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Volumn 43, Issue 1, 2014, Pages 193-210

Structural bioinformatics of the interactome

Author keywords

Machine learning; Network biology; Protein protein interaction; Structural systems biology

Indexed keywords

ARTICLE; BINDING AFFINITY; BIOLOGY; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; DRUG DEVELOPMENT; GENETIC ASSOCIATION; INTERACTOME; MACHINE LEARNING; MOLECULAR INTERACTION; PHENOTYPE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURAL BIOINFORMATICS;

EID: 84901979488     PISSN: 1936122X     EISSN: 19361238     Source Type: Book Series    
DOI: 10.1146/annurev-biophys-051013-022726     Document Type: Article
Times cited : (46)

References (199)
  • 1
    • 84862588440 scopus 로고    scopus 로고
    • Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes
    • Acuner Ozbabacan SE, KeskinO,Nussinov R,Gursoy A. 2012. Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. J. Struct. Biol. 179:338-466
    • (2012) J. Struct. Biol. , vol.179 , pp. 338-466
    • Acuner Ozbabacan, S.E.1    Keskin, O.2    Nussinov, R.3    Gursoy, A.4
  • 2
    • 77955480278 scopus 로고    scopus 로고
    • Revisiting date and party hubs: Novel approaches to role assignment in protein interaction networks
    • Agarwal S, Deane CM, Porter MA, Jones NS. 2010. Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PLoS Comput. Biol. 6:e10008177
    • (2010) PLoS Comput. Biol. , vol.6
    • Agarwal, S.1    Deane, C.M.2    Porter, M.A.3    Jones, N.S.4
  • 4
    • 84880993729 scopus 로고    scopus 로고
    • Drug-target interaction prediction through domaintuned network-based inference
    • Alaimo S, Pulvirenti A, Giugno R, Ferro A. 2013. Drug-target interaction prediction through domaintuned network-based inference. Bioinformatics 29:2004-88
    • (2013) Bioinformatics , vol.29 , pp. 2004-2088
    • Alaimo, S.1    Pulvirenti, A.2    Giugno, R.3    Ferro, A.4
  • 5
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • Aloy P, Ceulemans H, Stark A, Russell RB. 2003. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 332:989-988
    • (2003) J. Mol. Biol. , vol.332 , pp. 989-988
    • Aloy, P.1    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 6
    • 84871752376 scopus 로고    scopus 로고
    • Reverse engineering and analysis of large genome-scale gene networks
    • Aluru M, Zola J, Nettleton D, Aluru S. 2013. Reverse engineering and analysis of large genome-scale gene networks. Nucleic Acids Res. 41:e244
    • (2013) Nucleic Acids Res. , vol.41
    • Aluru, M.1    Zola, J.2    Nettleton, D.3    Aluru, S.4
  • 7
    • 84866390995 scopus 로고    scopus 로고
    • Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space
    • Arnold R, Boonen K, Sun MGF, Kim PM. 2012. Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. Methods 57:508-188
    • (2012) Methods , vol.57 , pp. 508-188
    • Arnold, R.1    Boonen, K.2    Sun, M.G.F.3    Kim, P.M.4
  • 8
    • 20844454090 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
    • Aytuna A, Gursoy A, Keskin O. 2005. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21:2850-555
    • (2005) Bioinformatics , vol.21 , pp. 2850-2565
    • Aytuna, A.1    Gursoy, A.2    Keskin, O.3
  • 9
    • 84881360450 scopus 로고    scopus 로고
    • Network pharmacology: An emerging field in cancer drug discovery
    • Azmi AS. 2013. Network pharmacology: An emerging field in cancer drug discovery. Curr. Drug Discov. Technol. 10:93-944
    • (2013) Curr. Drug Discov. Technol. , vol.10 , pp. 93-944
    • Azmi, A.S.1
  • 10
    • 78650345652 scopus 로고    scopus 로고
    • Proof of concept: Network and systems biology approaches aid in the discovery of potent anticancer drug combinations
    • Azmi AS, Wang Z, Philip PA, Mohammad RM, Sarkar FH. 2010. Proof of concept: Network and systems biology approaches aid in the discovery of potent anticancer drug combinations. Mol. Cancer Ther. 9:3137-444
    • (2010) Mol. Cancer Ther. , vol.9 , pp. 3137-3444
    • Azmi, A.S.1    Wang, Z.2    Philip, P.A.3    Mohammad, R.M.4    Sarkar, F.H.5
  • 11
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: A network-based approach to human disease
    • Barabasi A-L, Gulbahce N, Loscalzo J. 2011. Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 12:56-688
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 56-688
    • Barabasi, A.-L.1    Gulbahce, N.2    Loscalzo, J.3
  • 13
    • 24744435534 scopus 로고    scopus 로고
    • Kernel methods for predicting protein-protein interactions
    • Ben-Hur A,NobleWS. 2005. Kernel methods for predicting protein-protein interactions. Bioinformatics 21:i38-466
    • (2005) Bioinformatics , vol.21
    • Ben-Hur, A.1    Noble, W.S.2
  • 14
    • 20744456475 scopus 로고    scopus 로고
    • Correlation between gene expression profiles and protein-protein interactions within and across genomes
    • Bhardwaj N, Lu H. 2005. Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics 21:2730-388
    • (2005) Bioinformatics , vol.21 , pp. 2730-2398
    • Bhardwaj, N.1    Lu, H.2
  • 15
    • 79960884702 scopus 로고    scopus 로고
    • Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: The PICCOLO database
    • Bickerton GR, Higueruelo AP, Blundell TL. 2011. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. BMC Bioinform. 12:3133
    • (2011) BMC Bioinform. , vol.12 , pp. 3133
    • Bickerton, G.R.1    Higueruelo, A.P.2    Blundell, T.L.3
  • 16
    • 78249261016 scopus 로고    scopus 로고
    • Accumulation of driver and passenger mutations during tumor progression
    • Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, et al. 2010. Accumulation of driver and passenger mutations during tumor progression. Proc. Natl. Acad. Sci. USA 107:18545-500
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 18545-18510
    • Bozic, I.1    Antal, T.2    Ohtsuki, H.3    Carter, H.4    Kim, D.5
  • 17
    • 58149242456 scopus 로고    scopus 로고
    • An experimentally derived confidence score for binary protein-protein interactions
    • Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, et al. 2009. An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6:91-977
    • (2009) Nat. Methods , vol.6 , pp. 91-977
    • Braun, P.1    Tasan, M.2    Dreze, M.3    Barrios-Rodiles, M.4    Lemmens, I.5
  • 18
    • 39149114704 scopus 로고    scopus 로고
    • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    • Burger L, van Nimwegen E. 2008. Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol. Syst. Biol. 4:1-144
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 1-144
    • Burger, L.1    Van Nimwegen, E.2
  • 19
    • 84864402194 scopus 로고    scopus 로고
    • Leveraging models of cell regulation and GWAS data in integrative network-based association studies
    • Califano A, Butte AJ, Friend S, Ideker T, Schadt E. 2012. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat. Genet. 44:841-477
    • (2012) Nat. Genet. , vol.44 , pp. 841-477
    • Califano, A.1    Butte, A.J.2    Friend, S.3    Ideker, T.4    Schadt, E.5
  • 20
    • 84879935027 scopus 로고    scopus 로고
    • Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding
