Anish Man Singh Shrestha

Expanding the Repertoire of Associations Between Antibiotic Resistance Genes and Putative Mobile Genetic Element Carriers Using Metagenomic Long Reads

This study identifies new antibiotic resistance gene-mobile genetic element associations using metagenomic long reads from diverse environments.

DUMMEST: A simpler and faster model for frameshift-aware alignment of a DNA sequence to a protein family

DUMMEST improves frameshift-aware alignment of DNA sequences to protein families by combining simplicity and speed, outperforming existing methods in sensitivity and specificity.

PHIStruct: Improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings

PHIStruct improves phage-host interaction prediction by using structure-aware embeddings, achieving better precision and recall than sequence-only methods, especially at low sequence similarity.

DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms

This paper introduces a rapid differential gene expression analysis method for non-model organisms using quasi-mapping of RNA-seq reads to a protein database, achieving speeds > 1000x faster than assembly-based approaches.

Protein embeddings improve phage-host interaction prediction

The paper uses protein embeddings to predict phage-host interactions, showing improved performance over handcrafted features with ProtT5 achieving higher F1 scores.

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment

This paper presents a method for differential gene expression analysis in non-model organisms without transcriptome assembly by directly aligning RNA-seq reads to a proteome, improving speed and accuracy.