Bibliography¶
Differential Equations¶
Chen, T. et al. (1999). Modeling Gene Expression with Differential Equations. Pacific Symposium of Biocomputing.
Stochastic Modeling¶
Takeda, K. (2011). Green and red fluorescent proteins illuminate the mechanics of cell division. Link to video here.
Gillespie, D.T. (1977). Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry. Link.
Elowitz, M.B. et al. (2002) Stochastic Gene Expression in a Single Cell. Science.
Gore, J. Lecture 10: Stochastic modeling - The master equation, Fokker-Planck Equation, and the Gillespie algorithm. Link to lecture here
Network Properties¶
Guarracino, M.R. and A. Nebbia, (2009). Predicting protein-protein interactions with k-Nearest Neighbors classification algorithm. Conference Paper.
Pizzuti, C. and S.E. Rombo (2014). Algorithms and Tools for protein-protein interaction netowkrs clustering, which a special focus on population-based stochastic methods. Bioinformatics.
Xu, J. and Y. Li.(2006). Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics.
Ponomarenko, E.A. et al. (2016). The Size of the Human Proteome: The Width and Depth. Int J. Anal Chem.
Clustering Graphs¶
Scharl, T. and F. Leisch. (2008). Visualizing Gene Clusters using Neighborhood Graphs in R. Technical Report University of Munich.
Heyer, L.J. et al. (1999). Exploring Expression Data: Identification and Analysis of Coexpressed Genes. Genome Research.
Schaeffer, S.E. (2007) Graph Clustering. Computer Science Review.
Cho, R. et al. (1998). A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle. Molecular Cell.
Barabási, A.L. et al. (2011). Network Medicine: A Network-based Approach to Human Disease. Nat. Rev. Genet.
Chen, S-J. et al. (2019). Construction and Analysis of Protein-Protein Interaction Network of Heroin Use Disorder. Scientific Reports.
Newman, M. and M. Girvan. (2004). Finding and evaluating community structure in networks. Physical Review E.