T. Pupko

Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss

This study sequences and annotates the mitochondrial genome of Oikopleura dioica, revealing RNA editing, gene transfers to the nucleus, and tRNA losses, while highlighting sequencing challenges.

Evaluation of the Ability of AlphaFold to Predict the Three-Dimensional Structures of Antibodies and Epitopes

This study evaluates AlphaFold's ability to predict antibody structures and interactions, finding limitations in CDR regions and antigen binding predictions.

Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genus Xanthomonas

This study examines the genetic and functional diversity of Xanthomonas strains to understand their pathogenic, weakly pathogenic, and commensal lifestyles through genomic analysis and phylogenetic relationships.

Harnessing machine translation methods for sequence alignment

This paper introduces BetaAlign, a sequence alignment method using NLP techniques, which outperforms existing tools like MAFFT and MUSCLE.

Harnessing machine learning to unravel protein degradation in Escherichia coli

The paper uses a combination of experimental and machine learning methods to identify fast-degrading proteins in E. coli and explore factors influencing protein half-lives.

ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning

ModelTeller uses machine learning to select phylogenetic models for accurate branch-length estimation, outperforming traditional statistical methods on complex datasets.

Show me your secret(ed) weapons: a multifaceted approach reveals novel type III-secreted effectors of a plant pathogenic bacterium

This study identifies 51 T3E genes and seven novel T3Es in Acidovorax citrulli using bioinformatics and experimental validation, revealing its extensive T3E arsenal.