    • Cannistraci CV, Alanis-Lobato G, Ravasi T. 2013. Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding. Bioinformatics 29:i199-2099
    • (2013) Bioinformatics , vol.29
    • Cannistraci, C.V.1    Alanis-Lobato, G.2    Ravasi, T.3
  • 21
    • 84867908823 scopus 로고    scopus 로고
    • Large-scale prediction of drug-target interactions using protein sequences and drug topological structures
    • CaoDS, Liu S,XuQS, Lu HM,Huang JH, et al. 2012. Large-scale prediction of drug-target interactions using protein sequences and drug topological structures. Anal. Chim. Acta 752:1-100
    • (2012) Anal. Chim. Acta , vol.752 , pp. 1-100
    • Cao, D.S.1    Liu, S.2    Xu, Q.S.3    Lu, H.M.4    Huang, J.H.5
  • 23
    • 84878756325 scopus 로고    scopus 로고
    • Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli
    • Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO. 2013. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli. Science 340:1220-233
    • (2013) Science , vol.340 , pp. 1220-1233
    • Chang, R.L.1    Andrews, K.2    Kim, D.3    Li, Z.4    Godzik, A.5    Palsson, B.O.6
  • 24
    • 77952351365 scopus 로고    scopus 로고
    • Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity
    • Chen L, Qian Z, Fen K, Cai Y. 2010. Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity. J. Comput. Chem. 31:1766-766
    • (2010) J. Comput. Chem. , vol.31 , pp. 1766-1766
    • Chen, L.1    Qian, Z.2    Fen, K.3    Cai, Y.4
  • 25
    • 33644835242 scopus 로고    scopus 로고
    • Inferring protein interactions from experimental data by association probabilistic method
    • Chen L, Wu L-Y, Wang Y, Zhang X-S. 2006. Inferring protein interactions from experimental data by association probabilistic method. Proteins: Struct. Funct. Bioinform. 62:833-377
    • (2006) Proteins: Struct. Funct. Bioinform. , vol.62 , pp. 833-377
    • Chen, L.1    Wu, L.-Y.2    Wang, Y.3    Zhang, X.-S.4
  • 26
    • 61449249266 scopus 로고    scopus 로고
    • Sequence-based prediction of protein interaction sites with an integrative method
    • Chen X-W, Jeong JC. 2009. Sequence-based prediction of protein interaction sites with an integrative method. Bioinformatics 25:585-911
    • (2009) Bioinformatics , vol.25 , pp. 585-911
    • Chen, X.-W.1    Jeong, J.C.2
  • 27
    • 28944450149 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions using random decision forest framework
    • Chen X-W, LiuM. 2005. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics 21:4394-4000
    • (2005) Bioinformatics , vol.21 , pp. 4394-4000
    • Chen, X.-W.1    Liu, M.2
  • 28
    • 34547581834 scopus 로고    scopus 로고
    • 3D-partner: A web server to infer interacting partners and binding models
    • Chen Y-C, Lo Y-S, Hsu W-C, Yang J-M. 2007. 3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Res. 35:W561-677
    • (2007) Nucleic Acids Res. , vol.35
    • Chen, Y.-C.1    Lo, Y.-S.2    Hsu, W.-C.3    Yang, J.-M.4
  • 29
    • 84864003584 scopus 로고    scopus 로고
    • Prediction of chemical-protein interactions network with weighted network-based inference method
    • Cheng F, Zhou Y, Li W, Liu G, Tang Y. 2012. Prediction of chemical-protein interactions network with weighted network-based inference method. PLoS ONE 7:e410644
    • (2012) PLoS ONE , vol.7
    • Cheng, F.1    Zhou, Y.2    Li, W.3    Liu, G.4    Tang, Y.5
  • 32
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia of DNA Elements) Project
    • ENCODE Project Consortium
    • ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636-400
    • (2004) Science , vol.306 , pp. 636-400
  • 33
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review
    • Csermely P, Korcsmáros T, Kiss HJM, London G, NussinovR. 2013. Structure and dynamics of molecular networks: a novel paradigm of drug discovery. A comprehensive review. Pharmacol. Ther. 138:333-4088
    • (2013) Pharmacol. Ther. , vol.138 , pp. 333-4088
    • Csermely, P.1
  • 34
    • 84872790975 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions between viruses and human by an SVM model
    • Cui G, Fang C, Han K. 2012. Prediction of protein-protein interactions between viruses and human by an SVM model. BMC Bioinform. 13:S55
    • (2012) BMC Bioinform. , vol.13
    • Cui, G.1    Fang, C.2    Han, K.3
  • 35
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar T, Snel B, Huynen M, Bork P. 1998. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23:324-288
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 324-288
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 36
    • 68849117733 scopus 로고    scopus 로고
    • Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression
    • De Bodt S, Proost S, Vandepoele K, Rouze P, Van de Peer Y. 2009. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10:2888
    • (2009) BMC Genomics , vol.10 , pp. 2888
    • De Bodt, S.1    Proost, S.2    Vandepoele, K.3    Rouze, P.4    Van De Peer, Y.5
  • 37
  • 38
    • 77955505357 scopus 로고    scopus 로고
    • Protein-protein interactions essentials: Key concepts to building and analyzing interactome networks
    • De Las Rivas J, Fontanillo C. 2010. Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput. Biol. 6:e10008077
    • (2010) PLoS Comput. Biol. , vol.6
    • De Las Rivas, J.1    Fontanillo, C.2
  • 39
    • 0036580169 scopus 로고    scopus 로고
    • Two methods for assessment of the reliability of high throughput observations
    • Deane C, Salwinski L, Xenarios I, Eisenberg D. 2002. Two methods for assessment of the reliability of high throughput observations. Mol. Cell. Proteomics 1:349-566
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 349-566
    • Deane, C.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 40
    • 77951618528 scopus 로고    scopus 로고
    • Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens
    • Doolittle JM, Gomez SM. 2010. Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol. J. 7:822
    • (2010) Virol. J. , vol.7 , pp. 822
    • Doolittle, J.M.1    Gomez, S.M.2
  • 41
    • 84880398090 scopus 로고    scopus 로고
    • Pathogens use structuralmimicry of native host ligands as a mechanism for host receptor engagement
    • DraymanN,Glick Y, Ben-nun-Shaul O, ZerH, Zlotnick A, et al. 2013. Pathogens use structuralmimicry of native host ligands as a mechanism for host receptor engagement. Cell Host Microbe 14:63-733
    • (2013) Cell Host Microbe , vol.14 , pp. 63-733
    • Drayman, N.1    Glick, Y.2    Ben-Nun-Shaul, O.3    Zer, H.4    Zlotnick, A.5
  • 42
    • 84878242555 scopus 로고    scopus 로고
    • Structural systems pharmacology: The role of 3D structures in next-generation drug development
    • Duran-Frigola M, Mosca R, Aloy P. 2013. Structural systems pharmacology: the role of 3D structures in next-generation drug development. Chem. Biol. 20:674-844
    • (2013) Chem. Biol. , vol.20 , pp. 674-844
    • Duran-Frigola, M.1    Mosca, R.2    Aloy, P.3
  • 43
    • 79956299502 scopus 로고    scopus 로고
    • Supervised learning and prediction of physical interactions between human and HIV proteins
    • Dyer MD, Murali TM, Sobral BW. 2011. Supervised learning and prediction of physical interactions between human and HIV proteins. Infect. Genet. Evol. 11:917-233
