Projects

BioAI + Biosynthesis + Kaggle

BioAI

Interpretable Protein LLMs for Ubiquitination Prediction Built an ESM2-centered pipeline linking representation extraction, dimensionality reduction, and prediction. Developed interpretable models using embedding-based interpretation and attention-based analysis; contributed to code, data processing, and manuscripts.

Graph AI for Predicting Drug-Disease Links (Drug Repositioning) Built a multi-view heterogeneous GNN to integrate noisy similarity networks and meta-paths for drug-disease association prediction. Improved robustness via contrastive learning; led implementation, benchmarking, and manuscript preparation.

Multi-Omics for Cancer Biomarker Discovery Performed integrative analysis of WGS, RNA-seq, antibody-based protein profiling, and clinical metadata to support biomarker discovery and cross-cohort assessment. Contributed across data preprocessing, QC, statistical analysis, and result interpretation.

Integrative Multi-Omics in the Non-model Malaria Vector (Anopheles sinensis) Generated a de novo genome assembly and analyzed gene families associated with hematophagy and disease transmission. Integrated transcriptome, microRNA, metagenome, and resequencing data from pyrethroid-susceptible/resistant populations to infer resistance mechanisms (variants, selection, regulation, temporal expression); contributed end-to-end.

BioSynthesis + BioAI

Screening, Optimization, and Rational Design of Key Enzymes in Microbial Biosynthesis of Capsaicinoids Applied AI-driven approaches for enzyme screening and optimization in capsaicinoid biosynthesis pathways.

Identification, Optimization, and Rational Design of Functional Components from Pangolin Scales and Porcine Hooves Utilized computational methods to identify and optimize bioactive components for pharmaceutical applications.

Kaggle Competitions

My Kaggle Profile: https://www.kaggle.com/yujuanzhangai

  • Diabetes Prediction Challenge - Playground Series - Season 5, Episode 12 (Playground · 4206 Teams)
  • CAFA 6 Protein Function Prediction - Predict the biological function of a protein (Research · 2190 Teams)
  • Stanford RNA 3D Folding - Solve RNA structure prediction, one of biology’s remaining grand challenges (Featured · Code Competition · 1516 Teams)
  • Binary Prediction of Poisonous Mushrooms - Playground Series - Season 4, Episode 8 (Playground · 2422 Teams)
  • ISIC 2024 - Skin Cancer Detection with 3D-TBP - Identify cancers among skin lesions cropped from 3D total body photographs (Research · Code Competition · 2739 Teams)
  • NeurIPS 2024 - Predict New Medicines with BELKA - Predict small molecule-protein interactions for drug discovery (Research · Code Competition)