References
- Albert , R , Jeong , H and Barabási, , AL . 2000 . “Error and attack tolerance of complex networks.” . Nature London , 406 (6794) : 378 – 382 .
- Aloy , P and Russell , R . 2004 . “Taking the mystery out of biological networks.” . EMBO Rep. , 5 (4) : 349 – 350 .
- Aloy , P and Russell , RB . 2006 . “Structural systems biology: modelling protein interactions.” . Nat Rev. Mol. Cell Biol. , 7 (3) : 188 – 197 .
- Artzy‐Randrup , Y , Fleishman , S , Ben‐Tal , N and Stone , L . 2004 . “Comment on ‘Network motifs: simple building blocks of complex networks’ and ‘Superfamilies of evolved and designed networks.’” . Science , 305 (5687) : 1107
- Barabási , AL and Albert , R . 1999 . “Emergence of scaling in random networks.” . Science , 286 : 509 – 512 .
- Barabási , AL and Oltvai , ZN . 2004 . “Network biology: understanding the cell's functional organization.” . Nat. Rev. Genet. , 5 : 101 – 113 .
- Barrat , A , Barthelemy , M , Pastor‐Satorras , R and Vespignani , A . 2004 . “The architecture of complex weighted networks.” . Proc. Natl. Acad.Sci. U.S.A. , 101 (11) : 3747 – 3752 .
- Batada , NN . 2006 . “Stratus not altocumulus: a new view of the yeast protein interaction network.” . PLoS Biol. , 4 : e317
- Benfey , PN and Mitchell‐Olds , T . 2008 . “From genotype to phenotype: systems biology meets natural variation.” . Science , 320 (5875) : 495 – 497 .
- Berg , J , Lässig , M and Wagner , A . 2004 . “Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications.” . BMC Evol. Biol. , 4 : 14689 – 14694 .
- Berman , H , Henrick , K and Nakamura , H . 2003 . “Announcing the worldwide Protein Data Bank.” . Nat. Struct. Biol. , 10 (12) : 980 – 980 .
- Bertin , N . 2007 . “Confirmation of organized modularity in the yeast interactome.” . PLoS Biol. , 5 : e153
- Bloom , J and Adami , C . 2003 . “Apparent dependence of protein evolutionary rate on the number of interactions is linked to biases in protein‐protein interactions data sets.” . BMC Evol. Biol. , 3 : 21
- Bollobás, , B . 2001 . Random Graphs. , 2nd ed. , Cambridge, , England : Cambridge University Press .
- Box , GEP . 1976 . “Science and statistics.” . J. Am. Stat. Assoc. , 71 (356) : 791 – 799 .
- Braun , P . 2009 . “An experimentally derived confidence score for binary protein‐protein interactions.” . Nat. Methods , 6 (1) : 91 – 97 .
- Chiang , T , Scholtens , D , Sarkar , D , Gentleman , R and Huber , W . 2007 . “Coverage and error models of protein‐protein interaction data by directed graph analysis.” . Genome Biol. , 8 (9) : R1 86
- Ciliberti , S , Martin , OC and Wagner , A . 2007 . “Innovation and robustness in complex regulatory gene networks.” . Proc. Natl. Acad. Sci. U.S.A. , 104 (34) : 13591 – 13596 .
- Clauset , A , Shalizi , C and Newman , M . 2009 . “Power‐law distributions in empirical data.” .
- Collins , SR , Kemmeren , P , Zhao , X‐C , Greenblatt , JF , Spencer , F , Holstege , FCP , Weissman , JS and Krogan , NJ . 2007 . “Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.” . Mol. Cell Proteomics , 6 (3) : 439 – 450 .
- Conant , GC and Wolfe , KH . 2008 . “Turning a hobby into a job: how duplicated genes find new functions.” . Nat. Rev. Genet. , 9 (12) : 938 – 950 .
