http://bactra.org/notebooks Cosma's Notebooks en http://bactra.org/notebooks/2008/04/26#biochem-network-evol <P>Including: gene regulatory networks, protein interaction networks, signal transduction, and metabolism. <P>See also: <a href="gene-expression-data.html">Gene Expression Data Analysis</a>; <a href="signal-transduction.html">Signal Transduction, Control of Metabolism, and Gene Regulation</a> <ul>Recommended: <li>Ricard V. Sole, Romualdo Pastor-Satorras, Eric Smith and Thomas B. Kepler, "A Model of Large-Scale Proteome Evolution," <cite>Advances in Complex Systems</cite> <strong>5</strong> (2002): 43ff = <a href="http://arxiv.org/abs/cond-mat/0207311">cond-mat/0207311</a> <li>Alexei Vazquez, A. Flammini, A. Maritan, and A. Vespignani, "Modeling of protein interaction networks," <a href="http://arxiv.org/abs/cond-mat/0108043">cond-mat/0108043</a> <li>Carsten Wiuf, Markus Brameier, Oskar Hagberg and Michael P. H. Stumpf, "A likelihood approach to analysis of network data", <a href="http://dx.doi.org/10.1073/pnas.0600061103"><cite>Proceedings of the National Academy of Sciences</cite> (USA) <strong>103</strong> (2006): 7566--7570</a> [<a href="../weblog/466.html">My comments</a>. Shorter: A nice piece of work, though limited to what they call "duplication attachment" models, a limitation which is not really made clear by the abstract.] </ul> <ul>To read: <li>Johannes Berg, Michael L&auml;ssig, and Stana Radic, "On the evolution of gene regulation," <a href="http://arxiv.org/abs/cond-mat/0301574">cond-mat/0301574</a> <li>Eric Davidson <ul> <li><citE>Genomic Regulatory Systems: Development and Evolution</cite> <li><cite>The Regulatory Genome: Gene Regulatory Networks in Development and Evolution</cite> </ul> <li>Paul Francois and Vincent Hakim <ul> <li>"Design of genetic networks with specified functions by evolution <em>in silico</em>", <a href="http://dx.doi.org/10.1073/pnas.0304532101"><cite>PNAS</cite> <strong>101</strong> (2004): 580--585</a> <li>"A core genetic module : the Mixed Feedback Loop", <a href="http://arxiv.org/abs/q-bio.MN/0507044">q-bio.MN/0507044</a> </ul> <li>Ulrich Gerland and Terence Hwa, "On the Selection and Evolution of Regulatory DNA Motifs," <a href="http://arxiv.org/abs/physics/0112039">physics/0112039</a> <li>Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut and Luis Serrano, "Evolvability and hierarchy in rewired bacterial gene networks", <a href="http://dx.doi.org/10.1038/nature06847">Nature<.cite> <strong>452</strong> (2008): 840--845</a> <li>Anil G. Jegga, Alberto Inga, Daniel Menendez, Bruce J. Aronow, and Michael A. Resnick, "Functional evolution of the p53 regulatory network through its target response elements", <a href="http://dx.doi.org/10.1073/pnas.0704694105 "><cite>Proceedings of the National Academy of Sciences</cite> (USA) <strong>105</strong> (2008): 944--949</a> <li>David Juan, Florencio Pazos, and Alfonso Valenci, "High-confidence prediction of global interactomes based on genome-wide coevolutionary networks", <a href="http://dx.doi.org/10.1073/pnas.0709671105"><cite>Proceedings of the National Academy of Sciences</cite> (USA) <strong>105</strong> (2008): 934--939</a> <li>Ron Milo, Shalev Itzkovitz, Nadav Kashtan, Reuven Levitt, Shai Shen-Orr, Inbal Ayzenshtat, Michal Sheffer and Uri Alon, "Superfamilies of Evolved and