BI502 - Topics in the theory of Biological Networks

This course examines mathematical principles underlying the activity of various biological networks.
The subject matter ranges from abstract boolean networks to bacterial chemotaxis, systems neuroscience, and ecosystems.
We examine how interesting dynamical properties arise from simple rules and the geometry of network connections.
We focus particularly on the properties of adaptive networks networks whose geometry changes as a result of the activity of the network.
The final projects in this course are computer programs written in matlab, with an accompanying presentation.

1: Boolean networks
Review paper

2: Yeast Transcription network
Review paper – epistasis and missing heritability

3: Topological evolution of dynamical networks: Global Dynamics from Local Plasticity


Review: Evolving a conscious machine

4: Biological Graphs

5: Self Organized Criticality

6: Emergent complex neural dynamics

7: Neuronal Avalanches 2

8: Local learning rules: cellular adaptation synaptic scaling

8b: Dynamic stabilization of excitation and inhibition through nonlinear feedback inhibition

9: Robust networks for dynamic fixed points

10: Guest speaker:

11: Associative neural networks, energy landscapes, and stem cells


12: Role of sleep in the erasure of spurious memories

13: Dynamics of Sleep

14: Guest speaker:

15: Guest speaker:

16: Antihebbian plasticity and sparse memories

18: Case study – dynamics of vocal imitation in songbirds

19: Guest speaker

20: Optimality & Flux balance

21: Guest speaker:

22: Ecosystem Stability-Complexity debate

Alon, U., MG Surette, N. Barkai, and S. Leibler. “Robustness in bacterial chemotaxis.” Nature 397, no. 6715 (1999): 168–171.
Andalman, A.S., and M.S. Fee. “A basal ganglia-forebrain circuit in the songbird biases motor output to avoid vocal errors.”
Proceedings of the National Academy of Sciences 106, no. 30 (2009): 12518.
Bak, P., K. Chen, and M. Creutz. “Self-organized criticality in the game of life.”
Nature 342, no. 6251 (1989): 780–782.
Bak, P., C. Tang, and K. Wiesenfeld. “Self-organized criticality.”
Physical review A 38, no. 1 (1988): 364–374.
Baker, M.D., and J.B. Stock. “Signal transduction: Networks and integrated circuits in bacterial cognition.”
Current Biology 17, no. 23 (2007): R1021–R1024.
Barabási, A.L., and R. Albert. “Emergence of scaling in random networks.”
science 286, no. 5439 (AAAS 1999): 509.
Barkai, N., and S. Leibler. “Robustness in simple biochemical networks.”
Nature 387, no. 6636 (1997): 913–917.
Beggs, J.M., and D. Plenz. “Neuronal avalanches in neocortical circuits.”
Journal of Neuroscience 23, no. 35 (2003): 11167.
Berg, H.C., and E.M. Purcell. “Physics of chemoreception.”
Biophysical journal 20, no. 2 (1977): 193–219.
Bornholdt, S “Less is more in modeling large genetic networks.”
science 310, no. 5747 (2005): 449.
Bornholdt, S., and T. Rohlf. “Topological evolution of dynamical networks: Global criticality from local dynamics.”
Physical Review Letters 84, no. 26 (2000): 6114–6117.
Chialvo, D.R “Are our senses critical.”
Nature Physics 2 (2006): 301–302.
Crick, F., and G. Mitchison. “The function of dream sleep.”
Nature 304, no. 5922 (1983): 111–114.
Diesmann, M, M O Gewaltig, and A Aertsen. “Stable propagation of synchronous spiking in cortical neural networks..”
Nature 402, no. 6761 (December 2, 1999): 529–533.
Eguiluz, V.M., D.R. Chialvo, G.A. Cecchi, M. Baliki, and A.V. Apkarian. “Scale-free brain functional networks.”
Physical Review Letters 94, no. 1 (2005): 18102.
Enver, T., M. Pera, C. Peterson, and P.W. Andrews. “Stem cell states, fates, and the rules of attraction.”
Cell Stem Cell 4, no. 5 (2009): 387–397.
Fangting, L., L. Tao, L. Ying, O. Qi, and T. Chao. “The yeast cell-cycle network is robustly designed.”
Proceedings of the National Academy of Sciences (PNAS) 101, no. 14 (2004): 4781–4786.
Gardner, T.J., F. Naef, and F. Nottebohm. “Freedom and rules: the acquisition and reprogramming of a bird's learned song.”
science 308, no. 5724 (2005): 1046.
Goldenfeld, N., Kadanoff, L.P “Simple lessons from complexity.”
science 284, no. 5411 (1999): 87.
Guelzim, N., S. Bottani, P. Bourgine, and F. Képès. “Topological and causal structure of the yeast transcriptional regulatory network.”
Nature genetics 31, no. 1 (2002): 60–63.
Hahnloser, R.H.R., A.A. Kozhevnikov, and M.S. Fee. “An ultra-sparse code underliesthe generation of neural sequences in a songbird.”
Nature 419, no. 6902 (2002): 65–70.
Haldeman, C., and J.M. Beggs. “Critical branching captures activity in living neural networks and maximizes the number of metastable states.”
Physical Review Letters 94, no. 5 (2005): 58101.
Hao, Jiang, Xu-dong Wang, Yang Dan, Mu-ming Poo, and Xiao-hui Zhang. “An arithmetic rule for spatial summation of excitatory and inhibitory inputs in pyramidal neurons..”
Proceedings of the National Academy of Sciences 106, no. 51 (December 22, 2009): 21906–21911.
Hopfield, J.J “Neural networks and physical systems with emergent collective computational abilities.”
Proceedings of the National Academy of Sciences of the United States of America 79, no. 8 (1982): 2554.
Hopfield, J.J., DI Feinstein, and RG Palmer. “`Unlearning'has a stabilizing effect in collective memories” (1983).
Huang, S., G. Eichler, Y. Bar-Yam, and D.E. Ingber. “Cell fates as high-dimensional attractor states of a complex gene regulatory network.”
Physical Review Letters 94, no. 12 (2005): 128701.
Kauffman, SA. “Metabolic stability and epigenesis in randomly constructed genetic nets.”
Journal of theoretical biology 22, no. 3 (1969): 437–467.
Kinouchi, O., and M. Copelli. “Optimal dynamical range of excitable networks at criticality.”
Nature Physics 2, no. 5 (2006): 348–351.
Kondoh, M “Foraging adaptation and the relationship between food-web complexity and stability.”
science 299, no. 5611 (2003): 1388.
Krueger, J.M., D.M. Rector, S. Roy, H.P.A. Van Dongen, G. Belenky, and J. Panksepp. “Sleep as a fundamental property of neuronal assemblies.”
Nature Reviews Neuroscience 9, no. 12 (2008): 910–919.
Lauffenburger, D.A “Cell signaling pathways as control modules: Complexity for simplicity?.”
Proceedings of the National Academy of Sciences 97, no. 10 (2000): 5031.
Long, M.A., D.Z. Jin, and M.S. Fee. “Support for a synaptic chain model of neuronal sequence generation.”
Nature 468, no. 7322 (2010): 394–399.
Magnasco, M.O., O. Piro, and G.A. Cecchi. “Self-Tuned Critical Anti-Hebbian Networks.”
Physical Review Letters 102, no. 25 (2009): 258102.
Maher, B “Personal genomes: The case of the missing heritability..”
Nature 456, no. 7218 (2008): 18.
Malamud, B.D., G. Morein, and D.L. Turcotte. “Forest fires: an example of self-organized critical behavior.”
science 281, no. 5384 (1998): 1840.
Olveczky, BP, A.S. Andalman, and M.S. Fee. “Vocal experimentation in the juvenile songbird requires a basal ganglia circuit.”
PLoS Biol 3, no. 5 (2005): e153.
Petermann, T., T.C. Thiagarajan, M.A. Lebedev, M.A.L. Nicolelis, D.R. Chialvo, and D. Plenz. “Spontaneous cortical activity in awake monkeys composed of neuronal avalanches.”
Proceedings of the National Academy of Sciences 106, no. 37 (2009): 15921.
Plenz, D., and T.C. Thiagarajan. “The organizing principles of neuronal avalanches: cell assemblies in the cortex?.”
TRENDS in Neurosciences 30, no. 3 (2007): 101–110.
Ptashne, M., and A. Gann. “Transcriptional activation by recruitment.”
Nature 386, no. 6625 (1997): 569–577.
Purcell, E.M “Life at low Reynolds number.”
Am. J. Phys 45, no. 3 (1977): 11.
Rochefort, N.L., O. Garaschuk, R.I. Milos, M. Narushima, N. Marandi, B. Pichler, Y. Kovalchuk, and A. Konnerth. “Sparsification of neuronal activity in the visual cortex at eye-opening.”
Proceedings of the National Academy of Sciences 106, no. 35 (2009): 15049.
Rudoy, J.D., J.L. Voss, C.E. Westerberg, and K.A. Paller. “Strengthening individual memories by reactivating them during sleep.”
science 326, no. 5956 (2009): 1079.
Shew, W.L., H. Yang, T. Petermann, R. Roy, and D. Plenz. “Neuronal avalanches imply maximum dynamic range in cortical networks at criticality.”
The Journal of Neuroscience 29, no. 49 (2009): 15595.
Spruston, Nelson. “Pyramidal neurons: dendritic structure and synaptic integration..”
Nature Reviews Neuroscience 9, no. 3 (March 2008): 206–221.
Stellwagen, D., and R.C. Malenka. “Synaptic scaling mediated by glial TNF-$\alpha$.”
Nature 440, no. 7087 (2006): 1054–1059.
Stopfer, M., V. Jayaraman, and G. Laurent. “Intensity versus identity coding in an olfactory system.”
Neuron 39, no. 6 (2003): 991–1004.
Taubes, G “Evolving a conscious machine.”
DISCOVER-NEW YORK- 19 (1998): 72–79.
Turrigiano, G.G., K.R. Leslie, N.S. Desai, L.C. Rutherford, and S.B. Nelson. “Activity-dependent scaling of quantal amplitude in neocortical neurons.”
NATURE-LONDON- (1998): 892–895.
Vogels, T.P., K. Rajan, and LF Abbott. “Neural network dynamics.”
Annu. Rev. Neurosci. 28 (2005): 357–376.
Vyazovskiy, V.V., U. Olcese, E.C. Hanlon, Y. Nir, C. Cirelli, and G. Tononi. “Local sleep in awake rats.”
Nature 472, no. 7344 (2011): 443–447.
Watts, D.J., and S.H. Strogatz. “Collective dynamics of `small-world'networks.”
Nature 393, no. 6684 (1998): 440–442.