Hongli Du

Evolutionary Origins of Molecular Programs Underlying Brain Circuitry

This study reconstructs the evolutionary assembly of a conserved cortical axis across vertebrates using spatial transcriptomics and single-nucleus RNA-seq, revealing conserved molecular programs and convergent evolution in brain circuitry.

PepCleav: a classification method for evaluating the cleavability of peptide fragments presented by MHC class I

PepCleav evaluates peptide cleavability by classifying amino acids at proteasome and aminopeptidase sites, improving neoantigen identification with 84-89% cleavable peptide accuracy.

Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of HPV16

The paper analyzes mutation profiles, glycosylation sites, and codon usage bias in HPV16 genomes to understand lineage differences and adaptation mechanisms.

Molecular dynamics simulation study reveals effects of key mutations on spike protein structure in SARS-CoV-2

This study uses molecular dynamics simulations to analyze how key mutations in SARS-CoV-2 spike protein affect its structure and stability, finding that some mutations enhance stability while others increase solvent accessibility.

AutoVEM2: a flexible automated tool to analyze candidate key mutations and epidemic trends for virus

AutoVEM2 is a flexible automated tool for analyzing candidate key mutations and epidemic trends in viruses, demonstrating its effectiveness with SARS-CoV-2, HBV, and HPV-16.

Real-time monitoring epidemic trends and key mutations in SARS-CoV-2 evolution by an automated tool

The paper introduces an automated tool, AutoVEM, to monitor SARS-CoV-2 haplotype subgroup trends and key mutations, analyzing 131,576 genomes in 18 hours.

Prediction and Evolution of B Cell Epitopes of Surface Protein in SARS-CoV-2

The paper predicts and analyzes B cell epitopes in SARS-CoV-2 surface proteins, identifying conserved epitopes with potential applications in vaccine development and treatment.

Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins

The paper analyzes the evolution and molecular characteristics of over 16,000 SARS-CoV-2 genomes to reveal its epidemic trend and possible origins.

Integrated analysis of gene correlation reveals disordered relationship between metabolism and immunity in tumor microenvironment

The paper analyzes gene correlations between metabolism and immunity in tumor and normal tissues, finding reduced correlations in tumors and identifying key gene pairs with potential therapeutic implications.

Cas12a-based on-site and rapid nucleic acid detection of African swine fever

This paper develops a rapid, sensitive, and on-site ASFV detection system using RAA-Cas12a and lateral-flow strips, achieving femtomolar sensitivity in an hour.