Zebulun W. Arendsee

Sources and sinks of influenza A virus genomic diversity in swine from 2009 to 2022 in the United States

This study quantifies the sources and sinks of influenza A virus genomic diversity in U.S. swine from 2009 to 2022, showing regional hotspots and the role of swine transport in diversity spread.

classLog: Logistic regression for the classification of genetic sequences

The paper introduces a logistic regression pipeline for classifying genetic sequences, achieving high accuracy even with degraded data and identifying clade-defining mutations.

Foster thy young: Enhanced prediction of orphan genes in assembled genomes

The paper evaluates gene annotation pipelines for predicting orphan genes in genomes, finding that combining methods improves prediction accuracy, especially for Arabidopsis.

Landscape of the Dark Transcriptome Revealed through Re-mining Massive RNA-Seq Data

The paper re-mines RNA-Seq data to identify unannotated ORFs in yeast, revealing many likely protein-coding genes and providing a resource for further study.

Machine learning prediction and experimental validation of antigenic drift in H3 influenza A viruses in swine

This study uses machine learning to predict antigenic drift in swine influenza A viruses and validates predictions with experimental assays.

phylostratr: A framework for phylostratigraphy

The paper introduces phylostratr, an R package for phylostratigraphy, enabling automated and customizable analysis of gene evolutionary origins across species.

synder: inferring genomic orthologs from synteny maps

synder infers genomic orthologs by using synteny maps to trace features between genomes, demonstrated with Arabidopsis thaliana transcription factors.