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AI for RNAi Screen (Therapy development in AIVC)

Topics/Projects

  • (1) RNAi-AIVC (AI Virtual Cell based on RNAi pertubation)
    • 👍 2026 Cell - Deep-learning-based de novo discovery and design of therapeutics that reverse disease-associated transcriptional phenotypes. 公众号介绍
    • 2026 bioRxiv - Unified modeling of cellular responses to diverse perturbation types
    • 2024 Bioinformatics - Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data
    • 2021 Nature biotechnology - Prediction of Drug Efficacy from Transcriptional Profiles with Deep Learning
  • (2) ⭐️RNA Delivery️⭐️
    • 👍 2026 Cell - LUMI-lab: A foundation model-driven autonomous platform enabling discovery of ionizable lipid designs for mRNA delivery. 公众号介绍

Screen Methods

  • How to Read
    • 👍 TotalX (Total RNA-seq) 2026 NBT - Scalable single-cell total RNA sequencing unifies coding and noncoding transcriptomics.  公众号介绍
    • 👍 VASA-seq (Total RNA-seq) 2022 NBT - High-throughput total RNA sequencing in single cells using VASA-seq
    • DETECTOR-seq 2024 Clin. & Trans. Med. - Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles [Lu Lab Paper]
    • 👍 TRIBE (Interaction-seq) 2023 Nature Biotech. - Detection of transcriptome-wide microRNA–target interactions in single cells with agoTRIBE
  • 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]

Applications of RNAi-AIVC

  • siRNA Design/Prediction
    • 2024 Bioinformatics - OligoFormer: An accurate and robust prediction method for siRNA design. Bioinformatics [Lu Lab Paper]
  • small RNA Drug Synergy
    • 2025 Nature Communications - Building a unified model for drug synergy analysis powered by large language models
    • 2023 Nature Biotechnology - Predicting transcriptional outcomes of novel multigene perturbations with GEARS
  • small RNA Aptamer Screen
    • 👍 2026 Nature Biotechnology - Single-round evolution of RNA aptamers with GRAPE-LM
    • 2010 Nature Review | Drug Discovery - Aptamers as therapeutics