Embedded Files
Instructor: Prof. INDIKA Rajapakse
Teaching Assistant: STEPHEN Lindsly
Timeline and Suggested Readings
ASSIGNMENTS
ASSIGNMENTS
Problem Set 6: Helpful Code (MATLAB), Solution
Problem Set 9: Papers (You need to download to see highlighted sections), Solution
Final Problem Set: Video, MATLAB Data
PROBLEM OF THE DAY
PROBLEM OF THE DAY
NOTES, SLIDES, AND PAPERS
NOTES, SLIDES, AND PAPERS
Date: 9-3-2020
Date: 9-3-2020
Papers
Gordon, David E., et al. "A SARS-CoV-2 protein interaction map reveals targets for drug repurposing." Nature (2020): 1-13.
Hartwell, Leland H., et al. "From molecular to modular cell biology." Nature 402.6761 (1999): C47-C52.
Date: 9-8-2020
Date: 9-8-2020
Date: 9-10-2020
Date: 9-10-2020
Papers
Barabási, Albert-László. "Scale-free networks: a decade and beyond." Science 325.5939 (2009): 412-413.
Erdős, Paul, and Alfréd Rényi. "On the evolution of random graphs." Publ. Math. Inst. Hung. Acad. Sci 5.1 (1960): 17-60.
Watts, Duncan J., and Steven H. Strogatz. "Collective dynamics of ‘small-world’networks." Nature 393.6684 (1998): 440-442.
Date: 9-15-2020
Date: 9-15-2020
Papers
Steven Strogatz (2014). "What Should We Be Worried About?: Real Scenarios That Keep Scientists Up at Night" (edited by John Brockman)
Rajapakse, Indika, and Stephen Smale. "Emergence of function from coordinated cells in a tissue." Proceedings of the National Academy of Sciences 114.7 (2017): 1462-1467.
Date: 9-17-2020
Date: 9-17-2020
Papers
Liu, Yang-Yu, Jean-Jacques Slotine, and Albert-László Barabási. "Controllability of complex networks." Nature 473.7346 (2011): 167-173.
Rajapakse I, Groudine M, Mesbahi M. "Dynamics and control of state-dependent networks for probing genomic organization." Proceedings of the National Academy of Sciences. 2011 Oct 18;108(42):17257-62.
Date: 9-22-2020
Date: 9-22-2020
Books
Moler CB. "Numerical computing with MATLAB." Society for Industrial and Applied Mathematics; 2004 Jan 1.
Date: 9-24-2020
Date: 9-24-2020
Papers
Brin, Sergey, and Lawrence Page. "The anatomy of a large-scale hypertextual web search engine." (1998).
Lieberman-Aiden, Erez, et al. "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science 326.5950 (2009): 289-293.
Liu, Yang-Yu, Jean-Jacques Slotine, and Albert-László Barabási. "Controllability of complex networks." Nature 473.7346 (2011): 167-173.
Date: 9-29-2020
Date: 9-29-2020
Books
Moler CB. "Numerical computing with MATLAB." Society for Industrial and Applied Mathematics; 2004 Jan 1.
Date: 10-1-2020
Date: 10-1-2020
Papers
Rajapakse, Indika, and Mark Groudine. "On emerging nuclear order." Journal of Cell Biology 192.5 (2011): 711-721.
Ronquist, Scott, et al. "Algorithm for cellular reprogramming." Proceedings of the National Academy of Sciences 114.45 (2017): 11832-11837.
Tero, Atsushi, et al. "Rules for biologically inspired adaptive network design." Science 327.5964 (2010): 439-442.
Date: 10-6-2020
Date: 10-6-2020
Date: 10-8-2020
Date: 10-8-2020
Date: 10-13-2020
Date: 10-13-2020
Papers
Michael Elowitz and Stanislas Leibler. "A synthetic oscillatory network of transcriptional regulators." Nature, 403(6767): 335, 2000.
Timothy Gardner, Charles Cantor, and James Collins. "Construction of a genetic toggle switch in escherichiacoli." Nature, 403(6767): 339, 2000.
Egerstedt M. "Degrees of control." Nature. 2011 May;473(7346):158-9.
Date: 10-15-2020
Date: 10-15-2020
Papers
Liu, Yang-Yu, Jean-Jacques Slotine, and Albert-László Barabási. "Controllability of complex networks." Nature 473.7346 (2011): 167-173.
COMMENTARY
Egerstedt M. "Degrees of control." Nature. 2011 May;473(7346):158-9.
Rajapakse I, Groudine M, Mesbahi M. "Dynamics and control of state-dependent networks for probing genomic organization." Proceedings of the National Academy of Sciences. 2011 Oct 18;108(42):17257-62.
COMMENTARY
Abdallah, Chaouki T. "Mathematical controllability of genomic networks." Proceedings of the National Academy of Sciences 108.42 (2011): 17243-17244.
FUN readings.....
Buchanan, Mark. "The best is yet to come." Nature 447.7140 (2007): 39-39.
More papers: Connections in 2007
Date: 10-20-2020
Date: 10-20-2020
Papers
Ronquist S, Patterson G, Muir LA, Lindsly S, Chen H, Brown M, Wicha MS, Bloch A, Brockett R, Rajapakse I. "Algorithm for cellular reprogramming." Proceedings of the National Academy of Sciences. 2017 Nov 7;114(45):11832-7.
Alon, Uri. "Biological networks: the tinkerer as an engineer." Science 301.5641 (2003): 1866-1867.
Nurse, Paul, and Jacqueline Hayles. "The cell in an era of systems biology." Cell 144.6 (2011): 850-854.
