Power Laws, Scale-Free Networks and Genome Biology

Power Laws in Biological Networks.- Graphical Analysis of Biocomplex Networks and Transport Phenomena.- Large-Scale Topological Properties of Molecular Networks.- The Connectivity of Large Genetic Networks.- The Drosophila Protein Interaction Network May Be neither Power-Law nor Scale-Free.- Birth and Death Models of Genome Evolution.- Scale-Free Evolution.- Gene Regulatory Networks.- Power Law Correlations in DNA Sequences.- Analytical Evolutionary Model for Protein Fold Occurrence in Genomes, Accounting for the Effects of Gene Duplication, Deletion, Acquisition and Selective Pressure.- The Protein Universes.- The Role of Computation in Complex Regulatory Networks.- Neutrality and Selection in the Evolution of Gene Families.- Scaling Laws in the Functional Content of Genomes.

[1]  Eugene V Koonin,et al.  No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly , 2003, BMC Evolutionary Biology.

[2]  B Honig,et al.  An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. , 2000, Journal of molecular biology.

[3]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[4]  E. Koonin,et al.  The structure of the protein universe and genome evolution , 2002, Nature.

[5]  Rory A. Fisher,et al.  The Possible Modification of the Response of the Wild Type to Recurrent Mutations , 1928, The American Naturalist.

[6]  J. Onuchic,et al.  The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. , 2000, Advances in protein chemistry.

[7]  Eugene V Koonin,et al.  An apology for orthologs - or brave new memes , 2001, Genome Biology.

[8]  Charles DeLisi,et al.  ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations , 2003, BMC Bioinformatics.

[9]  Yunje Cho,et al.  Structure-based identification of a novel NTPase from Methanococcus jannaschii , 1999, Nature Structural Biology.

[10]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[11]  A. Force,et al.  The probability of duplicate gene preservation by subfunctionalization. , 2000, Genetics.

[12]  D J Lipman,et al.  Lineage-specific loss and divergence of functionally linked genes in eukaryotes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  C L Brooks,et al.  Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[14]  J. McGregor,et al.  The number of mutant forms maintained in a population , 1967 .

[15]  R. Solé,et al.  Evolving protein interaction networks through gene duplication. , 2003, Journal of theoretical biology.

[16]  Temple F. Smith,et al.  Comparison of the complete protein sets of worm and yeast: orthology and divergence. , 1998, Science.

[17]  Eduardo P C Rocha,et al.  An analysis of determinants of amino acids substitution rates in bacterial proteins. , 2004, Molecular biology and evolution.

[18]  A. Wagner.  How the global structure of protein interaction networks evolves , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[19]  W. Doolittle,et al.  Lateral genomics. , 1999, Trends in cell biology.

[20]  B. Bollobás.  The evolution of random graphs , 1984 .

[21]  I. Shmulevich,et al.  Computational and Statistical Approaches to Genomics , 2007, Springer US.

[22]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[23]  A. Fersht,et al.  Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Lawrence M. Krauss,et al.  Age Estimates of Globular Clusters in the Milky Way: Constraints on Cosmology , 2003, Science.

[25]  R. Nussinov,et al.  A 3D sequence-independent representation of the protein data bank. , 1995, Protein engineering.

[26]  D. M. Krylov,et al.  Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. , 2003, Genome research.

[27]  C. DeLisi,et al.  Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. , 2000, Physical review letters.

[28]  H. Scheraga,et al.  Statistical analysis of the physical properties of the 20 naturally occurring amino acids , 1985 .

[29]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[30]  M. Gerstein,et al.  The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties , 2002, Genome Biology.

[31]  Akinori Kidera,et al.  Relation between sequence similarity and structural similarity in proteins. Role of important properties of amino acids , 1985 .

[32]  L. Hood,et al.  Gene families: the taxonomy of protein paralogs and chimeras. , 1997, Science.

[33]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[34]  Chris Arney.  Sync: The Emerging Science of Spontaneous Order , 2007 .

[35]  S. N. Dorogovtsev,et al.  Scaling properties of scale-free evolving networks: continuous approach. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.

[36]  M. Levitt,et al.  A unified statistical framework for sequence comparison and structure comparison. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[37]  E. Koonin,et al.  Horizontal gene transfer in prokaryotes: quantification and classification. , 2001, Annual review of microbiology.

[38]  Christoph Adami,et al.  Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response , 2004, BMC Evolutionary Biology.

[39]  B. Birren,et al.  Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.

[40]  Sergey N. Dorogovtsev,et al.  Evolution of Networks: From Biological Nets to the Internet and WWW (Physics) , 2003 .

[41]  Albert-László Barabási,et al.  Statistical mechanics of complex networks , 2001, ArXiv.

[42]  Massimo Marchiori,et al.  Error and attacktolerance of complex network s , 2004 .

[43]  S. Jones,et al.  Prediction of protein-protein interaction sites using patch analysis. , 1997, Journal of molecular biology.

[44]  Mark Buchanan,et al.  Nexus: Small Worlds and the Groundbreaking Science of Networks , 2002 .

