Computational Biomedicine Lab @ PKU Documentation¶
Long noncoding RNAs (lncRNAs) play crucial roles in fine regulation of gene expression programs, and thus contribute to various biological progresses and pathogenesis in eukaryotic organisms. The Computational Biomedicine Group at Peking University focus their research interests on elucidating the biology and the clinical applications of special categories of lncRNAs, such as circRNAs and TE-derived lncRNAs, by both computational and experimental approaches.
circRNA tools and pipelines¶
- circFL-seq: Sequence full-length ordinary and fusion circRNAs at isoform resolution.
- ucircFL-seq: Profile high-accuracy full-length circRNAs with UMI-guided sequencing.
- DEBKS: Detect differentially expressed circRNAs from RNA-seq datasets.
Transposable elements derived RNAs tools and pipelines¶
- SERVE: Identify expressed endogenous retroviruses from transcriptome data.
- TEIRI: Identify transposable element-initiated RNAs by integrating multi-omics transcript evidence.
- Deep-TEIRI: Predict TE-initiated transcripts with a deep-learning model and RNA-seq coverage.
- TERA: Analyze transposable element-derived RNAs across supported reference genomes.
General Biomedical AI Models and Pipelines¶
MTM: Predict individualized tissue gene expression from another tissue of the same donor.
MTGT: Segment medical images with a multiscale text feature-guided Transformer.