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2012 Program
Pre-Reading List

(as of July 10, 2012)


POSTED 7-9-12 and 7-10-12 SUGGESTED PRE-READINGS FROM THE FOLLOWING LECTURERS:

Bernard Chazelle

1. Blondel V.D. and Tsitsiklis J.N. (2000) A survey of computational complexity results in systems and control. Automatica 36 (1249-1274).

2. Castellano C., Fortunato S., and Loreto V. (2009) Statistical physics of social dynamics. ArXiv:0710.3256

3. Chazelle B. (2012) Influence Systems and Natural Algorithms.
(Draft), CACM, to appear.

4. Chazelle B. (2012) The Dynamics of Influence Systems. ArXiv:1204.3946


Guy Theraulaz

1. Bonabeau E., Theraulaz G., Deneubourg J-L., Aron S., and Camazine S. (1997) Self-organization in social insects. TREE vo. 12, no. 5.

2. Theraulaz G., Bonabeau E., and Deneubourg J-L. (1998) Response threshold reinforcement and division of labour in insect societies. Proc. R. Soc. Lond. B 265, (327-332).

3. Theraulaz G. and Bonabeau E. (1999) A Brief History of Stigmergy. Artifical Life 5: 97-116.

4. Theraulaz G., Bonabeau E., Nicolis S., Sole R, Fourcassie V., Blanco S., Fournier R., Joly J-L., Fernandez P., Grimal A., Dalle P., and Deneubourg J-L. (2002) Spatial patterns in ant colonies. PNAS vol. 99 no. 15 (9645-9649).

5. Garnier S., Gautrais J., and Theraulaz G. (2007) The biological principles of swarm intelligence.
Swarm Intell I: 3-31.

6. Gautrais J., Ginelli F., Fournier R., Blanco S., Soria M., Chate H., and Theraulaz G. Deciphering interactions in moving animal groups.

POSTED 7-3-12
SUGGESTED PRE-READINGS FROM THE FOLLOWING LECTURER:

Hod Lipson

1. Bongard J., Zykov V., Lipson H. (2006) Resilient Machines Through Continuous Self-Modeling. Science 314:1118-1121.

2. Schmidt M and Lipson H. (2009) Distilling Free-Form Natural Laws from Experimental Data. Science 324:81-85.


POSTED 6-29-12 SUGGESTED PRE-READINGS AND REFERENCE MATERIALS FROM THE FOLLOWING LECTURER:

Tsvi Tlusty

1. Feynman, Lectures on Computation, Chapters 4-5

2. R. W. Hamming, Coding and Information Theory, Parentice Hall 1986

3. J. von Neumann, Probabilistic Logics and the Synthesis of Reliable Organisms from Unreliable Components, In Automata Studies, eds. C. E. Shannon and J. McCarthy, Princeton University Press, Annals of Mathematics Studies, No. 34, pp. 43-98, 1956.

4. Cover TM & Thomas JA (1991) Elements of information theory (Wiley-Interscience, Hoboken, NJ) - Ch. 13.

5. Berger T (1971) Rate distortion theory (Prentice-Hall, NJ).

+  the papers in Mans Ehrenberg reading List



POSTED 6-27-12 SUGGESTED PRE-READINGS FROM THE FOLLOWING LECTURER:

Mans Ehrenberg

Ninio, J. (1974) A semi-quantitative treatment of missense and nonsense suppression in the strA and ram ribosomal mutants of Escherichia coli. Evaluation of some molecular parameters of translation in vivo. Mol Biol. 84:297.

Ninio, J. (1975) Kinetic amplification of enzyme discrimination. Biochimie. 57:587.

Hopfield, JJ. (1974) Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci U S A. 71:4135.

Hopfield JJ, Yamane T, Yue V, Coutts SM. (1976) Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle. Proc Natl Acad Sci U S A. 73:1164.

Fersht AR. (1977) Editing mechanisms in protein synthesis. Rejection of valine by the isoleucyl-tRNA synthetase. Biochemistry. 16:1025.

Freter RR, Savageau MA. (1980) Proofreading systems of multiple stages for improved accuracy of biological discrimination. J Theor Biol. 85:99.

Ehrenberg, M. and Blomberg, C. (1980). Thermodynamic constraints on kinetic proofreading in biosynthetic pathways. Biophys. J. 31, 333-358.