[45]  T. Gisiger.  Scale invariance in biology: coincidence or footprint of a universal mechanism? , 2001, Biological reviews of the Cambridge Philosophical Society.

[46]  Benjamin A. Shoemaker,et al.  CDD: a database of conserved domain alignments with links to domain three-dimensional structure , 2002, Nucleic Acids Res..

[47]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[48]  Ruth Nussinov,et al.  MASS: multiple structural alignment by secondary structures , 2003, ISMB.

[49]  Sui Huang,et al.  Back to the biology in systems biology: what can we learn from biomolecular networks? , 2004, Briefings in functional genomics & proteomics.

[50]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[51]  D. Baker,et al.  Matching theory and experiment in protein folding. , 1999, Current opinion in structural biology.

[52]  Andrey Rzhetsky,et al.  Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome , 2001, Bioinform..

[53]  George Kingsley Zipf,et al.  Human Behaviour and the Principle of Least Effort: an Introduction to Human Ecology , 2012 .

[54]  J M Gauthier,et al.  Protein--protein interaction maps: a lead towards cellular functions. , 2001, Trends in genetics : TIG.

[55]  A. E. Hirsh,et al.  Evolutionary Rate in the Protein Interaction Network , 2002, Science.

[56]  K. Gajiwala,et al.  HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria. , 2000, Journal of molecular biology.

[57]  E. Koonin,et al.  Birth and death of protein domains: A simple model of evolution explains power law behavior , 2002, BMC Evolutionary Biology.

[58]  C. Peterson,et al.  Topological properties of citation and metabolic networks. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[59]  Michael Y. Galperin,et al.  Sequence — Evolution — Function , 2003, Springer US.

[60]  E I Shakhnovich,et al.  Specific nucleus as the transition state for protein folding: evidence from the lattice model. , 1994, Biochemistry.

[61]  E. Koonin,et al.  Conservation and coevolution in the scale-free human gene coexpression network. , 2004, Molecular biology and evolution.

[62]  C. Adami.  What is complexity? , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[63]  P. Erdos,et al.  On the evolution of random graphs , 1984 .

[64]  Martin H. Levinson.  Linked: The New Science of Networks , 2004 .

[65]  C. Adami,et al.  Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein–protein interactions data sets , 2003, BMC Evolutionary Biology.

[66]  Sheldon M. Ross,et al.  Introduction to probability models , 1975 .

[67]  Albert-László Barabási,et al.  Evolution of Networks: From Biological Nets to the Internet and WWW , 2004 .

[68]  Charles Gide,et al.  Cours d'économie politique , 1911 .

[69]  M. Huynen,et al.  The frequency distribution of gene family sizes in complete genomes. , 1998, Molecular biology and evolution.

[70]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[71]  Flavio Seno,et al.  Protein Structures and Optimal Folding from a Geometrical Variational Principle , 1998, cond-mat/9811246.

[72]  C. Sparrow.  The Fractal Geometry of Nature , 1984 .

[73]  Barry D Hughes,et al.  A model explaining the size distribution of gene and protein families. , 2004, Mathematical biosciences.

[74]  E. Koonin,et al.  The role of lineage-specific gene family expansion in the evolution of eukaryotes. , 2002, Genome research.

[75]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[76]  William H. Press,et al.  Numerical recipes , 1990 .

[77]  M. Gerstein,et al.  Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. , 2001, Journal of molecular biology.

[78]  J H Lakey,et al.  Measuring protein-protein interactions. , 1998, Current opinion in structural biology.

[79]  Eugene I Shakhnovich,et al.  Expanding protein universe and its origin from the biological Big Bang , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[80]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[81]  C. Ponting,et al.  Protein repeats: structures, functions, and evolution. , 2001, Journal of structural biology.

[82]  G. Petsko.  Homologuephobia , 2001, Genome Biology.

[83]  Eugene V Koonin,et al.  Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models , 2004, BMC Evolutionary Biology.

[84]  Hidemi Watanabe,et al.  A genomic timescale for the origin of eukaryotes , 2001, BMC Evolutionary Biology.

[85]  Vladimir A. Kuznetsov,et al.  Distribution Associated with Stochastic Processes of Gene Expression in a Single Eukaryotic Cell , 2001, EURASIP J. Adv. Signal Process..

[86]  Dennis P Wall,et al.  A simple dependence between protein evolution rate and the number of protein-protein interactions , 2003, BMC Evolutionary Biology.

[87]  Duncan J. Watts,et al.  Six Degrees: The Science of a Connected Age , 2003 .

[88]  S. Blair Hedges,et al.  The origin and evolution of model organisms , 2002, Nature Reviews Genetics.

[89]  A. E. Hirsh,et al.  Evolutionary rate depends on number of protein-protein interactions independently of gene expression level , 2004, BMC Evolutionary Biology.

[90]  B. Stec,et al.  MJ0109 is an enzyme that is both an inositol monophosphatase and the 'missing' archaeal fructose-1,6-bisphosphatase , 2000, Nature Structural Biology.

[91]  E V Koonin,et al.  Lineage-specific gene expansions in bacterial and archaeal genomes. , 2001, Genome research.

[92]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.