AI for cell-free RNA (cfRNA)
I. cfRNA - Basics
Basic cfRNA Features
(1) Add a preset of mRNAs+lncRNAs(RAG):
- ✅ 2025 Nature - An ultrasensitive method for detection of cell-free RNA
(2) Add Microbial RNAs:
- 2025 Nature Biotechnology - Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples
- ✅2022 eLife - Cancer type classification using plasma cell-free RNAs derived from human and microbes [Lu Lab Paper]
(3) Add Fragmented RNAs (and sncRNAs):
- ✅2025 Genome Biology - Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential [Lu Lab Paper]
(4) Add TE-RNAs:
- ✅2023 Nature BME - Nature Profiling of repetitive RNA sequences in the blood plasma of patients with cancer
II. Advanced Projects/Directions
1. cfRNA Modeling
- 👍 2025 Nature Machine Intelligence - A multimodal cell-free RNA language model for liquid biopsy applications
- 贺昶-毕业论文 (清华云：Lu Lab - Shared-R/3.Thesis/本科论文)
- See more AI models for RNA
2. cfRNA Features
Fragment Representation
- ✅ 2026 preprint - Semantic fragment representations for coordinate-free analysis of genomics data
- ✅ Fragmentome (DELFI): 2019 Nature - Genome-wide cell-free DNA fragmentation in patients with cancer
Fragment's End-motif
- ✅ [end-motif ] 2023 PNAS - Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs
MISC RNA Variances (AS, APA, chimeric, etc):
- ✅ 2023 Cell Rep Med. - Cell-free multi-omics analysis reveals potential biomarkers in gastrointestinal cancer patients’ blood
3. cfRNA - microbiome in blood
Virome & AI
- 👍 2025 Nature Genetics - Blood DNA virome associates with autoimmune diseases and COVID-19
- 👍 2024 Cell - Using Artificial Intelligence to Document the Hidden RNA Virosphere
cfRNA-microbial reads
- 2025 Nature Biotechnology - Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples
- 👍 2022 eLife - Cancer Type Classification Using Plasma Cell Free RNAs Derived from Human and Microbes [Lu Lab Paper]
- 2020 Nature - RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
- concerns: Gihawi, A. et al. Major data analysis errors invalidate cancer microbiome findings. mBio 14, e01607–23 (2023)
- response: Sepich-Poore, G. D. et al. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 43, 1127–1148 (2024).
4. Cell-of-origin (classify type of cancer)
- ✅ 2022 Nature Biotech - Cell types of origin of the cell-free transcriptome
- 2021 Nature - MicroRNA sequence codes for small extracellular vesicle release and cellular retention