    • (2011) Infect. Genet. Evol. , vol.11 , pp. 917-233
    • Dyer, M.D.1    Murali, T.M.2    Sobral, B.W.3
  • 45
    • 80555146675 scopus 로고    scopus 로고
    • Large-scale de novo prediction of physical protein-protein association
    • Elefsinioti A, Saraç OS, Hegele A, Plake C, Hubner NC, et al. 2011. Large-scale de novo prediction of physical protein-protein association. Mol. Cell. Proteomics 10:M111.0106299
    • (2011) Mol. Cell. Proteomics , vol.10
    • Elefsinioti, A.1
  • 46
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-900
    • (1999) Nature , vol.402 , pp. 86-900
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 47
    • 13844264506 scopus 로고    scopus 로고
    • IPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    • Finn RD, Marshall M, Bateman A. 2005. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21:410-122
    • (2005) Bioinformatics , vol.21 , pp. 410-122
    • Finn, R.D.1    Marshall, M.2    Bateman, A.3
  • 50
    • 84875903756 scopus 로고    scopus 로고
    • Toward a three-dimensional view of protein networks between species
    • Franzosa EA,Garamszegi S, Xia Y. 2012. Toward a three-dimensional view of protein networks between species. Front. Microbiol. 3:4288
    • (2012) Front. Microbiol. , vol.3 , pp. 4288
    • Franzosa, E.A.1    Garamszegi, S.2    Xia, Y.3
  • 51
    • 84872784853 scopus 로고    scopus 로고
    • From systems to structure: Bridging networks and mechanism
    • Fraser JS, Gross JD, Krogan NJ. 2013. From systems to structure: bridging networks and mechanism. Mol. Cell 49:222-311
    • (2013) Mol. Cell , vol.49 , pp. 222-311
    • Fraser, J.S.1    Gross, J.D.2    Krogan, N.J.3
  • 52
    • 12144289984 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 1.Method and assessment of docking accuracy
    • Friesner RA, Banks JL,Murphy RB, Halgren TA, Klicic JJ, et al. 2004. Glide: a new approach for rapid, accurate docking and scoring. 1.Method and assessment of docking accuracy. J. Med. Chem. 47:1739-499
    • (2004) J. Med. Chem. , vol.47 , pp. 1739-1499
    • Friesner, R.A.1    Banks, J.L.2    Murphy, R.B.3    Halgren, T.A.4    Klicic, J.J.5
  • 53
    • 84875275699 scopus 로고    scopus 로고
    • Human diseases through the lens of network biology
    • Furlong LI. 2013. Human diseases through the lens of network biology. Trends Genet. 29:150-599
    • (2013) Trends Genet. , vol.29 , pp. 150-599
    • Furlong, L.I.1
  • 54
    • 78651081229 scopus 로고    scopus 로고
    • Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected
    • GaoM, Skolnick J. 2010. Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc. Natl. Acad. Sci. USA 107:22517-222
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 22517-22232
    • Gaom Skolnick, J.1
  • 55
  • 56
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R800
    • (2004) Genome Biol. , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3    Bolstad, B.4    Dettling, M.5
  • 57
    • 84877639844 scopus 로고    scopus 로고
    • Learning a peptide-protein binding affinity predictor with kernel ridge regression
    • Giguere S, Marchand M, Laviolette F, Drouin A, Corbeil J. 2013. Learning a peptide-protein binding affinity predictor with kernel ridge regression. BMC Bioinform. 14:822
    • (2013) BMC Bioinform. , vol.14 , pp. 822
    • Giguere, S.1    Marchand, M.2    Laviolette, F.3    Drouin, A.4    Corbeil, J.5
  • 58
    • 79958035893 scopus 로고    scopus 로고
    • Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses
    • Gilman SR, Iossifov I, Levy D, RonemusM,WiglerM, VitkupD. 2011. Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron 70:898-9077
    • (2011) Neuron , vol.70 , pp. 898-9077
    • Gilman, S.R.1    Iossifov, I.2    Levy, D.3    Ronemus, M.4    Wigler, M.5    Vitkup, D.6
  • 59
    • 84872045007 scopus 로고    scopus 로고
    • Chapter 4: Protein interactions and disease
    • Gonzalez MW, Kann MG. 2012. Chapter 4: Protein interactions and disease. PLoS Comput. Biol. 8:e10028199
    • (2012) PLoS Comput. Biol. , vol.8
    • Gonzalez, M.W.1    Kann, M.G.2
  • 60
    • 84875464398 scopus 로고    scopus 로고
    • Mapping monomeric threading to protein-protein structure prediction
    • Guerler A,Govindarajoo B, Zhang Y. 2013. Mapping monomeric threading to protein-protein structure prediction. J. Chem. Inf. Model. 53:717-255
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 717-255
    • Guerler, A.1    Govindarajoo, B.2    Zhang, Y.3
  • 61
    • 84881117528 scopus 로고    scopus 로고
    • Cancer networks and beyond: Interpreting mutations using the human interactome and protein structure
    • Gulati S, Cheng TMK, Bates PA. 2013. Cancer networks and beyond: Interpreting mutations using the human interactome and protein structure. Semin. Cancer Biol. 23:219-266
    • (2013) Semin. Cancer Biol. , vol.23 , pp. 219-266
    • Gulati, S.1    Cheng, T.M.K.2    Bates, P.A.3
  • 63
    • 41149141724 scopus 로고    scopus 로고
    • Predicting biological networks from genomic data
    • Harrington ED, Jensen LJ, Bork P. 2008. Predicting biological networks from genomic data. FEBS Lett. 582:1251-588
    • (2008) FEBS Lett. , vol.582 , pp. 1251-1588
    • Harrington, E.D.1    Jensen, L.J.2    Bork, P.3
  • 64
    • 61849137243 scopus 로고    scopus 로고
    • Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery
    • Hohman M, GregoryK,Chibale K, Smith PJ, Ekins S, Bunin B. 2009. Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery. Drug Discov. Today 14:261-700
    • (2009) Drug Discov. Today , vol.14 , pp. 261-700
    • Hohman, M.1    Gregory, K.2    Chibale, K.3    Smith, P.J.4    Ekins, S.5    Bunin, B.6
  • 65
    • 84862683667 scopus 로고    scopus 로고
    • Computational structural analysis of protein interactions and networks
    • Hooda Y, Kim PM. 2012. Computational structural analysis of protein interactions and networks. Proteomics 12:1697-7055
    • (2012) Proteomics , vol.12 , pp. 1697-7055
    • Hooda, Y.1    Kim, P.M.2
  • 67
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • Hopkins AL. 2008. Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol. 4:682-900
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 682-900
    • Hopkins, A.L.1
  • 69
    • 84865545263 scopus 로고    scopus 로고
    • A computational framework for boosting confidence in high-throughput protein-protein interaction datasets
    • Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, et al. 2012. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biol. 13:R766
    • (2012) Genome Biol. , vol.13
    • Hosur, R.1    Peng, J.2    Vinayagam, A.3    Stelzl, U.4    Xu, J.5
  • 70
    • 84871735758 scopus 로고    scopus 로고
    • Human protein-protein interaction prediction by a novel sequencebased co-evolution method: Co-evolutionary divergence
    • Hsin Liu C, Li K-C, Yuan S. 2013. Human protein-protein interaction prediction by a novel sequencebased co-evolution method: co-evolutionary divergence. Bioinformatics 29:92-988
    • (2013) Bioinformatics , vol.29 , pp. 92-988
    • Hsin Liu, C.1    Li, K.-C.2    Yuan, S.3
  • 71
    • 84879892154 scopus 로고    scopus 로고
    • Compound promiscuity: What can we learn from current data?