Date: 10-22-2020
Date: 10-22-2020
Papers
Rajapakse I, Perlman MD, Scalzo D, Kooperberg C, Groudine M, Kosak ST. "The emergence of lineage-specific chromosomal topologies from coordinate gene regulation." Proceedings of the National Academy of Sciences. 2009 Apr 21;106(16):6679-84.
COMMENTARY
Misteli T. "Self-organization in the genome." Proceedings of the National Academy of Sciences. 2009 Apr 28;106(17):6885-6.
Rajapakse I, Groudine M, Mesbahi M. "What can systems theory of networks offer to biology?" PLoS Comput Biol. 2012 Jun 28;8(6):e1002543.
Date: 10-27-2020
Date: 10-27-2020
Controllability Metrics for Networks: Controllability Gramian
Large networks and graph limits (see chapter 8) : This is very TECHNICAL!
Papers
Ronquist S, Patterson G, Muir LA, Lindsly S, Chen H, Brown M, Wicha MS, Bloch A, Brockett R, Rajapakse I. "Algorithm for cellular reprogramming." Proceedings of the National Academy of Sciences. 2017 Nov 7;114(45):11832-7.
Donnat C, Holmes S. "Tracking network dynamics: A survey using graph distances." The Annals of Applied Statistics. 2018;12(2):971-1012.
Date: 10-29-2020
Date: 10-29-2020
Extra Readings
Hardy, Godfrey H. "Mendelian proportions in a mixed population." Science 28.706 (1908): 49-50.
Hardy, G. H. "A Mathematician’s Apology." University of Alberta Mathematical Sciences Society. (2005).
Rajapakse, Indika, Lindsey Muir, and Paul Martin. "Hardy’s “Small” Discovery Remembered." Notices of the AMS 55.3 (2008).
Date: 11-3-2020
Date: 11-3-2020
In-class Network Visualization Example (MATLAB)
Data Generated: nodes_cent.csv and edges_cent.csv
Papers
Proctor, Joshua L., Steven L. Brunton, and J. Nathan Kutz. "Dynamic mode decomposition with control." SIAM Journal on Applied Dynamical Systems 15.1 (2016): 142-161.
Date: 11-5-2020
Date: 11-5-2020
Papers
Proctor, Joshua L., Steven L. Brunton, and J. Nathan Kutz. "Dynamic mode decomposition with control." SIAM Journal on Applied Dynamical Systems 15.1 (2016): 142-161.
Date: 11-10-2020
Date: 11-10-2020
Book Chapter: Dynamic Mode Decomposition: Data-Driven Modeling of Complex Systems
MATLAB Code: DMD Function and DMD Example
Papers
Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. "The human transcription factors." Cell. 2018 Feb 8;172(4):650-65.
Kunert-Graf JM, Eschenburg K, Galas D, Kutz JN, Rane S, Brunton BW. "Extracting reproducible time-resolved resting state networks using dynamic mode decomposition." Frontiers in computational neuroscience. 2019;13:75.
Date: 11-12-2020
Date: 11-12-2020
Papers
Benson, Austin R., David F. Gleich, and Jure Leskovec. "Higher-order organization of complex networks." Science 353.6295 (2016): 163-166.
Chen C, Rajapakse I. "Tensor Entropy for Uniform Hypergraphs." IEEE Transactions on Network Science and Engineering. (2020).
Date: 11-17-2020
Date: 11-17-2020
Papers
Ng AY, Jordan MI, Weiss Y. "On spectral clustering: Analysis and an algorithm." In Advances in neural information processing systems (2002) (pp. 849-856).
Date: 11-19-2020
Date: 11-19-2020
Papers
Bassett, Danielle S., and Olaf Sporns. "Network neuroscience." Nature neuroscience 20.3 (2017): 353-364.
Date: 12-01-2020
Date: 12-01-2020
Entropy (from biology): Please read the yellow highlighted section
Entropy
Papers
Chen, Pin-Yu, et al. "Fast incremental von neumann graph entropy computation: Theory, algorithm, and applications." International Conference on Machine Learning. PMLR, 2019.
Supplementary materials
Dan Spielman's excellent lecture notes for his semester-long course on Spectral Graph Theory. The notes include a number of helpful plots.
Date: 12-03-2020
Date: 12-03-2020
Emergence: Alan Turing's paper "The chemical basis of morphogenesis " is a beautiful example of a network system which can guide us to talk about emergence. Please read these pages carefully and internalize the ideas! I will discuss tomorrow.
Application: Dynamics of Obesity
Problem Set 9
Papers
Rajapakse, Indika, and Stephen Smale. "Emergence of function from coordinated cells in a tissue." Proceedings of the National Academy of Sciences 114.7 (2017): 1462-1467.
Cucker F, Smale S. On the mathematics of emergence. Japanese Journal of Mathematics. 2007 Mar 1;2(1):197-227.
Application: Wound Healing
Date: 12-08-2020
Date: 12-08-2020
Matrix World : The Picture of All Matrices
Papers
Chen C, Surana A, Bloch A, Rajapakse I. Controllability of Hypergraphs. Submitted (2020).
Strogatz SH. "Exploring complex networks." nature. 2001 Mar;410(6825):268-76.
Hartwell, Leland H., et al. "From molecular to modular cell biology." Nature 402.6761 (1999): C47-C52.
Extra (don't read)
Aral, Sinan, and Dylan Walker. "Identifying influential and susceptible members of social networks." Science 337.6092 (2012): 337-341.
Shimada, Yutaka, et al. "Graph distance for complex networks." Scientific reports 6 (2016): 34944.
Report abuse