- Cordero , OX and Hogeweg , P . 2006 . “Feed‐forward loop circuits as a side effect of genome evolution.” . Mol. Biol. Evol. , 23 (10) : 1931 – 1936 .
- Davidson , EH and Erwin , DH . 2006 . “Gene regulatory networks and the evolution of animal body plans.” . Science , 311 (5762) : 796 – 800 .
- de Silva , E , Thorne , T , Ingram , P , Agrafioti , I , Swire , J , Wiuf , C and Stumpf , M . 2006 . “The effects of incomplete protein interaction data on structural and evolutionary inferences.” . BMC Evol. Biol. , 4 : 39
- Deeds , EJ , Ashenberg , O and Shakhnovich , EI . 2006 . “A simple physical model for scaling in protein‐protein interaction networks.” . Proc. Natl. Acad. Sci. U.S.A. , 103 (2) : 311 – 316 .
- Des Marais , DL and Rausher , MD . 2008 . “Escape from adaptive conflict after duplication in an anthocyanin pathway gene.” . Nature London , 454 (7205) : 762 – 765 .
- Doyle , JC , Alderson , DL , Li , L , Low , S , Roughan , M , Shalunov , S , Tanaka , R and Willinger , W . 2005 . “The robust yet fragile nature of the internet.” . Proc. Natl. Acad. Sci. U.S.A. , 102 (41) : 14497 – 14502 .
- Drummond , DA , Bloom , JD , Adami , C , Wilke , CO and Arnold , FH . 2005 . “Why highly expressed proteins evolve slowly.” . Proc. Natl. Acad. Sci. U.S.A. , 102 : 14338 – 14343 .
- Durand , D , Halldórsson , BV and Vernot , B . 2006 . “A hybrid micro‐macroevolutionary approach to gene tree reconstruction.” . J. Comput. Biol. , 13 (2) : 320 – 335 .
- Dutkowski , J and Tiuryn , J . 2007 . “Identification of functional modules from conserved ancestral protein‐protein interactions.” . Bioinformatics , 23 (13) : i149 – i158 .
- Evlampiev , K and Isambert , H . 2007 . “Modeling protein network evolution under genome duplication and domain shuffling.” . BMC Systems Biology , 1 (1) : 49
- Evlampiev , K and Isambert , H . 2008 . “Conservation and topology of protein interaction networks under duplication‐divergence evolution.” . Proc. Natl. Acad. Sci. U.S.A. , 105 (29) : 9863 – 9868 .
- Fields , S . 2005 . “High‐throughput two‐hybrid analysis: the promise and the peril.” . FEBS J. , 272 (21) : 5391 – 5399 .
- Finn , RD , Marshall , M and Bateman , A . 2005 . “iPfam: visualization of protein‐protein interactions in PDB at domain and amino acid resolutions.” . Bioinformatics , 21 : 410 – 412 .
- Fong , JH , Keating , AE and Singh , M . 2004 . “Predicting specificity in bzip coiled‐coil protein interactions.” . Genome Biol. , 5 (2) : R11
- Force , A , Lynch , M , Pickett , F , Amoresa , A , Yana , Y and Postlethwait , J . 1999 . “Preservation of duplicate genes by complementary, degenerative mutations.” . Genetics , 151 : 1531 – 1545 .
- Fraser , H , Hirsh , A , Steinmetz , L , Scharfe , C and Feldman , M . 2002 . “Evolutionary rate in the protein interaction network.” . Science , 296 : 750 – 752 .
- Fraser , HB . 2005 . “Modularity and evolutionary constraint on proteins.” . Nat. Genet. , 37 : 351 – 352 .
- Gavin , A‐C . 2006 . “Proteome survey reveals modularity of the yeast cell machinery.” . Nature London , 440 (7084) : 631 – 636 .
