Shawn W. Polson

Multi-site Assessment of Methods for Cell Preservation Upstream of Single Cell RNA Sequencing

This study evaluates three cell preservation methods for scRNA-seq across multiple sites, showing concordant cell type results but platform-specific gene expression differences and better granulocyte retention with preservation methods.

Single amino acid substitution in DNA Polymerase I dramatically alters infection dynamics of bacteriophage T7

This study shows that a single amino acid substitution in phage T7's DNA polymerase I significantly affects infection dynamics in the T7-E. coli system.

Ribonucleotide reductases recapitulate biogeographic patterns within virioplankton according to ocean biogeochemistry

The paper examines the distribution of ribonucleotide reductase (RNR) genes in marine viruses and links their patterns to ocean biogeochemistry.

An integrative proteotranscriptomics approach reveals new ADAM9 substrates and downstream pathways

This study identifies new ADAM9 substrates and downstream pathways using an integrative proteotranscriptomics approach in HCT116 cells.

EXTENDING PROTEIN LANGUAGE MODELS TO A VIRAL GENOMIC SCALE USING BIOLOGICALLY INDUCED SPARSE ATTENTION

This paper extends protein language models to a viral genomic scale using sparse attention, improving embeddings for long-range interprotein interactions.

EVRCEPT: EV RNA Cargo Enrichment Prediction Tool to predict enrichment of RNA into Extracellular Vesicles

EVRCEPT predicts RNA enrichment in extracellular vesicles using sequence features and provides RBP interactions, aiding in therapeutic RNA design.

Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.

The paper isolates and compares 16 bacteriophages targeting Bradyrhizobium spp., revealing host species-dependent diversity and identifying three new phage species.

Genomic diversity and global distribution of four new prasinoviruses from the tropical North Pacific

The paper describes four new prasinoviruses infecting Micromonas commoda from the North Pacific, revealing genomic diversity and potential host adaptation mechanisms.

Fine-Tuning Protein Language Models Unlocks the Potential of Underrepresented Viral Proteomes

This study fine-tunes pre-trained protein language models on viral protein sequences to improve their performance on downstream tasks and representation quality.

Deletion of Fibroblast growth factor 9 globally and in skeletal muscle results in enlarged tuberosities at sites of deltoid tendon attachments

This study shows that deletion of Fgf9 in mice leads to enlarged deltoid tuberosities, suggesting a role for Fgf9 in muscle-bone interactions during development.

PASV: Automatic protein partitioning and validation using conserved residues

PASV automates validation and partitioning of protein-coding sequences using conserved residues, achieving high accuracy in classifying RNR, AOX, and PTOX sequences.

Iroki: automatic customization and visualization of phylogenetic trees

Iroki automates the customization and visualization of phylogenetic trees using metadata, enabling easier exploration of microbial ecology data.

Reannotation of the ribonucleotide reductase in a cyanophage reveals life history strategies within the virioplankton

The paper reannotates an RNR gene in a cyanophage, revealing it belongs to Class I rather than Class II, and suggests this reannotation impacts understanding of viral life strategies.

Fast and sensitive protein sequence homology searches using hierarchical cluster BLAST

The paper introduces a method to speed up protein sequence homology searches with minimal loss of sensitivity and specificity by using hierarchical clustering of reference databases.