Paul P. Gardner

The paper assesses genomic indicators of gene function in the human genome, finding that transcriptional activity and evolutionary conservation are strongest predictors of functional regions.

This study identifies potential vaccine antigens in Staphylococcus aureus using computational methods, prioritizing 304 candidates based on sequence, structure, localization, and immunology features.

This study evaluates protein-coding sequence detection tools, finding most are inaccurate and inefficient, with only three out of nine performing better than a naive scheme.

This study examines if academic department affiliations affect bioinformatic tool accuracy, finding no strong association after correcting for multiple testing.

This study assesses the classification of human non-coding RNA genes by analyzing conservation and expression of 15 small ncRNA families to identify potential misclassified pseudogenes and functional ncRNAs.

LazyPair predicts protein-protein interactions and their types using random forests trained on residue properties, outperforming existing methods in accuracy and scalability.

This paper evaluates factors predicting bioinformatic software accuracy and finds that sustained development, not citations or journal impact, is most indicative of accuracy.

The paper shows that modifying synonymous codons in translation initiation sites can tune protein yield in recombinant protein production.

Razor identifies signal peptides from toxins using N-terminal residues, revealing conserved features across kingdoms and discovering toxin-like signal peptides in defensive proteins.

The paper investigates genomic features associated with functional genes and finds evolutionary conservation and transcriptional activity are the strongest indicators of functionality.

The paper introduces TIsigner and SoDoPE, web tools for optimizing recombinant protein expression and solubility, with linked functionality for gene optimization.

The paper introduces a new predictor, SWI, for protein solubility using B-factors and develops a web tool, SoDoPE, to maximize solubility and expression.

The paper presents the tuatara genome, highlighting its evolutionary significance and unique features compared to other vertebrates.

This study compares the mutational robustness of proteins and RNAs using evolutionary, structural, and functional approaches, finding they have similar robustness with proteins slightly more robust on average.

The paper evaluates metagenome and amplicon analysis tools by meta-analyzing benchmarking studies to identify accurate sequence-to-taxonomy mapping software.

The paper uses machine learning to identify genetic signatures of host adaptation in Salmonella enterica strains associated with extraintestinal disease.