Jonathan Allen

Addressing the dynamic nature of reference data: a new nt database for robust metagenomic classification

The paper develops new Centrifuge-compatible nt databases to improve metagenomic classification accuracy by addressing reference database inconsistencies and growth challenges.

GENTANGLE: integrated computational design of gene entanglements

GENTANGLE is a computational tool for designing overlapping gene pairs in microbial genomes, enabling safer genetic engineering through gene entanglements.

Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies

The paper shows that passaging SARS-CoV-2 viral stocks under antiserum selection pressure increases genetic diversity and antibody escape mutations, making them more representative of circulating viruses.

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-based Featurization Method

This paper introduces a ligand-based featurization method to map human protein pockets and identify potential drug interactions by clustering proteins and evaluating compound associations.

A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2

This paper introduces a computational pipeline to identify and characterize binding sites and interacting chemotypes in SARS-CoV-2 proteins using structural modeling and cheminformatic techniques.

PDBspheres - a method for finding 3D similarities in local regions in proteins

PDBspheres identifies and evaluates structural similarities in protein regions near ligands using a library of over 2 million spheres and the LGA algorithm.

Model Choice Metrics to Optimize Profile-QSAR Performance

This paper evaluates pQSAR 2.0's performance on GPCR and safety targets, finding it improves models on some assays but not all, with compound assay coverage being a key factor.