- Gentleman , R and Huber , W . 2007 . “Making the most of high‐throughput protein‐interaction data.” . Genome Biol. , 8 (10) : 112
- Gibson , TA and Goldberg , DS . 2009a . “Questioning the ubiquity of neofunctionalization.” . PLOS Comput. Biol. , 5 (1) : e1000252
- Gibson , TA and Goldberg , DS . 2009b . “Reverse engineering the evolution of protein interaction networks.” . Pacific Symposium on Biocomputing, , : 190 – 202 .
- Gilchrist , MA , Salter , LA and Wagner , A . 2004 . “A statistical framework for combining and interpreting proteomic datasets.” . Bioinformatics , 20 (5) : 689 – 700 .
- Goh , K‐I , Cusick , ME , Valle , D , Childs , B , Vidal , M and Barabasi , A‐L . 2007 . “The human disease network.” . Proc. Natl. Acad. Sci. U.S.A. , 104 (21) : 8685 – 8690 .
- Hahn , M , Conant , G and Wagner , A . 2004 . “Molecular evolution in large genetic networks: does connectivity equal constraint?” . J. Mol. Evol. , 58 : 203 – 211 .
- Hakes , L , Lovell , SC , Oliver , SG and Robertson , DL . 2007a . “Specificity in protein interactions and its relationship with sequence diversity and coevolution.” . Proc. Natl. Acad. Sci. U.S.A. , 104 (19) : 7999 – 8004 .
- Hakes , L , Pinney , JW , Lovell , SC , Oliver , SG and Robertson , DL . 2007b . “All duplicates are not equal: the difference between small‐scale and genome duplication.” . Genome Biol. , 8 (10) : R209
- Hakes , L , Pinney , JW , Robertson , DL and Lovell , SC . 2008 . “Protein‐protein interaction networks and biology—what's the connection?” . Nat. Biotechnol. , 26 (1) : 69 – 72 .
- Han , JDJ . 2004 . “Evidence for dynamically organized modularity in the yeast protein‐protein interaction network.” . Nature , 430 : 88 – 93 .
- Han , JDJ , Dupuy , D , Bertin , N , Cusick , ME and Vidal , M . 2005 . “Effect of sampling on topology predictions of protein‐protein interaction networks.” . Nat. Biotechnol. , 23 : 839 – 844 .
- Hartwell , LH , Hopfield , JJ , Leibler , S and Murray , AW . 1999 . “From molecular to modular cell biology.” . Nature London , 402 (6761) : C47 – C52 .
- He , X and Zhang , J . 2005 . “Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution.” . Genetics , 169 (2) : 1157 – 1164 .
- Hughes , AL . 2005 . “Gene duplication and the origin of novel proteins.” . Proc. Natl. Acad. Sci. U.S.A. , 102 (25) : 8791 – 8792 .
- Ihmels , J , Collins , SR , Schuldiner , M , Krogan , NJ and Weissman , JS . 2007 . “Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.” . Mol. Syst. Biol. , 3 : 86
- Ito , TEA . 2001 . “A comprehensive two‐hybrid analysis to explore the yeast protein interactome.” . Proc. Natl. Acad. Sci. U.S.A. , 98 : 4569 – 4574 .
- Janin , J , Rodier , F , Chakrabarti , P and Bahadur , RP . 2007 . “Macromolecular recognition in the Protein Data Bank.” . Acta Crystallogr., Sect. D: Biol. Crystallogr. , 63 (1) : 1 – 8 .
- Jensen , LJ . 2008 . “STRING 8—a global view on proteins and their functional interactions in 630 organisms.” . Nucleic Acids Res. , http://nar.oxfordjournals.org/cgi/content/abstract/gkn760v1
- Jeong , H , Mason , SP , Barabási, , A‐L and Oltvai , ZN . 2001 . “Lethality and centrality in protein networks.” . Nature London , 411 (6833) : 41 – 42 .
- Joyce , P and Marjoram , P . 2008 . “Approximately sufficient statistics and Bayesian computation.” . Stat. Appl. Genet. Mol. Biol. , 7 (1) : 26
- Keller , EF . 2005 . “Revisiting “scale‐free” networks.” . BioEssays , 27 (10) : 1060 – 1068 .
