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References: Graph Theory Fundamentals

  1. Graph Theory - Wikipedia - Comprehensive introduction to graph theory covering fundamental definitions, types of graphs, basic properties, and historical development from Euler's bridges of Konigsberg.

  2. Centrality - Wikipedia - Explains key centrality measures including degree, betweenness, closeness, and eigenvector centrality, with mathematical definitions and interpretations for identifying important network nodes.

  3. Scale-Free Network - Wikipedia - Describes networks with power-law degree distributions, the Barabasi-Albert preferential attachment model, and why biological networks like protein interaction networks exhibit scale-free properties.

  4. Networks: An Introduction - Mark Newman - Oxford University Press - Authoritative textbook on network science covering graph fundamentals, centrality measures, community detection, random graphs, and applications to biological and social networks.

  5. Graph Theory and Its Applications (3rd Edition) - Jonathan Gross - CRC Press - Rigorous mathematical treatment of graph theory including trees, traversals, planarity, connectivity, and network flow algorithms relevant to computational biology applications.

  6. NetworkX Documentation - NetworkX Developers - Official documentation for the Python graph analysis library, covering graph creation, algorithms for centrality, shortest paths, and community detection used throughout bioinformatics.

  7. Graph Theory Tutorial - TutorialsPoint - Accessible tutorial covering vertices, edges, adjacency matrices, graph traversal algorithms, and basic graph properties with worked examples and visual illustrations.

  8. Barabasi Lab: Network Science Textbook - Albert-Laszlo Barabasi - Free online textbook covering network science fundamentals including random networks, scale-free models, communities, and spreading phenomena with interactive visualizations.

  9. D3.js Graph Gallery - D3 Graph Gallery - Examples and code for interactive network visualizations using D3.js, demonstrating force-directed layouts, adjacency matrices, and arc diagrams for graph data.

  10. vis-network Documentation - vis.js Community - Reference documentation for the vis-network JavaScript library used to create interactive graph visualizations, covering nodes, edges, physics simulation, and layout algorithms.