Joshua Chang Mell

The paper identifies disease-specific alleles and gene duplications in H. influenzae by analyzing protein sequences and clinical metadata from 1,600 genomes.

This study identifies coding and non-coding small RNAs in Bacteroides fragilis outer membrane vesicles that modulate inflammatory responses in intestinal epithelial cells, with ETBF OMVs showing immunosuppressive effects.

Scorpio improves DNA sequence embeddings using contrastive learning, enhancing performance in taxonomic classification, AMR gene detection, and promoter identification across diverse datasets.

The paper introduces a linked-pair long-read sequencing strategy for targeted resequencing, enabling efficient enrichment of genomic regions with haplotype information.

The paper introduces a deep learning model for microbial DNA sequence analysis, achieving phenotypic prediction and sequence visualization with performance comparable to conventional methods.

The paper introduces a topic modeling approach to analyze 16S rRNA amplicon data, linking microbial co-occurrence patterns to functional and environmental features.

The paper presents a pipeline using PacBio CCS to sequence full-length 16S rRNA genes for species-level microbiome analysis, showing high accuracy in mock communities and variation in sinonasal microbiomes.

This paper evaluates a topic model approach for analyzing microbiome data, showing it captures dynamic behavior and identifies gut configurations in time-series data.