- Kelley , BP , Yuan , B , Lewitter , F , Sharan , R , Stockwell , BR and Ideker , T . 2004 . “Pathblast: a tool for alignment of protein interaction networks.” . Nucleic Acids Res. , 32 : W83 – W88 .
- Keskin , O , Gursoy , A , Ma , B and Nussinov , R . 2008 . “Principles of protein‐protein interactions: what are the preferred ways for proteins to interact?.” . Chem. Rev. Washington, D.C. , 108 (4) : 1225 – 1244 .
- Kim , PM , Korbel , JO and Gerstein , MB . 2007 . “Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.” . Proc. Natl. Acad. Sci. U.S.A. , 104 (51) : 20274 – 20279 .
- Kim , PM , Lu , LJ , Xia , Y and Gerstein , MB . 2006 . “Relating three‐dimensional structures to protein networks provides evolutionary insights.” . Science , 314 (5807) : 1938 – 1941 .
- Krogan , NJ . 2006 . “Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.” . Nature London , 440 (7084) : 637 – 643 .
- Kuo , PD , Banzhaf , W and Leier , A . 2006 . “Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence.” . BioSystems , 85 (3) : 177 – 200 .
- Kupiec , M , Sharan , R and Ruppin , E . 2007 . “Genetic interactions in yeast: is robustness going bust?.” . Mol. Syst. Biol. , : 3
- Levin , SA , Grenfell , B , Hastings , A and Perelson , AS . 1997 . “Mathematical and computational challenges in population biology and ecosystems science.” . Science , 275 (5298) : 334 – 343 .
- Levy , ED , Erba , EB , Robinson , CV and Teichmann , SA . 2008 . “Assembly reflects evolution of protein complexes.” . Nature London , 453 (7199) : 1262 – 1265 .
- Li , W‐H , Yang , J and Gu , X . 2005 . “Expression divergence between duplicate genes.” . Trends Genet. , 21 (11) : 602 – 607 .
- Lynch , M . 2007a . “The evolution of genetic networks by non‐adaptive processes.” . Nat Rev. Genet. , 8 (10) : 803 – 813 .
- Lynch , M . 2007b . “The frailty of adaptive hypotheses for the origins of organismal complexity.” . Proc. Natl. Acad. Sci. U.S.A. , 104 : 8597 – 8604 .
- Lynch , M . 2007c . The Origins of Genome Architecture. , Sunderland, MA : Sinauer Associates .
- Marjoram , P and Tavaré, , S . 2006 . “Modern computational approaches for analysing molecular genetic variation data.” . Nat. Rev. Genet. , 7 (10) : 759 – 770 .
- Masloy , S and Sneppen , K . 2002 . “Specificity and stability in topology of protein networks.” . Science , 296 (5569) : 910 – 913 .
- Maslov , S , Sneppen , K , Eriksen , K and Yan , K . 2004 . “Upstream plasticity and downstream robustness in evolution of molecular networks.” . BMC Evol. Biol. , 4 : 9
- Mason , O and Verwoerd , M . 2007 . “Graph theory and networks in biology.” . Syst. Biol. , 4 (2) : 89 – 119 .
- May , RM . 2004 . “Uses and abuses of mathematics in biology.” . Science , 303 (5659) : 790 – 793 .
- Mazurie , A , Bottani , S and Vergassola , M . 2005 . “An evolutionary and functional assessment of regulatory network motifs.” . Genome Biol , 6 : R35
- Middendorf , M , Ziv , E , Adams , C , Hom , J , Koytcheff , R , Levovitz , C , Woods , G , Chen , I and Wiggins , C . 2004 . “Discriminative topological features reveal biological network mechanisms.” . BMC Bioinf. , 5 (1) : 181
- Middendorf , M , Ziv , E and Wiggins , C . 2005 . “Inferring network mechanisms: the Drosophila melanogaster protein interaction network.” . Proc. Natl. Acad. Sci. U.S.A. , 102 (9) : 3192 – 3197 .
