Introduction to Biological Network Analysis II: Protein-Protein Interaction Networks: From Graphs to

on YouTube ↗01h 07m

" summary

Describes where protein‑protein interaction data come from (yeast two‑hybrid, co‑IP with mass spectrometry), catalogs public databases and Gene Ontology use, and quantifies noise: high false positive/negative rates, context dependence and biased sampling. Covers function‑prediction methods that actually work: semantic similarity, neighborhood counting, diffusion/random‑walk distances, flow/max‑flow and iterative probabilistic models (reporting ~98% precision in cross‑validation for one method), and stresses modeling missing edges and experimental context.

AI-written summary · about

" chapters (29)

1. 0:00Intro
2. 0:41Protein-Protein Interactions
3. 1:58Computational biologists love PPI networks. Why?
4. 3:28About PPI data
5. 4:19Yeast 2-Hybrid Assays
6. 7:51Co-Immunoprecipitation
7. 11:07Inferring PPIs
8. 14:19Orthologs and Interologs
9. 15:11Be Afraid ... Be Very Afraid
10. 16:52Once a Hub, Always a Hub
11. 18:31Repositories of PPI data
12. 18:42Quality of data matters
13. 19:51Bigger question: missing data
14. 20:56Network Visualization Tools
15. 21:41Network Visualization Problem
16. 25:24The Gene Ontology (GO)
17. 28:27Distances in GO
18. 30:01Many other sources of functional annotation
19. 31:45Function prediction based on graph properties
20. 35:47Can be more sophisticated
21. 41:09Use local neighborhood structure
22. 44:06Graph Cut Approaches
23. 46:26Functional Flow
24. 49:12Use Local Community Structure
25. 49:59Redefine "distance"
26. 54:04Redefine "function prediction"
27. 55:56Degree Distributions
28. 57:06Centrality and Essentiality
29. 58:37Summary

" related talks

• 33mNetwork Data Integration Enables Precision MedicineNatasa Przulj · Network Biology 2016
• 43mPanel on Interpretability in the Biological SciencesAnshul Kundaje, Jack Gallant, Debbie Marks · Interpretable Machine Learning in Natural and Social Sciences (2022)
• 36mFormatting Biological Big Data to Enable (Personalized) Systems PharmacologyPatrick Aloy · From Algorithms to Discovery in Genome-Scale Biology and Medicine 2022
• 39mIdentifying Disease Mechanisms Using Gene Networks as PriorsAnna Goldberg · Network Biology 2016
• 32mDynamic and Integrative Biological Network Research of AgingTijana Milenkovic · Network Biology 2016
• 44mNetwork Propagation as a Tool for Deciphering Disease MechanismsRoded Sharan · Network Biology 2016
• 01h 19mAnalyzing Genetic Networks Using Neural NetworksManu Flores · PyData Los Angeles 2019
• 22mThe Nexus of Innovation: How Knowledge Graphs Fuel AI Scientific BreakthroughsPooja Arora · LambdaConf 2024