AI for RNAi Screen (Therapy development in AIVC)

Topics/Projects

• (1) siRNA prediction
  • 2024 Bioinformatics - OligoFormer: An accurate and robust prediction method for siRNA design. Bioinformatics [Lu Lab Paper]
• (2) RNAi pertubation based AIVC (AI Virtual Cell)
  • 👍2026 bioRxiv - Unified modeling of cellular responses to diverse perturbation types
  • 2021 Nature biotechnology - Prediction of Drug Efficacy from Transcriptional Profiles with Deep Learning
• (3) Drug Synergy
  • 2025 Nature Communications - Building a unified model for drug synergy analysis powered by large language models
• (4) sRNA aptamer screen
  • 👍 2026 Nature Biotechnology - Single-round evolution of RNA aptamers with GRAPE-LM
  • 2010 Nature Review | Drug Discovery - Aptamers as therapeutics

Screen Methods

• How to Write
  • 2022 Nature Review - High-content CRISPR screening. 
  • 2012 PNAS - Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy [Lu Lab Paper]
• How to Read
  • 👍 VASA-seq (Total RNA-seq) 2022 NBT - High-throughput total RNA sequencing in single cells using VASA-seq
  • 👍 TRIBE (Interaction-seq) 2023 Nature Biotech. - Detection of transcriptome-wide microRNA–target interactions in single cells with agoTRIBE