    • Hu Y, Bajorath J. 2013. Compound promiscuity: What can we learn from current data? Drug Discov. Today 18:644-500
    • (2013) Drug Discov. Today , vol.18 , pp. 644-500
    • Hu, Y.1    Bajorath, J.2
  • 72
    • 77952305592 scopus 로고    scopus 로고
    • Large-scale prediction of protein-protein interactions from structures
    • HueM, Riffle M, Vert J-P, NobleW. 2010. Large-scale prediction of protein-protein interactions from structures. BMC Bioinform. 11:1444
    • (2010) BMC Bioinform. , vol.11 , pp. 1444
    • Hue, M.1    Riffle, M.2    Vert, J.-P.3    Noble, W.4
  • 73
    • 84872409290 scopus 로고    scopus 로고
    • Predicting PDZ domain mediated protein interactions from structure
    • Hui S, Xing X, Bader GD. 2013. Predicting PDZ domain mediated protein interactions from structure. BMC Bioinform. 14:277
    • (2013) BMC Bioinform. , vol.14 , pp. 277
    • Hui, S.1    Xing, X.2    Bader, G.D.3
  • 75
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker T, Ozier O, Schwikowski B, Siegel AF. 2002. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18:S233-400
    • (2002) Bioinformatics , vol.18
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 76
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker T, Sharan R. 2008. Protein networks in disease. Genome Res. 18:644-522
    • (2008) Genome Res. , vol.18 , pp. 644-522
    • Ideker, T.1    Sharan, R.2
  • 77
    • 84879784821 scopus 로고    scopus 로고
    • Targeting protein-protein interactions as an anticancer strategy
    • Ivanov AA, Khuri FR, Fu H. 2013. Targeting protein-protein interactions as an anticancer strategy. Trends Pharmacol. Sci. 34:393-4000
    • (2013) Trends Pharmacol. Sci. , vol.34 , pp. 393-4000
    • Ivanov, A.A.1    Khuri, F.R.2    Fu, H.3
  • 78
    • 40549145513 scopus 로고    scopus 로고
    • Enhancing the prediction of protein pairings between interacting families using orthology information
    • Izarzugaza J, Juan D, Pons C, Pazos F, Valencia A. 2008. Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinform. 9:355
    • (2008) BMC Bioinform. , vol.9 , pp. 355
    • Izarzugaza, J.1    Juan, D.2    Pons, C.3    Pazos, F.4    Valencia, A.5
  • 79
    • 84861310336 scopus 로고    scopus 로고
    • From protein interaction networks to novel therapeutic strategies
    • Jaeger S, Aloy P. 2012. From protein interaction networks to novel therapeutic strategies. IUBMB Life 64:529-377
    • (2012) IUBMB Life , vol.64 , pp. 529-377
    • Jaeger, S.1    Aloy, P.2
  • 80
    • 0036141992 scopus 로고    scopus 로고
    • Relatingwhole-genome expression data with protein-protein interactions
    • Jansen R, Greenbaum D, Gerstein M. 2002. Relatingwhole-genome expression data with protein-protein interactions. Genome Res. 12:37-466
    • (2002) Genome Res. , vol.12 , pp. 37-466
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 81
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-533
    • (2003) Science , vol.302 , pp. 449-533
    • Jansen, R.1    Yu, H.2    Greenbaum, D.3    Kluger, Y.4    Krogan, N.J.5
  • 82
    • 80052054208 scopus 로고    scopus 로고
    • Recent advances in protein-protein interaction prediction: Experimental and computational methods
    • Jessulat M, Pitre S, Gui Y, Hooshyar M, Omidi K, et al. 2011. Recent advances in protein-protein interaction prediction: experimental and computational methods. Expert Opin. Drug Discov. 6:921-355
    • (2011) Expert Opin. Drug Discov. , vol.6 , pp. 921-355
    • Jessulat, M.1    Pitre, S.2    Gui, Y.3    Hooshyar, M.4    Omidi, K.5
  • 83
    • 84870316384 scopus 로고    scopus 로고
    • Studying protein-protein interaction networks: A systems view on diseases
    • Jordan F, Nguyen T-P, LiuW-C. 2012. Studying protein-protein interaction networks: a systems view on diseases. Brief. Funct. Genomics 11:497-5044
    • (2012) Brief. Funct. Genomics , vol.11 , pp. 497-5044
    • Jordan, F.1    Nguyen, T.-P.2    Liu, W.-C.3
  • 84
    • 29144461552 scopus 로고    scopus 로고
    • Predicting protein-protein interaction by searching evolutionary tree automorphism space
    • Jothi R, Kann MG, Przytycka TM. 2005. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics 21:i241-500
    • (2005) Bioinformatics , vol.21
    • Jothi, R.1    Kann, M.G.2    Przytycka, T.M.3
  • 85
    • 38949168935 scopus 로고    scopus 로고
    • High-confidence prediction of global interactomes based on genomewide coevolutionary networks
    • Juan D, Pazos F, Valencia A. 2008. High-confidence prediction of global interactomes based on genomewide coevolutionary networks. Proc. Natl. Acad. Sci. USA 105:934-399
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 934-399
    • Juan, D.1    Pazos, F.2    Valencia, A.3
  • 86
    • 74549134502 scopus 로고    scopus 로고
    • Human cancer protein-protein interaction network: A structural perspective
    • Kar G, Gursoy A, Keskin O. 2009. Human cancer protein-protein interaction network: a structural perspective. PLoS Comput. Biol. 5:e10006011
    • (2009) PLoS Comput. Biol. , vol.5
    • Kar, G.1    Gursoy, A.2    Keskin, O.3
  • 87
    • 84856657449 scopus 로고    scopus 로고
    • Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs
    • Kar G, Keskin O, Nussinov R, Gursoy A. 2011. Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J. Proteome Res. 11:1196-2077
    • (2011) J. Proteome Res. , vol.11 , pp. 1196-2077
    • Kar, G.1    Keskin, O.2    Nussinov, R.3    Gursoy, A.4
  • 88
    • 84884483881 scopus 로고    scopus 로고
    • Advances in integrative modeling of biomolecular complexes
    • Karaca E, Bonvin AMJJ. 2013. Advances in integrative modeling of biomolecular complexes. Methods 59:372-811
    • (2013) Methods , vol.59 , pp. 372-811
    • Karaca, E.1    Bonvin, A.M.J.J.2
  • 89
    • 84876575373 scopus 로고    scopus 로고
    • Assessment of high-confidence protein-protein interactome in yeast
    • Karagoz K, Arga KY. 2013. Assessment of high-confidence protein-protein interactome in yeast. Comput. Biol. Chem. 45:1-88
    • (2013) Comput. Biol. Chem. , vol.45 , pp. 1-88
    • Karagoz, K.1    Arga, K.Y.2
  • 91
    • 84876009220 scopus 로고    scopus 로고
    • Interpretation of genomic variants using a unified biological network approach
    • Khurana E, Fu Y,Chen J,GersteinM. 2013. Interpretation of genomic variants using a unified biological network approach. PLoS Comput. Biol. 9:e10028866
    • (2013) PLoS Comput. Biol. , vol.9
    • Khurana, E.1    Fu, Y.2    Chen, J.3    Gerstein, M.4
  • 92
    • 82155179340 scopus 로고    scopus 로고
    • Structural and functional protein network analyses predict novel signaling functions for rhodopsin
    • Kiel C, Vogt A, Campagna A, Chatr-aryamontri A, Swiatek-de Lange M, et al. 2011. Structural and functional protein network analyses predict novel signaling functions for rhodopsin. Mol. Syst. Biol. 7:5511
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 5511
    • Kiel, C.1    Vogt, A.2    Campagna, A.3    Chatr-Aryamontri, A.4    Swiatek-De Lange, M.5
  • 93
    • 33845875196 scopus 로고    scopus 로고
    • Relating three-dimensional structures to protein networks provides evolutionary insights
    • Kim PM, Lu LJ, Xia Y, Gerstein MB. 2006. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314:1938-411
    • (2006) Science , vol.314 , pp. 1938-1421
    • Kim, P.M.1    Lu, L.J.2    Xia, Y.3    Gerstein, M.B.4
  • 94
    • 33749337098 scopus 로고    scopus 로고
    • The many faces of protein-protein interactions: A compendium of interface geometry
    • KimWK, Henschel A, Winter C, Schroeder M. 2006. The many faces of protein-protein interactions: a compendium of interface geometry. PLoS Comput. Biol. 2:e1244
    • (2006) PLoS Comput. Biol. , vol.2
    • Kimwk Henschel, A.1    Winter, C.2    Schroeder, M.3
  • 95
    • 84877674140 scopus 로고    scopus 로고
    • IDDI: Integrated domain-domain interaction and protein interaction analysis system
    • Kim Y, Min B, Yi G-S. 2012. IDDI: integrated domain-domain interaction and protein interaction analysis system. Proteome Sci. 10(Suppl. 1):S99
    • (2012) Proteome Sci. , vol.10 , Issue.SUPPL. 1
    • Kim, Y.1    Min, B.2    Yi, G.-S.3
  • 96
    • 84883534356 scopus 로고    scopus 로고
    • Bridging the gap between genotype and phenotype via network approaches
    • Kim Y-A, Przytycka TM. 2013. Bridging the gap between genotype and phenotype via network approaches. Front. Genet. 3:2277
    • (2013) Front. Genet. , vol.3 , pp. 2277
    • Kim, Y.-A.1    Przytycka, T.M.2
  • 97
    • 79953645463 scopus 로고    scopus 로고
    • Identifying causal genes and dysregulated pathways in complex diseases
    • KimY-A,Wuchty S,PrzytyckaTM.2011. Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput. Biol. 7:e10010955
    • (2011) PLoS Comput. Biol. , vol.7
    • Kim, Y.-A.1    Wuchty, S.2    Przytycka, T.M.3
  • 98
    • 33847377573 scopus 로고    scopus 로고
    • A robustness-based approach to systems-oriented drug design
    • Kitano H. 2007. A robustness-based approach to systems-oriented drug design. Nat. Rev. Drug Discov. 6:202-100
    • (2007) Nat. Rev. Drug Discov. , vol.6 , pp. 202-100
    • Kitano, H.1
  • 101
    • 1842765629 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using support vector machines
    • Koike A, Takagi T. 2004. Prediction of protein-protein interaction sites using support vector machines. Protein Eng. Des. Sel. 17:165-733
    • (2004) Protein Eng. Des. Sel. , vol.17 , pp. 165-733
    • Koike, A.1    Takagi, T.2
  • 102
    • 4344645978 scopus 로고    scopus 로고
    • Can the pharmaceutical industry reduce attrition rates?
