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AI for RNAi Screen (Therapy development in AIVC)

RNAi based AIVC (AI Virtual Cell)

1. siRNA Design (on/off-target & Toxicity Prediction)

  • 2024 Bioinformatics - OligoFormer: An accurate and robust prediction method for siRNA design. Bioinformatics [Lu Lab Paper]
  • 2010 Nature Review Drug Discovery - Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application

2. Drug Synergy Prediction

  • [Transcriptional Profile] 2026 Cell - Deep-learning-based de novo discovery and design of therapeutics that reverse disease-associated transcriptional phenotypes. 公众号介绍
  • [Transcriptional Profile] 2021 Nature biotechnology - Prediction of Drug Efficacy from Transcriptional Profiles with Deep Learning
  • 👍 [Synergy] 2025 Nature Communications - Building a unified model for drug synergy analysis powered by large language models
  • 👍 [Synergy] 2023 Nature Biotechnology - Predicting transcriptional outcomes of novel multigene perturbations with GEARS

3. AIVC

  • 👍 [AIVC Perspective] 2024 Cell - How to build the virtual cell with artificial intelligence - Priorities and opportunities
  • [Resources of Perturbation Datasets] 2026 bioRxiv - Unified modeling of cellular responses to diverse perturbation types

Screen Methods (Wetlab) for RNAi based AIVC

How to Read (Total RNA-seq)

  • 👍 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 (High-throughput Perturbation)

  • 👍 2025 Nature Biotechnology - Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling
  • 👍 2026 Cell - CRISPR screens identify targets to rescue age-related T cell dysfunction in cancer
  • Screen Method Introduction
    • 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]

Novel small RNA (Aptamer) Drug Screen/Discovery

  • [Aptamer] 2026 Nature Biotechnology - Single-round evolution of RNA aptamers with GRAPE-LM
  • [Aptamer] 2010 Nature Review | Drug Discovery - Aptamers as therapeutics