Appendices
C
Glossary
Genomic Foundation Models
Introduction
Preface
Part I: Data & Pre-DL Methods
1
Sequencing: From Reads to Variants
2
The Genomic Data Landscape
3
GWAS & Polygenic Scores
4
Deleteriousness Scores
Part II: CNN Seq-to-Function Models
5
Regulatory Prediction
6
Transcriptional Effects
7
Splicing Prediction
Part III: Transformers Models
8
Sequence Representation & Tokens
9
Protein Language Models
10
DNA Foundation Models
11
Long-range Hybrid Model
Part IV: GFMs & Multi-omics
12
Genomic FMs: Principles & Practice
13
Variant Effect Prediction
14
Multi-omics & Systems Context
Part V: Reliability & Interpretation
15
Model Evaluation & Benchmarks
16
Confounders in Model Training
17
Interpretability & Mechanisms
Part VI: Applications
18
Clinical Risk Prediction
19
Pathogenic Variant Discovery
20
Drug Discovery & Biotech
References
Appendices
A
Deep Learning Primer for Genomics
B
Additional Resources
C
Glossary
Appendices
C
Glossary
Appendix C — Glossary
Warning
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Term
Definition
B
Additional Resources