- Milo , R , Itzkovitz , S , Kashtan , N , Levitt , R , Shen‐Orr , S , Ayzenshtat , I , Sheffer , M and Alon , U . 2004 . “Superfamilies of evolved and designed networks.” . Science , 303 : 1538 – 1542 .
- Milo , R , Shen‐Orr , S , Itzkovitz , S , Kashtan , N , Chklovskii , D and Alon , U . 2002 . “Network motifs: simple building blocks of complex networks.” . Science , 298 (5594) : 824 – 827 .
- Mintseris , J and Weng , Z . 2005 . “Structure, function, and evolution of transient and obligate protein‐protein interactions.” . Proc. Natl. Acad. Sci. U.S.A. , 102 (31) : 10930 – 10935 .
- Monica , M . 2005 . “Genomes, phylogeny and evolutionary systems biology.” . Proc. Natl. Acad. Sci. U.S.A. , 102 : 6630 – 6635 .
- Nei , M . 2007 . “The new mutation theory of phenotypic evolution.” . Proc. Natl. Acad. Sci. U.S.A. , 104 (30) : 12235 – 12242 .
- Nei , M and Rooney , AP . 2005 . “Concerted and birth‐and‐death evolution of multigene families.” . Annu. Rev. Genet. , 39 (1) : 121 – 152 .
- Newman , MEJ . 2002 . “Assortative mixing in networks.” . Phys. Rev. Lett. , 89 : 208701
- Onnela , J‐P , Saramäki , J , Kertész , J and Kaski , K . 2005 . “Intensity and coherence of motifs in weighted complex networks.” . Phys. Rev. E , 71 (6) : 065103
- Orchard , S . 2007 . “The minimum information required for reporting a molecular interaction experiment (MIMIx).” . Nat. Biotechnol. , 25 (8) : 894 – 898 .
- Pal , C , Papp , B and Hurst , LD . 2001 . “Highly expressed genes in yeast evolve slowly.” . Genetics , 158 : 927 – 931 .
- Pal , C , Papp , B and Lercher , MJ . 2006 . “An integrated view of protein evolution.” . Nat. Rev. Genet. , 7 (5) : 337 – 348 .
- Parrish , J . 2007 . “A proteome‐wide protein interaction map for Campylobacterjejuni.” . Genome Biol. , 8 (7) : R130
- Pastor‐Satorras , R , Smith , E and Solé, , RV . 2003 . “Evolving protein interaction networks through gene duplication.” . J. Theor. Biol. , 222 (2) : 199 – 210 .
- Pereira‐Leal , J , Levy , E , Kamp , C and Teichmann , S . 2007 . “Evolution of protein complexes by duplication of homomeric interactions.” . Genome Biol. , 8 (4) : R51
- Pfeiffer , T , Soyer , OS and Bonhoeffer , S . 2005 . “The evolution of connectivity in metabolic networks.” . PLoS Biol. , 3 (7)
- Pinney , JW , Amoutzias , GD , Rattray , M and Robertson , DL . 2007 . “Reconstruction of ancestral protein interaction networks for the bZIP transcription factors.” . Proc. Natl. Acad. Sci. U.S.A. , 104 : 20449 – 20453 .
- Presser , A , Elowitz , MB , Kellis , M and Kishony , R . 2008 . “The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication.” . Proc. Natl. Acad. Sci. U.S.A. , 105 (3) : 950 – 954 .
- Przulj , N . 2007 . “Biological network comparison using graphlet degree distribution.” . Bioinformatics , 23 (2) : e177 – e183 .
- Rain , J‐C . 2001 . “The protein‐protein interaction map of Helicobacter pylori.” . Nature London , 409 : 211 – 215 .
- Ratmann , O , Andrieu , C , Wiuf , C and Richardson , S . 2009 . “Model criticism with likelihood‐free inference, with an application to protein network evolution.” . Proc. Nat. Acad. Sci. U.S.A., , 106 : 10576 – 10581 .
