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Volumn , Issue , 2009, Pages 145-170

Statistical null models for biological network analysis

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EID: 77957815696     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9781848164345_0008     Document Type: Chapter
Times cited : (3)

References (50)
  • 2
    • 33747150019 scopus 로고    scopus 로고
    • Complex networks and simple models in biology
    • E. de Silva and M. P. H. Stumpf, Complex networks and simple models in biology. J. Roy. Soc. Interface. 2, 419-340, (2005).
    • (2005) J. Roy. Soc. Interface , vol.2
    • de Silva, E.1    Stumpf, M.P.H.2
  • 3
    • 0036435908 scopus 로고    scopus 로고
    • Co-evolutionary analysis reveals insights into proteinprotein interactions
    • C. S. Goh and F. E. Cohen, Co-evolutionary analysis reveals insights into proteinprotein interactions. J. Mol. Biol. 324, 177-192, (2002).
    • (2002) J. Mol. Biol , vol.324 , pp. 177-192
    • Goh, C.S.1    Cohen, F.E.2
  • 4
    • 17444387503 scopus 로고    scopus 로고
    • Comparative analysis of the saccaromyces cerevisiae and caenorhabditis elegans protein interaction networks
    • bf 5, 23
    • I. Agraoti, J. Swire, J. Abbott, D. Huntley, S. Butcher and M. P. H. Stumpf, Comparative analysis of the saccaromyces cerevisiae and caenorhabditis elegans protein interaction networks. BMC Evolutionary Biology. bf 5, 23, (2005).
    • (2005) BMC Evolutionary Biology
    • Agraoti, I.1    Swire, J.2    Abbott, J.3    Huntley, D.4    Butcher, S.5    Stumpf, M.P.H.6
  • 5
    • 34249945479 scopus 로고    scopus 로고
    • Specićity in protein interactions and its relationship with sequence diversity and coevolution
    • L. Hakes, S. C. Lovell, S. G. Oliver and D. L. Robertson, Specićity in protein interactions and its relationship with sequence diversity and coevolution. Proc. Natl. Acad. Sci. USA. 104, 7999-8004, (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 7999-8004
    • Hakes, L.1    Lovell, S.C.2    Oliver, S.G.3    Robertson, D.L.4
  • 10
    • 33845262280 scopus 로고    scopus 로고
    • The effects of incomplete protein interaction data on structural and evolutionary inferences
    • E. de Silva, T. Thorne, P. Ingram, I. Agraoti, J. Swire, C. Wiuf and M. P. H. Stumpf, The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biology. 4, 39, (2006).
    • (2006) BMC Biology , vol.4 , pp. 39
    • de Silva, E.1    Thorne, T.2    Ingram, P.3    Agraoti, I.4    Swire, J.5    Wiuf, C.6    Stumpf, M.P.H.7
  • 13
    • 14744273317 scopus 로고    scopus 로고
    • Inferring network mechanisms: The drosophila melanogaster protein interaction network
    • M. Middendorf, Z. Etay and C. Wiggins, Inferring network mechanisms: The drosophila melanogaster protein interaction network. Proc. Natl. Acad. Sci. USA. 102 3192-3197, (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 3192-3197
    • Middendorf, M.1    Etay, Z.2    Wiggins, C.3
  • 14
    • 36949017519 scopus 로고    scopus 로고
    • Using likelihood-free inference to compare evolutionary dynamics of the protein networks of h. pylori and p. falciparum
    • O. Ratmann, O. Jorgensen, T. Hinkley, M. P. H. Stumpf, S. Richardson and C. Wiuf, Using likelihood-free inference to compare evolutionary dynamics of the protein networks of h. pylori and p. falciparum. PLoS Comput. Biol. 3, 2266-2278, (2007).
