Shuhui Song

BacLLM improves protein sequence representations for antimicrobial resistance analysis by integrating functional knowledge and enhancing resistance gene identification and mechanism prediction.

InfluProto predicts cross-species transmission of influenza A virus using prototype learning, showing high accuracy in host classification and detecting reassortment effects.

ImmuneLens links transcriptional states and TCR clonotypes using disentangled multimodal learning to improve antigen-specificity prediction and reveal T cell heterogeneity in immunotherapy.

Influ-BERT improves IAV subtype identification by using domain-adaptive pretraining and achieves high F1-scores across underrepresented subtypes.

The paper introduces the GSA Family, a platform for sharing multi-omics and multimodal data, with expanded databases and improved features.

HaploThread constructs and visualizes haplotype networks from large sequence datasets using multi-threaded algorithms and a plugin system.

RCoV19 integrates SARS-CoV-2 genome data, monitors variants, and provides risk pre-warning tools for COVID-19 response.

This paper develops a machine learning model using LightGBM to predict high-risk SARS-CoV-2 variants based on haplotype network features, achieving high accuracy in identifying variants of concern and interest.

SoyOmics integrates soybean multi-omics data to support functional studies and molecular breeding by providing a centralized database with analysis tools.

McAN constructs haplotype networks using a minimum-cost arborescence approach, achieving speeds two orders of magnitude faster than existing methods.

The paper describes the 2019nCoVR resource, which curates and analyzes SARS-CoV-2 genomes, variants, and haplotypes globally, providing daily updates and integration with literature and databases.

This study identifies PRKCG as a glioma biomarker through multi-omics integration, showing its association with glioma progression and survival outcomes when combined with MGMT.

SR4R provides a processed SNP database for rice, offering four reference SNP panels for population genetics and genomic breeding.