- Ratmann , O , Jørgensen , O , Hinkley , T , Stumpf , MP , Richardson , S and Wiuf , C . 2007 . “Using likelihood‐free inference to compare evolutionary dynamics of the protein networks of H pylori and P. falciparum.” . PLOS Comput. Biol. , 3 (2007) : 11
- Ravasz , E , Somera , AL , Mongru , DA , Oltvai , ZN and Barabasi , AL . 2002 . “Hierarchical organization of modularity in metabolic networks.” . Science , 297 : 1551 – 1555 .
- Reguly , T . 2006 . “Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.” . J. Biol. , 5 (4) : 11
- Reyes , L , Conde , E , Lopez , T , Santillán , C and Izaguirre , R . 2008 . “Statistical selection of relevant features to classify random, scale free and exponential networks..” . Innovations in Hybrid Intelligent Systems, , : 454 – 461 .
- Rice , J , Kershenbaum , A and Stolovitzky , G . 2005 . “Lasting impressions: motifs in protein‐protein maps may provide footprints of evolutionary events.” . Proc. Natl. Acad. Sci. U.S.A. , 102 (9) : 3173 – 3174 .
- Rosenberg , NA and Nordborg , M . 2002 . “Genealogical trees, coalescent theory and the analysis of genetic polymorphisms.” . Nat. Rev. Genet. , 3 (5) : 380 – 390 .
- Rual , J . 2005 . “Towards a proteome‐scale map of the human protein‐protein interaction network.” . Nature London , 437 : 1173 – 1178 .
- Russell , RB and Aloy , P . 2008 . “Targeting and tinkering with interaction networks.” . Nat. Chem. Biol. , 4 (11) : 666 – 673 .
- Sato , S , Shimoda , Y , Muraki , A , Kohara , M , Nakamura , Y and Tabata , S . 2007 . “A large‐scale protein protein interaction analysis in Synechocystis sp. PCC6803.” . DNA Res. , 14 (5) : 207 – 216 .
- Scholtens , D , Chiang , T , Huber , W and Gentleman , R . 2007 . “Estimating node degree in bait‐prey graphs.” . Bioinformatics, , http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm565v1
- Scholtens , D and Gentleman , R . 2004 . “Making sense of high‐throughput protein‐protein interaction data.” . Stat. Appl. Genet. Mol. Biol. , 3 (1) : 39 http://www.bepress.com/sagmb/vol3/iss1/art39
- Shimoda , Y , Shinpo , S , Kohara , M , Nakamura , Y , Tabata , S and Sato , S . 2008 . “A large scale analysis of protein protein interactions in the nitrogen‐fixing bacterium Mesorhizobium loti.” . DNA Res., , http://dnaresearch.oxfordjournals.org/cgi/content/abstract/dsm028v1
- Soyer , O and Bonhoeffer , S . 2006 . “Evolution of complexity in signaling pathways.” . Proc. Natl. Acad. Sci. U.S.A. , 103 : 16337 – 16342 .
- Stelzl , U . 2005 . “A human protein‐protein interaction network: a resource for annotating the proteome.” . Cell , 122 (6) : 957 – 968 .
- Stumpf , M , Ingram , P , Nouvel , I and Wiuf , C . 2005 . “Statistical model selection methods applied to biological networks.” . Trans. Comp. Sys.Biol. , 3 : 65 – 77 .
- Stumpf , M , Kelly , W , Thorne , T and Wiuf , C . 2007 . “Evolution at the system level: the natural history of protein interaction networks.” . Trends Ecol. Evol. , 22 : 366 – 373 .
- Stumpf , MP H and Thorne , T . 2007 . “Multimodel inference of network properties from incomplete data.” . J. Integr. Bioinformatics , 3 (32)
- Teichmann , S . 2002 . “The constraints protein‐protein interactions place on sequence divergence.” . J. Mol. Biol. , 324 : 399 – 407 .