    • Kola I, Landis J. 2004. Can the pharmaceutical industry reduce attrition rates? Nat. Rev. Drug Discov. 3:711-166
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 711-166
    • Kola, I.1    Landis, J.2
  • 103
    • 0034745504 scopus 로고    scopus 로고
    • Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach
    • Koonin EV, Wolf YI, Aravind L. 2001. Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res. 11:240-522
    • (2001) Genome Res. , vol.11 , pp. 240-522
    • Koonin, E.V.1    Wolf, Y.I.2    Aravind, L.3
  • 104
    • 24344441167 scopus 로고    scopus 로고
    • Localization of protein-binding sites within families of proteins
    • Korkin D, Davis FP, Sali A. 2005. Localization of protein-binding sites within families of proteins. Protein Sci. 14:2350-600
    • (2005) Protein Sci. , vol.14 , pp. 2350-2600
    • Korkin, D.1    Davis, F.P.2    Sali, A.3
  • 105
    • 81055140589 scopus 로고    scopus 로고
    • From in silico target prediction to multi-target drug design: Current databases, methods and applications
    • Koutsoukas A, Simms B, Kirchmair J, Bond PJ,WhitmoreAV, et al. 2011. From in silico target prediction to multi-target drug design: Current databases, methods and applications. J. Proteomics 74:2554-744
    • (2011) J. Proteomics , vol.74 , pp. 2554-2744
    • Koutsoukas, A.1    Simms, B.2    Kirchmair, J.3    Bond, P.J.4    Whitmore, A.V.5
  • 106
    • 34548232365 scopus 로고    scopus 로고
    • Inference ofmacromolecular assemblies from crystalline state
    • Krissinel E,Henrick K. 2007. Inference ofmacromolecular assemblies from crystalline state. J. Mol. Biol. 372:774-977
    • (2007) J. Mol. Biol. , vol.372 , pp. 774-977
    • Krissinel, E.1    Henrick, K.2
  • 107
    • 84862233055 scopus 로고    scopus 로고
    • Templates are available to model nearly all complexes of structurally characterized proteins
    • Kundrotas PJ, Zhu Z, Janin J, Vakser IA. 2012. Templates are available to model nearly all complexes of structurally characterized proteins. Proc. Natl. Acad. Sci. USA 109:9438-411
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 9438-9421
    • Kundrotas, P.J.1    Zhu, Z.2    Janin, J.3    Vakser, I.A.4
  • 109
    • 84862625522 scopus 로고    scopus 로고
    • Constructing structural networks of signaling pathways on the proteome scale
    • Kuzu G, Keskin O, Gursoy A, Nussinov R. 2012. Constructing structural networks of signaling pathways on the proteome scale. Curr. Opin. Struct. Biol. 22:367-777
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 367-777
    • Kuzu, G.1    Keskin, O.2    Gursoy, A.3    Nussinov, R.4
  • 110
    • 84863598108 scopus 로고    scopus 로고
    • Bioinformatics and variability in drug response: A protein structural perspective
    • Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. 2012. Bioinformatics and variability in drug response: a protein structural perspective. J. R. Soc. Interface 9:1409-377
    • (2012) J. R. Soc. Interface , vol.9 , pp. 1409-1387
    • Lahti, J.L.1    Tang, G.W.2    Capriotti, E.3    Liu, T.4    Altman, R.B.5
  • 111
    • 84860851412 scopus 로고    scopus 로고
    • Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks
    • Lee MJ, Ye AS, Gardino AK, Heijink AM, Sorger PK, et al. 2012. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 149:780-944
    • (2012) Cell , vol.149 , pp. 780-944
    • Lee, M.J.1    Ye, A.S.2    Gardino, A.K.3    Heijink, A.M.4    Sorger, P.K.5
  • 112
    • 77953255983 scopus 로고    scopus 로고
    • A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers
    • Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, LimWK, et al. 2010. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol. Syst. Biol. 6:3777
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 3777
    • Lefebvre, C.1    Rajbhandari, P.2    Alvarez, M.J.3    Limwk, B.P.4
  • 113
    • 72949117638 scopus 로고    scopus 로고
    • Predicting protein-protein interactions in the context of protein evolution
    • Lewis ACF, Saeed R, Deane CM. 2010. Predicting protein-protein interactions in the context of protein evolution. Mol. Biosyst. 6:55-644
    • (2010) Mol. Biosyst. , vol.6 , pp. 55-644
    • Lewis, A.C.F.1    Saeed, R.2    Deane, C.M.3
  • 114
    • 84878952113 scopus 로고    scopus 로고
    • Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: Application to human brain tissues
    • Li Y, Xu J, Chen H, Zhao Z, Li S, et al. 2013. Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: application to human brain tissues. PLoS ONE 8:e658711
    • (2013) PLoS ONE , vol.8
    • Li, Y.1    Xu, J.2    Chen, H.3    Zhao, Z.4    Li, S.5
  • 115
    • 84866939028 scopus 로고    scopus 로고
    • Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis
    • Liang Y, Wu H, Lei R, Chong RA, Wei Y, et al. 2012. Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis. J. Biol. Chem. 287:33533-444
    • (2012) J. Biol. Chem. , vol.287 , pp. 33533-33454
    • Liang, Y.1    Wu, H.2    Lei, R.3    Chong, R.A.4    Wei, Y.5
  • 116
    • 78650821937 scopus 로고    scopus 로고
    • Large-scale discovery and characterization of protein regulatory motifs in eukaryotes
    • Lieber DS, Elemento O, Tavazoie S. 2010. Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS ONE 5:e144444
    • (2010) PLoS ONE , vol.5
    • Lieber, D.S.1    Elemento, O.2    Tavazoie, S.3
  • 117
    • 84884182082 scopus 로고    scopus 로고
    • Inferring homologous protein-protein interactions through pair position specific scoring matrix
    • Lin C-Y, Chen Y-C, Lo Y-S, Yang J-M. 2013. Inferring homologous protein-protein interactions through pair position specific scoring matrix. BMC Bioinform. 14(Suppl. 2):S111
    • (2013) BMC Bioinform. , vol.14 , Issue.SUPPL. 2
    • Lin, C.-Y.1    Chen, Y.-C.2    Lo, Y.-S.3    Yang, J.-M.4
  • 118
    • 84872678121 scopus 로고    scopus 로고
    • Heterogeneous data integration by tree-augmented naïve Bayes for protein-protein interactions prediction
    • Lin X, Chen X-w. 2013. Heterogeneous data integration by tree-augmented naïve Bayes for protein-protein interactions prediction. Proteomics 13:261-688
    • (2013) Proteomics , vol.13 , pp. 261-688
    • Lin, X.1    Chen, X.-W.2
  • 119
    • 84870311707 scopus 로고    scopus 로고
    • Proteome-wide prediction of protein-protein interactions from high-throughput data
    • LiuZ-P,ChenL. 2012. Proteome-wide prediction of protein-protein interactions from high-throughput data. Protein Cell 3:508-200
    • (2012) Protein Cell , vol.3 , pp. 508-200
    • Liu, Z.-P.1    Chen, L.2
  • 120
    • 84862510972 scopus 로고    scopus 로고
    • Large-scale prediction and testing of drug activity on side-effect targets
    • Lounkine E, Keiser MJ,Whitebread S, Mikhailov D, Hamon J, et al. 2012. Large-scale prediction and testing of drug activity on side-effect targets. Nature 486:361-677
    • (2012) Nature , vol.486 , pp. 361-677
    • Lounkine, E.1    Keiser, M.J.2    Whitebread, S.3    Mikhailov, D.4    Hamon, J.5
  • 121