    • (2007) PLoS Comput. Biol , vol.3 , pp. 2266-2278
    • Ratmann, O.1    Jorgensen, O.2    Hinkley, T.3    Stumpf, M.P.H.4    Richardson, S.5    Wiuf, C.6
  • 15
    • 34250322596 scopus 로고    scopus 로고
    • Evolution at the system level: The natural history of protein interaction networks
    • M. P. H. Stumpf, W. P. Kelly, T. Thorne and C. Wiuf, Evolution at the system level: the natural history of protein interaction networks. Trends Ecol. Evol. 22, 366-373, (2007).
    • (2007) Trends Ecol. Evol , vol.22 , pp. 366-373
    • Stumpf, M.P.H.1    Kelly, W.P.2    Thorne, T.3    Wiuf, C.4
  • 17
    • 0036681932 scopus 로고    scopus 로고
    • The structure and function of networks
    • M. Newman, The structure and function of networks. Comp. Phys. Comm. 147, 40-45, (2002).
    • (2002) Comp. Phys. Comm , vol.147 , pp. 40-45
    • Newman, M.1
  • 19
    • 0742275434 scopus 로고    scopus 로고
    • Mathematical results on scale-free graphs. In S Bornholdt and H Schuster, editors
    • Wiley-VCH
    • B. Bollobas and O. Riordan, Mathematical results on scale-free graphs. In S Bornholdt and H Schuster, editors, Handbook of Graphs and Networks, 1-34. Wiley-VCH, (2003).
    • (2003) Handbook of Graphs and Networks , pp. 1-34
    • Bollobas, B.1    Riordan, O.2
  • 22
    • 0001510996 scopus 로고
    • Random graphs
    • E. Gilbert, Random graphs. Ann. of Math. Stats. 30, 1141-1144, (1959).
    • (1959) Ann. of Math. Stats , vol.30 , pp. 1141-1144
    • Gilbert, E.1
  • 23
    • 0000664045 scopus 로고
    • The asymptotic number of labeled graphs with given degree sequence
    • E. Bender and E. Canfield, The asymptotic number of labeled graphs with given degree sequence. J. Comb. Theory A. 24, 296-307, (1978).
    • (1978) J. Comb. Theory A , vol.24 , pp. 296-307
    • Bender, E.1    Canfield, E.2
  • 24
    • 84990671447 scopus 로고
    • A critical point for random graphs with a given degree distribution
    • M. Molloy and B. Reed, A critical point for random graphs with a given degree distribution. Rand. Struct. Algorithms. 6, 161-179, (1995).
    • (1995) Rand. Struct. Algorithms , vol.6 , pp. 161-179
    • Molloy, M.1    Reed, B.2
  • 25
    • 0032286776 scopus 로고    scopus 로고
    • The size of the giant component of a random graph with a given degree sequence
    • M. Molloy and B. Reed, The size of the giant component of a random graph with a given degree sequence. Comb. Probab. Comput. 7, 295-305, (1998).
    • (1998) Comb. Probab. Comput , vol.7 , pp. 295-305
    • Molloy, M.1    Reed, B.2
  • 26
    • 0035420732 scopus 로고    scopus 로고
    • Random graphs with arbitrary degree distributions and their applications
    • N. Newman, S. Strogatz and D. Watts, Random graphs with arbitrary degree distributions and their applications. Phys. Rev. E. 64, 026118, (2001).
    • (2001) Phys. Rev. E , vol.64
    • Newman, N.1    Strogatz, S.2    Watts, D.3
  • 27
    • 0242425399 scopus 로고    scopus 로고
    • Random graphs as models of networks. In S Bornholdt and H Schuster, editors
    • Wiley-VCH
    • M. Newman, Random graphs as models of networks. In S Bornholdt and H Schuster, editors, Handbook of Graphs and Networks. Wiley-VCH, (2003).
    • (2003) Handbook of Graphs and Networks
    • Newman, M.1
  • 30
    • 39149116715 scopus 로고    scopus 로고
    • Generating confidence intervals on biological networks
    • T. Thorne and M. P. H. Stumpf, Generating confidence intervals on biological networks BMC Bioinformatics. 8, 467, (2007).
