Paul D. Thomas

SNPWay: streamlined SNP-to-function and pathway over-representation analysis

SNPWay provides a streamlined workflow for SNP-to-function and pathway over-representation analysis using integrated tools and a web server.

Unveiling the Functional Fate of Duplicated Genes Through Expression Profiling and Structural Analysis

This study tests the least diverged orthologue conjecture by analyzing sequence and expression data across multiple species, finding that the least diverged orthologue tends to retain ancestral functions.

Updates to the Alliance of Genome Resources Central Infrastructure

The paper updates the Alliance of Genome Resources' central infrastructure, adding tools and enhancing data management and curation capabilities.

On the automatic annotation of gene functions using observational data and phylogenetic trees

This paper develops a probabilistic model using phylogenetic trees and Gene Ontology annotations to predict gene functions, showing scalability and agreement with biological intuition.

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

The paper introduces CausalTAB, an updated format for representing causal signaling interactions, enhancing the precision and coverage of signaling network modeling.