    • 22244447463 scopus 로고    scopus 로고
    • Assessing the limits of genomic data integration for predicting protein networks
    • Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M. 2005. Assessing the limits of genomic data integration for predicting protein networks. Genome Res. 15:945-533
    • (2005) Genome Res. , vol.15 , pp. 945-533
    • Lu, L.J.1    Xia, Y.2    Paccanaro, A.3    Yu, H.4    Gerstein, M.5
  • 122
    • 84855182281 scopus 로고    scopus 로고
    • Gene Ontology-driven inference of protein-protein interactions using inducers
    • Maetschke SR, Simonsen M, Davis MJ, Ragan MA. 2012. Gene Ontology-driven inference of protein-protein interactions using inducers. Bioinformatics 28:69-755
    • (2012) Bioinformatics , vol.28 , pp. 69-755
    • Maetschke, S.R.1    Simonsen, M.2    Davis, M.J.3    Ragan, M.A.4
  • 123
    • 39149143293 scopus 로고    scopus 로고
    • A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas
    • Mani KM, LefebvreC,WangK, Lim WK, Basso K, et al. 2008. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol. Syst. Biol. 4:1-99
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 1-99
    • Mani, K.M.1    Lefebvre, C.2    Wang, K.3    Lim, W.K.4    Basso, K.5
  • 125
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, et al. 2006. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform. 7(Suppl. 1):S77
    • (2006) BMC Bioinform. , vol.7 , Issue.SUPPL. 1
    • Margolin, A.A.1    Nemenman, I.2    Basso, K.3    Wiggins, C.4    Stolovitzky, G.5
  • 126
    • 13444262436 scopus 로고    scopus 로고
    • Predicting protein-protein interactions using signature products
    • Martin S, Roe D, Faulon JL. 2005. Predicting protein-protein interactions using signature products. Bioinformatics 21:218-266
    • (2005) Bioinformatics , vol.21 , pp. 218-266
    • Martin, S.1    Roe, D.2    Faulon, J.L.3
  • 127
    • 0035211290 scopus 로고    scopus 로고
    • Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs"
    • Matthews L, Vaglio P, Reboul J, Ge H, Davis B, et al. 2001. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 11:2120-266
    • (2001) Genome Res. , vol.11 , pp. 2120-2266
    • Matthews, L.1    Vaglio, P.2    Reboul, J.3    Ge, H.4    Davis, B.5
  • 128
  • 131
    • 84878858665 scopus 로고    scopus 로고
    • INstruct: A database of high-quality 3D structurally resolved protein interactome networks
    • Meyer MJ, Das J, Wang X, Yu H. 2013. INstruct: a database of high-quality 3D structurally resolved protein interactome networks. Bioinformatics 29:1577-799
    • (2013) Bioinformatics , vol.29 , pp. 1577-1799
    • Meyer, M.J.1    Das, J.2    Wang, X.3    Yu, H.4
  • 132
    • 77955411868 scopus 로고    scopus 로고
    • Computational tools for the interactive exploration of proteomic and structural data
    • Morris JH, Meng EC, FerrinTE. 2010. Computational tools for the interactive exploration of proteomic and structural data. Mol. Cell. Proteomics 9:1703-155
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 1703-1165
    • Morris, J.H.1    Meng, E.C.2    Ferrin, T.E.3
  • 133
    • 84871967106 scopus 로고    scopus 로고
    • Interactome3D: Adding structural details to protein networks
    • Mosca R, Ceol A, Aloy P. 2013. Interactome3D: adding structural details to protein networks. Nat. Methods 10:47-533
    • (2013) Nat. Methods , vol.10 , pp. 47-533
    • Mosca, R.1    Ceol, A.2    Aloy, P.3
  • 134
    • 70049112107 scopus 로고    scopus 로고
    • Pushing structural information into the yeast interactome by high-throughput protein docking experiments
    • Mosca R, Pons C, Fernandez-Recio J, Aloy P. 2009. Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput. Biol. 5:e10004900
    • (2009) PLoS Comput. Biol. , vol.5
    • Mosca, R.1    Pons, C.2    Fernandez-Recio, J.3    Aloy, P.4
  • 135
    • 79960164372 scopus 로고    scopus 로고
    • Protein-protein complex structure predictions by multimeric threading and template recombination
    • Mukherjee S, Zhang Y. 2011. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure 19:955-666
    • (2011) Structure , vol.19 , pp. 955-666
    • Mukherjee, S.1    Zhang, Y.2
  • 136
    • 84872570833 scopus 로고    scopus 로고
    • Evaluation of physical and functional protein-protein interaction prediction methods for detecting biological pathways
    • Muley VY, Ranjan A. 2013. Evaluation of physical and functional protein-protein interaction prediction methods for detecting biological pathways. PLoS ONE 8:e543255
    • (2013) PLoS ONE , vol.8
    • Muley, V.Y.1    Ranjan, A.2
  • 137
    • 52149097555 scopus 로고    scopus 로고
    • Regulatory networks define phenotypic classes of human stem cell lines
    • Muller F-J, Laurent LC, Kostka D, Ulitsky I, Williams R, et al. 2008. Regulatory networks define phenotypic classes of human stem cell lines. Nature 455:401-55
    • (2008) Nature , vol.455 , pp. 401-455
    • Muller, F.-J.1    Laurent, L.C.2    Kostka, D.3    Ulitsky, I.4    Williams, R.5
  • 138
    • 84874500187 scopus 로고    scopus 로고
    • Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions
    • Ochoa D, Garcia-Gutiérrez P, Juan D, Valencia A, Pazos F. 2013. Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions. Mol. Biosyst. 9:70-766
    • (2013) Mol. Biosyst. , vol.9 , pp. 70-766
    • Ochoa, D.1    Garcia-Gutiérrez, P.2    Juan, D.3    Valencia, A.4    Pazos, F.5
  • 141
    • 41149167511 scopus 로고    scopus 로고
    • Network medicine
    • Pawson T, Linding R. 2008. Network medicine. FEBS Lett. 582:1266-700
    • (2008) FEBS Lett. , vol.582 , pp. 1266-1700
    • Pawson, T.1    Linding, R.2
  • 143
    • 66549120787 scopus 로고    scopus 로고
    • Is protein classification necessary? Toward alternative approaches to function annotation
    • Petrey D, Honig B. 2009. Is protein classification necessary? Toward alternative approaches to function annotation. Curr. Opin. Struct. Biol. 19:363-688
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 363-688
    • Petrey, D.1    Honig, B.2
  • 145
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated nonredundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61-655
    • (2007) Nucleic Acids Res. , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 146
    • 77649182705 scopus 로고    scopus 로고
    • Unveiling the role of network and systems biology in drug discovery
    • Pujol A, Mosca R, Farrés J, Aloy P. 2010. Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol. Sci. 31:115-233
    • (2010) Trends Pharmacol. Sci. , vol.31 , pp. 115-233
    • Pujol, A.1    Mosca, R.2    Farrés, J.3    Aloy, P.4
  • 147
    • 84878574165 scopus 로고    scopus 로고
    • Deciphering the host-pathogen protein interface in chikungunya virus-mediated sickness
    • Rana J, Sreejith R, Gulati S, Bharti I, Jain S, Gupta S. 2013. Deciphering the host-pathogen protein interface in chikungunya virus-mediated sickness. Arch. Virol. 158:1159-722
    • (2013) Arch. Virol. , vol.158 , pp. 1159-1722
    • Rana, J.1    Sreejith, R.2    Gulati, S.3    Bharti, I.4    Jain, S.5    Gupta, S.6
