Biochemical Network Evolution

Last update: 27 Jul 2026 11:53
First version: 20 August 2007

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Including: gene regulatory networks, protein interaction networks, signal transduction, and metabolism.

See also:
• Analysis of Network Data
• Complex Networks
• Gene Expression Data Analysis
• Molecular Biology
• Signal Transduction, Control of Metabolism, and Gene Regulation

Recommended, bigger picture:
• Ricard V. Sole, Romualdo Pastor-Satorras, Eric Smith and Thomas B. Kepler, "A Model of Large-Scale Proteome Evolution," Advances in Complex Systems 5 (2002): 43ff = cond-mat/0207311
• Alexei Vazquez, A. Flammini, A. Maritan, and A. Vespignani, "Modeling of protein interaction networks," cond-mat/0108043
• Carsten Wiuf, Markus Brameier, Oskar Hagberg and Michael P. H. Stumpf, "A likelihood approach to analysis of network data", Proceedings of the National Academy of Sciences (USA) 103 (2006): 7566--7570 [My comments. 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.]

Recommended, close-ups:
• Adrián López García de Lomana, Qasim K. Beg, G. de Fabritiis and Jordi Villà-Freixa, "Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks", arxiv:1004.3138
• Sergei Maslov and Kim Sneppen, "Specificity and Stability in Topology of Protein Networks", Science 296 (2002): 910--913
• Ali Zarrinpar, Sang-Hyun Park and Wendell A. Lim, "Optimization of Specificity in a Cellular Protein Interaction Network by Negative Selection", Nature 426 (2003): 676--680

To read:
• Johannes Berg, Michael Lässig, and Stana Radic, "On the evolution of gene regulation," cond-mat/0301574
• Eric Davidson
  • Genomic Regulatory Systems: Development and Evolution
  • The Regulatory Genome: Gene Regulatory Networks in Development and Evolution
• Paul Francois and Vincent Hakim
  • "Design of genetic networks with specified functions by evolution in silico", PNAS 101 (2004): 580--585
  • "A core genetic module : the Mixed Feedback Loop", q-bio.MN/0507044
• Ulrich Gerland and Terence Hwa, "On the Selection and Evolution of Regulatory DNA Motifs," physics/0112039
• 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", Nature<.cite> 452 (2008): 840--845
• 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", Proceedings of the National Academy of Sciences (USA) 105 (2008): 944--949
• David Juan, Florencio Pazos, and Alfonso Valenci, "High-confidence prediction of global interactomes based on genome-wide coevolutionary networks", Proceedings of the National Academy of Sciences (USA) 105 (2008): 934--939
• J. Kim, P. L. Krapivsky, B. Kahng and Sidney Redner, "Evolving Protein Interaction Networks," cond-mat/0203167
• Ron Milo, Shalev Itzkovitz, Nadav Kashtan, Reuven Levitt, Shai Shen-Orr, Inbal Ayzenshtat, Michal Sheffer and Uri Alon, "Superfamilies of Evolved and Designed Networks", Science 303 (2004): 1538--1542
• Michael C. Oldham, Steve Horvath and Daniel H. Geschwind, "Conservation and evolution of gene coexpression networks in human and chimpanzee brains", Proceedings of the National Academy of Sciences (USA) 103 (2006): 17973--17978
• J. Podani, Z. N. Oltvai, H. Jeong, B. Tombor, A.-L. Barabasi and E. Szathmary, "Comparable system-level organization of Archaea and Eukaryotes," Nature Genetics 29 (2001): 54--56 = cond-mat/0110370
• Aviva Presser, Michael B. Elowitz, Manolis Kellis,, and Roy Kishony, "The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication", Proceedings of the National Academy of sciences (USA) 105 (2008): 950--954
• 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", q-bio.PE/0605050
• Gabriele Scheler, "Dynamic re-wiring of protein interaction: The case of transactivation", q-bio.MN/0609014
• Ricard V. Solé, Isaac Salazar-Ciudad and Jordi Garcia-Fernández, "Landscapes, Gene Networks and Pattern Formation: On the Cambrian Explosion," SFI Working Paper 00-08-046
• Michael P. H. Stumpf, P. J. Ingram, I. Nouvel and Carsten Wiuf, "Statistical model selection methods applied to biological networks", Transactions in Computational Systems Biology forthcoming (2005) = q-bio.MN/0506013
• Annie E. Tsong, Brian B. Tuch, Hao Li and Alexander D. Johnson, "Evolution of alternative transcriptional circuits with identical logic", Nature 443 (2006): 415--420
• Hiroki R. Ueda and John B. Hogenesch, "Principles in the Evolution of Metabolic Networks", q-bio.MN/0503038
• 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", PNAS 100 (2003): 15428--15433
• Andreas Wagner, "How the global structure of protein interaction networks evolves," cond-mat/0207043
• Andreas Wagner and Jeremiah Wright, "Compactness and Cycles in Signal Transduction and Transcriptional Regulation Networks: A Signature of Natural Selection?", Advances in Complex Systems 7 (2004): 419--432