR is a public database of COVID-19 CXR and CT images, which are automatically extracted from COVID-19-relevant articles from the PubMed Central Open Access (PMC-OA) Subset.

19 and Me: COVID-19 Risk Score Calculator is a tool that synthesizes reported COVID-19 geographic case data and rapidly evolving scientific research to help you ballpark how much risk this disease poses to you.