  • 148
    • 33847064282 scopus 로고    scopus 로고
    • Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    • Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, et al. 2006. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol. 5:111
    • (2006) J. Biol. , vol.5 , pp. 111
    • Reguly, T.1    Breitkreutz, A.2    Boucher, L.3    Breitkreutz, B.J.4    Hon, G.C.5
  • 149
    • 54249117223 scopus 로고    scopus 로고
    • Targeting and tinkering with interaction networks
    • Russell RB, Aloy P. 2008. Targeting and tinkering with interaction networks. Nat. Chem. Biol. 4:666-733
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 666-733
    • Russell, R.B.1    Aloy, P.2
  • 150
    • 24144476642 scopus 로고    scopus 로고
    • The inference of protein-protein interactions by coevolutionary analysis is improved by excluding the information about the phylogenetic relationships
    • Sato T, Yamanishi Y, Kanehisa M, Toh H. 2005. The inference of protein-protein interactions by coevolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21:3482-899
    • (2005) Bioinformatics , vol.21 , pp. 3482-3899
    • Sato, T.1    Yamanishi, Y.2    Kanehisa, M.3    Toh, H.4
  • 151
    • 70249134919 scopus 로고    scopus 로고
    • Molecular networks as sensors and drivers of common human diseases
    • Schadt EE. 2009. Molecular networks as sensors and drivers of common human diseases. Nature 461:218-233
    • (2009) Nature , vol.461 , pp. 218-233
    • Schadt, E.E.1
  • 153
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homologymodeling server
    • Schwede T, Kopp J, Guex N, Peitsch MC. 2004. SWISS-MODEL: An automated protein homologymodeling server. Nucleic Acids Res. 31:3381-855
    • (2004) Nucleic Acids Res. , vol.31 , pp. 3381-3855
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 155
    • 34247586171 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    • Shoemaker BA, Panchenko AR. 2007. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput. Biol. 3:e433
    • (2007) PLoS Comput. Biol. , vol.3
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 156
    • 34047202181 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part I. Experimental techniques and databases
    • Shoemaker BA, Panchenko AR. 2007. Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput. Biol. 3:e422
    • (2007) PLoS Comput. Biol. , vol.3
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 157
    • 84857784008 scopus 로고    scopus 로고
    • IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
    • Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, et al. 2012. IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res. 40:D834-400
    • (2012) Nucleic Acids Res. , vol.40
    • Shoemaker, B.A.1    Zhang, D.2    Tyagi, M.3    Thangudu, R.R.4    Fong, J.H.5
  • 158
    • 77954278629 scopus 로고    scopus 로고
    • Struct2Net: A web service to predict protein-protein interactions using a structure-based approach
    • Singh R, Park D, Xu J, Hosur R, Berger B. 2010. Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Res. 38:W508-155
    • (2010) Nucleic Acids Res. , vol.38
    • Singh, R.1    Park, D.2    Xu, J.3    Hosur, R.4    Berger, B.5
  • 159
    • 0035943340 scopus 로고    scopus 로고
    • Correlated sequence-signatures as markers of protein-protein interaction
    • Sprinzak E, Margalit H. 2001. Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol. 311:681-922
    • (2001) J. Mol. Biol. , vol.311 , pp. 681-922
    • Sprinzak, E.1    Margalit, H.2
  • 160
    • 0037432528 scopus 로고    scopus 로고
    • How reliable are experimental protein-protein interaction data?
    • Sprinzak E, Sattath S, Margalit H. 2003. How reliable are experimental protein-protein interaction data? J. Mol. Biol. 327:919-233
    • (2003) J. Mol. Biol. , vol.327 , pp. 919-233
    • Sprinzak, E.1    Sattath, S.2    Margalit, H.3
  • 161
    • 13444257903 scopus 로고    scopus 로고
    • 3did: Interacting protein domains of known three-dimensional structure
    • Stein A, Russell RB, Aloy P. 2005. 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 33:D413-177
    • (2005) Nucleic Acids Res. , vol.33
    • Stein, A.1    Russell, R.B.2    Aloy, P.3
  • 163
    • 80052411919 scopus 로고    scopus 로고
    • Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
    • Tuncbag N, Gursoy A, Nussinov R, Keskin O. 2011. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat. Protoc. 6:1341-544
    • (2011) Nat. Protoc. , vol.6 , pp. 1341-1544
    • Tuncbag, N.1    Gursoy, A.2    Nussinov, R.3    Keskin, O.4
  • 164
    • 72949088633 scopus 로고    scopus 로고
    • Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: The p53 example
    • Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R. 2009. Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example. Mol. Biosyst. 5:1770-788
    • (2009) Mol. Biosyst. , vol.5 , pp. 1770-1788
    • Tuncbag, N.1    Kar, G.2    Gursoy, A.3    Keskin, O.4    Nussinov, R.5
  • 165
    • 79952676403 scopus 로고    scopus 로고
    • Literature curation of protein interactions: Measuring agreement across major public databases
    • Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. 2010. Literature curation of protein interactions: measuring agreement across major public databases. Database 2010:baq0266
    • (2010) Database , vol.2010
    • Turinsky, A.L.1    Razick, S.2    Turner, B.3    Donaldson, I.M.4    Wodak, S.J.5
  • 166
  • 167
    • 29244477844 scopus 로고    scopus 로고
    • A human protein atlas for normal and cancer tissues based on antibody proteomics
    • Uhlén M, Björling E, Agaton C, Szigyarto CA-K, Amini B, et al. 2005. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 4:1920-322
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1920-1332
    • Uhlén, M.B.1
  • 168
    • 78149460182 scopus 로고    scopus 로고
    • DEGAS: De novo discovery of dysregulated pathways in human diseases
    • Ulitsky I, Krishnamurthy A, Karp RM, Shamir R. 2010. DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS ONE 5:e133677
    • (2010) PLoS ONE , vol.5
    • Ulitsky, I.1    Krishnamurthy, A.2    Karp, R.M.3    Shamir, R.4
  • 169
    • 84878583033 scopus 로고    scopus 로고
    • The development of a universal in silico predictor of protein-protein interactions
    • Valente GT, Acencio ML,Martins C, LemkeN. 2013. The development of a universal in silico predictor of protein-protein interactions. PLoS ONE 8:e655877
    • (2013) PLoS ONE , vol.8
    • Valente, G.T.1    Acencio, M.L.2    Martins, C.3    Lemke, N.4
  • 170
    • 80054881553 scopus 로고    scopus 로고
    • Gaussian interaction profile kernels for predicting drug-target interaction
    • van Laarhoven T, Nabuurs SB, Marchiori E. 2011. Gaussian interaction profile kernels for predicting drug-target interaction. Bioinformatics 27:3036-433
    • (2011) Bioinformatics , vol.27 , pp. 3036-3433
    • Van Laarhoven, T.1    Nabuurs, S.B.2    Marchiori, E.3
  • 171
