Genomic Structural Variation: INDEL(deletion, insertion, duplication, inversion)
Segmental duplication and copy-number variants (CNV)
GWAS (Genome-wide association studies): 罕见病、单基因分析
LD (Linkage Disequilibrium) 连锁不平衡
similarities
associations
DNA-protein interaction
- cis-element
- trans-element
- TF (Transcription factor)
- TRF (Transcription regulation factor)
Captured/targeted sequencing
CLIP-seq
- PAR-CLIP
- HITS-CLIP
Introduction to neural network
Architectures
- Multilayer perception
- Convolutional neural network
- recurrent neural network
- self-attention mechanism, transformer
Application of LLM in Biomedicine
- linguistics ⇒ bioinformatics
- Grammars
- regular grammars
- context-free grammars
- context-sensitive grammars
- unrestricted grammars
- SCFG (context-free) ⇒ transformer (context sensitive)
- Evoformer, a transformer used in protein folding (AlphaFold2)