Designed Networks", <a href="http://dx.doi.org/10.1126/science.1089167"><citE>Science</cite> <strong>303</strong> (2004): 1538--1542</a> <li>Michael C. Oldham, Steve Horvath and Daniel H. Geschwind, "Conservation and evolution of gene coexpression networks in human and chimpanzee brains", <a href="http://dx.doi.org/10.1073/pnas.0605938103"><cite>Proceedings of the National Academy of Sciences</cite> (USA) <strong>103</strong> (2006): 17973--17978</a> <li>J. Podani, Z. N. Oltvai, H. Jeong, B. Tombor, A.-L. Barabasi and E. Szathmary, "Comparable system-level organization of Archaea and Eukaryotes," <cite>Nature Genetics</cite> <strong>29</strong> (2001): 54--56 = <a href="http://arxiv.org/abs/cond-mat/0110370">cond-mat/0110370</a> <li>Aviva Presser, Michael B. Elowitz, Manolis Kellis,, and Roy Kishony, "The evolutionary dynamics of the <em>Saccharomyces cerevisiae</em> protein interaction network after duplication", <a href="http://dx.doi.org/10.1073/pnas.0707293105"><cite>Proceedings of the National Academy of sciences</cite> (USA) <strong>105</strong> (2008): 950--954</a> <li>Alejandro F. Rozenfeld, Sophie Arnaud-Haond, Emilio Hernandez-Garcia, Victor M. Eguiluz, Manuel A. Matias, Ester Serrao, and Carlos M. Duarte, "Spectrum of genetic diversity and networks of clonal plant populations", <a href="http://arxiv.org/abs/q-bio.PE/0605050">q-bio.PE/0605050</a> <li>Gabriele Scheler, "Dynamic re-wiring of protein interaction: The case of transactivation", <a href="http://arxiv.org/abs/q-bio.MN/0609014">q-bio.MN/0609014</a> <li>Ricard V. Sol&eacute;, Isaac Salazar-Ciudad and Jordi Garcia-Fern&aacute;ndez, "Landscapes, Gene Networks and Pattern Formation: On the Cambrian Explosion," <a href="http://www.santafe.edu/sfi/publications/Abstracts/00-08-046abs.html">SFI Working Paper 00-08-046</a> <li>Michael P. H. Stumpf, P. J. Ingram, I. Nouvel and Carsten Wiuf, "Statistical model selection methods applied to biological networks", <cite>Transactions in Computational Systems Biology</cite> <strong>forthcoming</strong> (2005) = <a href="http://arxiv.org/abs/q-bio.MN/0506013">q-bio.MN/0506013</a> <li>Annie E. Tsong, Brian B. Tuch, Hao Li and Alexander D. Johnson, "Evolution of alternative transcriptional circuits with identical logic", <a href="http://dx.doi.org/10.1038/nature05099"><cite>Nature</cite> <strong>443</strong> (2006): 415--420</a> <li>Hiroki R. Ueda and John B. Hogenesch, "Principles in the Evolution of Metabolic Networks", <a href="http://arxiv.org/abs/q-bio.MN/0503038">q-bio.MN/0503038</a> <li>Christian von Mering, Evgeny M. Zdobnov, Sophia Tsoka, Francesca D. Ciccarelli, Jose B. Pereira-Leal, Christos A. Ouzounis and Peer Bork, "Genome Evolution Reveals Biochemical Networks and Functional Modules", <a href="http://www.pnas.org/cgi/doi/10.1073/pnas.2136809100"><cite>PNAS</cite> <strong>100</strong> (2003): 15428--15433</a> <li>Andreas Wagner, "How the global structure of protein interaction networks evolves," <a href="http://arxiv.org/abs/cond-mat/0207043">cond-mat/0207043</a> <li>Andreas Wagner and Jeremiah Wright, "Compactness and Cycles in Signal Transduction and Transcriptional Regulation Networks: A Signature of Natural Selection?", <a href="http://dx.doi.org/10.1142/S0219525904000251"><cite>Advances in Complex Systems</cite> <strong>7</strong> (2004): 419--432</a> </ul>