    • (2007) BMC Bioinformatics , vol.8 , pp. 467
    • Thorne, T.1    Stumpf, M.P.H.2
  • 36
    • 0842291785 scopus 로고    scopus 로고
    • No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolić interactors tend to evolve slowly
    • I. K. Jordan, Y. I. Wolf and E. V. Koonin, No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolić interactors tend to evolve slowly. BMC Evol. Biol. 3, 1, (2003).
    • (2003) BMC Evol. Biol , vol.3 , pp. 1
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3
  • 37
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • D. Drummond, A. Raval and C. Wilke, A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23, 327-337, (2006).
    • (2006) Mol. Biol. Evol , vol.23 , pp. 327-337
    • Drummond, D.1    Raval, A.2    Wilke, C.3
  • 40
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • A. Wagner, The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18, 1283-1292, (2001).
    • (2001) Mol. Biol. Evol , vol.18 , pp. 1283-1292
    • Wagner, A.1
  • 41
    • 33745004625 scopus 로고    scopus 로고
    • Computational approaches for predicting protein-protein interactions: A survey
    • J. Yu and F. Fotouhi, Computational approaches for predicting protein-protein interactions: A survey. J. Med. Sys. 30, 39-44, (2006).
    • (2006) J. Med. Sys , vol.30 , pp. 39-44
    • Yu, J.1    Fotouhi, F.2
  • 43
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of proteinprotein interaction
    • F. Pazos and A. Valencia, Similarity of phylogenetic trees as indicator of proteinprotein interaction. Protein Engineering. 14, 609-614, (2001).
    • (2001) Protein Engineering , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 44
    • 24644502565 scopus 로고    scopus 로고
    • Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome
    • F. Pazos, J. Ranea, D. Juan and M. J. E. Sternberg, Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J. Mol. Biol. 352, 1002-15, (2005).
    • (2005) J. Mol. Biol , vol.352 , pp. 1002-1015
    • Pazos, F.1    Ranea, J.2    Juan, D.3    Sternberg, M.J.E.4
  • 45
    • 24144476642 scopus 로고    scopus 로고
    • The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships
    • T. Sato, Y. Yamanishi, M. Kanehisa and H. Toh, The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics. 21, 3482-3489, (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3482-3489
    • Sato, T.1    Yamanishi, Y.2    Kanehisa, M.3    Toh, H.4
  • 46
    • 0037436412 scopus 로고    scopus 로고
    • Exploiting the co-evolution of interacting proteins to discover interaction specićity
    • A. Ramani and E. Marcotte, Exploiting the co-evolution of interacting proteins to discover interaction specićity. J. Mol. Biol. 327, 273-84, (2003).
    • (2003) J. Mol. Biol , vol.327 , pp. 273-284
    • Ramani, A.1    Marcotte, E.2
  • 47
    • 33646381380 scopus 로고    scopus 로고
    • Comparative genomics and genome evolution in yeast
    • K. Wolfe, Comparative genomics and genome evolution in yeast. Phil. Trans. Roy. Soc. Lond. B. Biol. Sci. 361, 403-412, (2006).
    • (2006) Phil. Trans. Roy. Soc. Lond. B. Biol. Sci , vol.361 , pp. 403-412
    • Wolfe, K.1
  • 48
    • 33845452848 scopus 로고    scopus 로고
    • A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    • D. Fitzpatrick, M. Logue, J. Stajich and G. Butler, A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol. 6, 99, (2006).
    • (2006) BMC Evol. Biol , vol.6 , pp. 99
    • Fitzpatrick, D.1    Logue, M.2    Stajich, J.3    Butler, G.4
  • 49
    • 0000122573 scopus 로고
    • Phylip-phylogeny inference package (version 3. 2)
    • J. Felsenstein, Phylip-phylogeny inference package (version 3. 2). Cladistics. 5, 164-166, (1989).
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 50
    • 0030683599 scopus 로고    scopus 로고
    • Paml: A program package for phylogenetic analysis by maximum likelihood
    • Z. Yang, Paml: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in Biosciences. 13, 555-556, (1997).
    • (1997) Computer Applications in Biosciences , vol.13 , pp. 555-556
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.