Startup Readings
A1. RNAfinder
(适合生物和计算背景的同学）
Novelty: TE-RNA, mbRNA, dsRNA, cfRNA
- cfRNAfinder
- dsRNAfinder & TE-cfRNA
- 2025 bioRXiv - Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions
- 2023 Nature BME - Nature Profiling of repetitive RNA sequences in the blood plasma of patients with cancer
- MB-cfRNA (Microbial cfRNA)
- 2025 Nature Genetics - Blood DNA virome associates with autoimmune diseases and COVID-19
- 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- 2020 Nature - RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
- MB-RNA Struture
- 2021 Genome Biology - Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes
- 2025 Genome Biology - Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential [Lu Lab Paper]
- 2024 Nature Biotechnology - RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators
- cf-Rfam Database
- New AI model for RNA Code (motif & structure)
- 2024 Nature Machine Intelligence - An interpretable RNA foundation model for exploring functional RNA motifs in plants
- 2021 Nature - MicroRNA sequence codes for small extracellular vesicle release and cellular retention
- More: dsRNA code
A2. RNAfinder - Applications
A2.1 [Medicine] Precision Medicine
(适合医学和生物背景的同学）（合作： Hospitals）
- Cell-free multi-omics analysis reveals potential biomarkers in gastrointestinal cancer patients’ blood. Cell Reports Medicine 2023 [Lu Lab Paper]
- dsRNAome Manuscript [Lu Lab Paper]
- More: Immune Diseases Cell 2021; SLE Cell 2022; modENCODE Science 2010
A2.2 [Ribozyme] Structure Prediction & Ribozyme Design
(适合生物和计算背景的同学）（合作： Structure lab)
- 2024 Nature Methods - [RfamGen]Deep generative design of RNA family sequences
- 2024 Nature machine intelligence - A 5′ UTR language model for decoding untranslated regions of mRNA and function predictions
B1. RNAtalk
(适合生物和计算背景的同学）（合作： Biology lab）
Novelty: Novel RNA-centered (TE-RNA, mbRNA, sRNA; DT2)
- Type I. Novel Seq-tech
- VASA-seq NBT 2022 （DT2 - [Lu Lab]）
- MUSIC-seq Nature 2024
- UDA-seq Nature Methods 2025
- More: RIC-seq Nature 2020/2023; GRID-seq NBT 2017, etc
- Type II-A. Novel AI Model
- 2023 Nature Methods - SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
- 2021 NAR - ImmReg: the regulon atlas of immune-related pathways across cancer types
- Type II-B. Benchmark & Database
- 2024 Nature Methods - Benchmarking algorithms for single-cell multi-omics prediction and integration
B2. RNAtalk - Applications
B2.1 [RNA-RNA] siRNA Drug Design
(适合生物和计算背景的同学）
(合作： Drug Companies）
- UDA-seq Nature Methods 2025
- High-throughput Seq Data: 2024 Nature Biotechnology - Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling
- AI Model: 2024 Bioinformatics - OligoFormer: An accurate and robust prediction method for siRNA design. Bioinformatics [Lu Lab Paper]
More Readings about Guide RNAs:
2025 Nature Biotechnology - Improved RNA base editing with guide RNAs mimicking highly edited endogenous ADAR substrates
2024 Nature Biotechnology - Tracking-seq reveals the heterogeneity of off-target effects in CRISPR–Cas9-mediated genome editing
B2.2 [RNA-Ligand] Small-molecule Drug Design
(适合计算和生物背景的同学）
(合作： Drug Companies, Computation Labs, Chemistry Labs)
- Generation of 3D molecules in pockets via a language model. Nature Machine Intelligence, 2024
- RNAsmol: RNA–ligand interaction scoring via data perturbation and augmentation modeling. Nature Computational Science 2025 [Lu Lab Paper]
B2.3 [RNA-Protein] RBP & Post-transcriptional Regulation
(适合生物和计算背景的同学）
- 2015 Nature Biotech. - DeepBind: Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
- POSTAR3 - NAR 2022 [Lu Lab Paper]
- RBPgroup - Genome Biology 2017 [Lu Lab Paper]