Johansson M., Zhang J., Ehrenberg M. (2011) Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection. (2012) PNAS 109:131

Johansson M, Lovmar M, Ehrenberg M. (2008) Rate and accuracy of bacterial protein synthesis revisited. Curr Opin Microbiol. 11:141-7.



POSTED 6-15-12 SUGGESTED PRE-READINGS AND REFERENCE MATERIALS FROM THE FOLLOWING LECTURERS:

Arup Chakraborty

1 Please go to the following web site,  http://www.ragoninstitute.org/outreach_education.html#, and watch the video on basic immunology (not the other ones, unless there is interest).  I will provide a more detailed version of this in the first hour of my lectures.  It may also be useful to read the introductory chapters of Immunobiology, C. Janeway, Garland.

References 2 and 3 are for background as I shall use some concepts therein, although in a very different context.

2 Halabi, N., Rivoire, O., Leibler, S. & Ranganathan, R. Protein sectors: evolutionary units of three‐dimensional structure. Cell. 138, 774‐786 (2009).

3 Mora, T. and Bialek, W. (2011). Are biological systems poised at criticality? J. Stat. Phys. 144, 268 - 302.


Arnold Levine

If you have the opportunity to look over the following three books before you arrive, they will serve as helpful references. These books also will be available in our library during the program.

1 Field’s Virology, 5th Edition

2 Principles of Molecular Virology 4th Ed. Alan J. Cann

3 Introduction to Modern Virology (Sixth Edition)


POSTED 6-11-12 SUGGESTED PRE-READINGS FROM THE FOLLOWING LECTURER:

Przemyslaw Prusinkiewicz

Reading suggestions (in the order of importance):

1 Przemyslaw Prusinkiewicz and Brendan Lane [to appear]. Modeling Morphogenesis in Multicellular Structures with Cell Complexes and L-systems.
(Note: this is the manuscript of a book chapter to appear).

2 Richard S. Smith, Soazig Guyomarc'h, Therese Mandel, Didier Reinhardt, Cris Kuhlemeier, and Przemyslaw Prusinkiewicz [2006]. A plausible model of phyllotaxis. Proceedings of the National Academy of Sciences 103 (5), pp. 1301-1306

3 Anne-Gaelle Rolland-Lagan and Przemyslaw Prusinkiewicz [2005]. Reviewing models of auxin canalization in the context of leaf vein pattern formation in Arabidopsis. The Plant Journal, volume 44, pp. 854-865.

4 Emmanuelle M. Bayer, Richard S. Smith, Therese Mandel, Naomi Nakayama, Michael Sauer, Przemyslaw Prusinkiewicz, and Cris Kuhlemeier [2009]. Integration of transport-based models for phyllotaxis and midvein formation. Genes & Development 23(3), pp. 373-384, 2009.

5 Przemyslaw Prusinkiewicz and Adam Runions [2012]. Computational models of plant development and form. New Phytologist 193, pp. 549-569, 2012.


POSTED 6-4-12
SUGGESTED PRE-READINGS FROM THE FOLLOWING LECTURER:

Dario Floreano

S. Wischmann, D. Floreano and L. Keller. Historical contingency affects signaling strategies and competitive abilities in evolving populations of simulated robots, in PNAS, vol. 109, num. 3, p. 864-868, 2012.

D. Floreano and L. Keller. Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection, in PLOS Biology, vol. 8, num. 1, p. e100029, 2010.

S. Mitri, D. Floreano and L. Keller. The Evolution of Information Suppression in Communicating Robots with Conflicting Interests, in PNAS, vol. 106, num. 37, p. 15786-15790, 2009.


POSTED 5-30-12
SUGGESTED PRE-READINGS FROM THE FOLLOWING LECTURERS:

Guillaume Bonfante

Chapters 1 - 6 of the book "Compatibility and Complexity From a Programming Perspective," by Neil D. Jones, MIT Press, 1997.

For those who have the time, also recommended is the book "Computer Viruses: from theory to applications," by Eric Filiol, Springer, 2005. If your time is limited, it is recommended you focus especially on the section "The Virus Formalization: F. Cohen and L. Adleman (1984-1989)."

Enrico Coen

"Generation of Spatial Patterns Through Cell Polarity Switching"

"Generation of Leaf Shape Through Early Patterns of Growth and Tissue Polarity"

"Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth"