Xianglilan Zhang

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

Protein Function Prediction via Contig-Aware Multi-Level Feature Integration

This paper introduces CAML, a deep learning model that improves protein function prediction by integrating sequence, structure, and contig-level CDS topology features, achieving significant performance gains over existing methods.

Coding nucleic acid sequences with graph convolutional network

This paper introduces a graph convolutional network for analyzing nucleic acid sequences, outperforming existing methods in phage-related tasks.

Mining bacterial NGS data vastly expands the complete genomes of temperate phages

This study expands the number of complete temperate phage genomes by over 100-fold using a novel computational method applied to bacterial NGS data.

HyperVR--A hybrid prediction framework for virulence factors and antibiotic resistance genes in microbial data

HyperVR predicts virulence factors and antibiotic resistance genes in microbial data using gene sequences, achieving high precision and recall without strict thresholds.

A framework to trace microbial engraftment at the strain level during fecal microbiota transplantation

The paper introduces PStrain-tracer, a software package to track microbial strain engraftment during FMT using shotgun metagenomic data, revealing strain-specific engraftment patterns and failure determinants.