- Teichmann , SA and Babu , M . 2004 . “Gene regulatory network growth by duplication.” . Nat. Genet. , 36 : 492 – 496 .
- Titz , B , Rajagopala , SV , Goll , J , Häuser , R , McKevitt , MT , Palzkill , T and Uetz , P . 2008 . “The binary protein interactome of Treponema pallidum—the Syphilis spirochete.” . PLoS ONE , 3 (5) : e2292 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=23 86257
- Uetz , PEA . 2000 . “A comprehensive analysis of protein‐protein interaction networks in Saccharomyces cerevisiae.” . Nature London , 403 : 623 – 627 .
- van Hoof, , A . 2005 . “Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication.” . Genetics , 171 : 1455 – 1461 .
- Vazquez , A . 2004 . “The topological relationship between the large‐scale attributes and local interaction patterns of complex networks.” . Proc. Natl. Acad. Sci. U.S.A. , 101 : 17940 – 17945 .
- Vazquez , A , Flammini , A , Maritan , A and Vespignani , A . 2003 . “Modeling of protein interaction networks.” . ComPlexUs , 1 : 38 – 44 .
- von Mering , C , Krause , R , Snel , B , Cornell , M , Oliver , S , Fields , S and Bork , P . 2002 . “Comparative assessment of large‐scale data sets of protein‐protein interactions.” . Nature London , 417 : 399 – 403 .
- Wagner , A . 2000 . “Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implication for the neutralist‐selectionist debate.” . Proc. Natl. Acad. Sci. U.S.A. , 97 (12) : 6579 – 6584 .
- Wagner , A . 2001 . “The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes.” . Mol. Biol. Evol. , 18 (7) : 1283 – 1292 .
- Wagner , A . 2003a . “Does Selection Mold Molecular Networks?.” . Sci. STKE , 2003 (202) : pe41
- Wagner , A . 2003b . “How the global structure of protein interaction networks evolves.” . Proc. R. Soc. London, Ser. B , 270 (1514) : 457 – 466 .
- Wagner , A . 2008 . “Neutralism and selectionism: a network‐based reconciliation?.” . Wot Rev. Genet. , 9 (12) : 965 – 974 .
- Wang , Z and Zhang , J . 2007 . “In search of the biological significance of modular structures in protein networks.” . PLoS Computational Biology, , : 3
- Watts , DJ and Strogatz , SH . 1998 . “Collective dynamics of ‘small‐world’ networks.” . Nature , 393 : 440 – 442 .
- Wilson , D . 2009 . “Superfamily‐sophisticated comparative genomics, data mining, visualization and phylogeny.” . Nucleic Acids Res. , 37 : D380 – 386 .
- Winter , C , Henschel , A , Kim , WK and Schroeder , M . 2006 . “SCOPPI: a structural classification of protein‐protein interfaces.” . Nuc. Acids Res. , 34 : D310 – 314 .
- Wiuf , C , Brameier , M , Hagberg , O and Stumpf , M . 2006 . “A likelihood approach to analysis of network data.” . Proc. Natl. Acad. Sci. U.S.A. , 103 (20) : 7566 – 7570 .
- Wiuf , C and Ratmann , O . 2009 . “Evolutionary analysis of protein interaction networks.” . In Statistical and Evolutionary Analysis of Biological Networks. , 17 – 43 . Imperial College Press .
- Wodak , SJ , Pu , S , Vlasblom , J and Seraphin , B . 2009 . “Challenges and rewards of interaction proteomics.” . Mol. Cell Proteomics , 8 (1) : 3 – 18 .
- Yu , H . 2008 . “High‐quality binary protein interaction map of the yeast interactome network.” . Science , 322 (5898) : 104 – 110 .
- Yu , H , Xia , Y , Trifonov , V and Gerstein , M . 2006 . “Design principles of molecular networks revealed by global comparisons and composite motifs.” . Genome Biol. , 7 (7) : R55