    • 84856532705 scopus 로고    scopus 로고
    • De novo discovery of mutated driver pathways in cancer
    • Vandin F, Upfal E, Raphael BJ. 2012. De novo discovery of mutated driver pathways in cancer. Genome Res. 22:375-855
    • (2012) Genome Res. , vol.22 , pp. 375-855
    • Vandin, F.1    Upfal, E.2    Raphael, B.J.3
  • 172
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • Vidal M, Cusick ME, Barabási A-L. 2011. Interactome networks and human disease. Cell 144:986-988
    • (2011) Cell , vol.144 , pp. 986-988
    • Vidal, M.1    Cusick, M.E.2    Barabási, A.-L.3
  • 174
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • vonMeringC,KrauseR, SnelB,Cornell M, Oliver SG, et al. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399-4033
    • (2002) Nature , vol.417 , pp. 399-4033
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5
  • 175
    • 79951789553 scopus 로고    scopus 로고
    • Machine learning in drug discovery and development
    • Wale N. 2011. Machine learning in drug discovery and development. Drug Dev. Res. 72:112-199
    • (2011) Drug Dev. Res. , vol.72 , pp. 112-199
    • Wale, N.1
  • 176
    • 33745800831 scopus 로고    scopus 로고
    • Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes
    • Wang K, Nemenmann I, Banerjee N, Margolin A, Califano A. 2006. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes. Lect. Notes Comput. Sci. 3909:348-622
    • (2006) Lect. Notes Comput. Sci. , vol.3909 , pp. 348-622
    • Wang, K.1    Nemenmann, I.2    Banerjee, N.3    Margolin, A.4    Califano, A.5
  • 177
    • 70249108504 scopus 로고    scopus 로고
    • Genome-wide identification of post-translational modulators of transcription factor activity in human B cells
    • Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, et al. 2009. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat. Biotechnol. 27:829-377
    • (2009) Nat. Biotechnol. , vol.27 , pp. 829-377
    • Wang, K.1    Saito, M.2    Bisikirska, B.C.3    Alvarez, M.J.4    Lim, W.K.5
  • 178
    • 84863010950 scopus 로고    scopus 로고
    • Three-dimensional reconstruction of protein networks provides insight into human genetic disease
    • Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H. 2012. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat. Biotechnol. 30:159-644
    • (2012) Nat. Biotechnol. , vol.30 , pp. 159-644
    • Wang, X.1    Wei, X.2    Thijssen, B.3    Das, J.4    Lipkin, S.M.5    Yu, H.6
  • 179
    • 79951788562 scopus 로고    scopus 로고
    • Towards the prediction of protein interaction partners using physical docking
    • Wass MN, Fuentes G, Pons C, Pazos F, Valencia A. 2011. Towards the prediction of protein interaction partners using physical docking. Mol. Syst. Biol. 7:4699
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 4699
    • Wass, M.N.1    Fuentes, G.2    Pons, C.3    Pazos, F.4    Valencia, A.5
  • 180
    • 77952720637 scopus 로고    scopus 로고
    • Genome-wide association studies and beyond
    • Witte JS. 2010. Genome-wide association studies and beyond. Annu. Rev. Public Health 31:9-200
    • (2010) Annu. Rev. Public Health , vol.31 , pp. 9-200
    • Witte, J.S.1
  • 181
    • 79953100964 scopus 로고    scopus 로고
    • Structure-based systems biology for analyzing off-target binding
    • Xie L, Xie L, Bourne PE. 2011. Structure-based systems biology for analyzing off-target binding. Curr. Opin. Struct. Biol. 21:189-999
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 189-999
    • Xie, L.1    Xie, L.2    Bourne, P.E.3
  • 182
    • 78651306870 scopus 로고    scopus 로고
    • The protein common interface database (ProtCID) a comprehensive database of interactions of homologous proteins in multiple crystal forms
    • Xu Q, Dunbrack RL. 2011. The protein common interface database (ProtCID) - A comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Res. 39:D761-700
    • (2011) Nucleic Acids Res. , vol.39
    • Xu, Q.1    Dunbrack, R.L.2
  • 183
    • 80053022680 scopus 로고    scopus 로고
    • Transferring network topological knowledge for predicting protein-protein interactions
    • Xu Q, Xiang EW, Yang Q. 2011. Transferring network topological knowledge for predicting protein-protein interactions. Proteomics 11:3818-255
    • (2011) Proteomics , vol.11 , pp. 3818-3265
    • Xu, Q.1    Xiang, E.W.2    Yang, Q.3
  • 184
    • 79952345084 scopus 로고    scopus 로고
    • Analysis of multiple compoundprotein interactions reveals novel bioactive molecules
    • Yabuuchi H, Niijima S, Takematsu H, Ida T, Hirokawa T, et al. 2011. Analysis of multiple compoundprotein interactions reveals novel bioactive molecules. Mol. Syst. Biol. 7:4722
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 4722
    • Yabuuchi, H.1    Niijima, S.2    Takematsu, H.3    Ida, T.4    Hirokawa, T.5
  • 186
    • 84883162967 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis
    • You Z-H, Lei Y-K, Zhu L, Xia J,Wang B. 2013. Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis. BMC Bioinform. 14:S100
    • (2013) BMC Bioinform. , vol.14
    • You, Z.-H.1    Lei, Y.-K.2    Zhu, L.3    Xia, J.4    Wang, B.5
  • 187
    • 84884590545 scopus 로고    scopus 로고
    • A novel method based on new adaptive LVQ neural network for predicting protein-protein interactions from protein sequences
    • Yousef A, Moghadam Charkari N. 2013. A novel method based on new adaptive LVQ neural network for predicting protein-protein interactions from protein sequences. J. Theor. Biol. 336:231-399
    • (2013) J. Theor. Biol. , vol.336 , pp. 231-399
    • Yousef, A.1    Moghadam Charkari, N.2
  • 188
    • 77950545785 scopus 로고    scopus 로고
    • Predicting protein-protein interactions in unbalanced data using the primary structure of proteins
    • Yu C-Y, Chou L-C, Chang D. 2010. Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. BMC Bioinform. 11:1677
    • (2010) BMC Bioinform. , vol.11 , pp. 1677
    • Yu, C.-Y.1    Chou, L.-C.2    Chang, D.3
  • 189
    • 84860525022 scopus 로고    scopus 로고
    • Inferring high-confidence human protein-protein interactions
    • Yu X, Wallqvist A, Reifman J. 2012. Inferring high-confidence human protein-protein interactions. BMC Bioinform. 13:799
    • (2012) BMC Bioinform. , vol.13 , pp. 799
    • Yu, X.1    Wallqvist, A.2    Reifman, J.3
  • 190
    • 84886313848 scopus 로고    scopus 로고
    • PPlevo: Protein-protein interaction prediction from PSSM based evolutionary information
    • Zahiri J, Yaghoubi O, Mohammad-NooriM, Ebrahimpour R, Masoudi-Nejad A. 2013. PPlevo: protein-protein interaction prediction from PSSM based evolutionary information. Genomics 102:237-422
    • (2013) Genomics , vol.102 , pp. 237-422
    • Zahiri, J.1    Yaghoubi, O.2    Mohammad-Noori, M.3    Ebrahimpour, R.4    Masoudi-Nejad, A.5
  • 191
    • 84879684780 scopus 로고    scopus 로고
    • Kaposi's sarcoma: A computational approach through protein-protein interaction and gene regulatory networks analysis
    • Zaman A, Rahaman MH, Razzaque S. 2013. Kaposi's sarcoma: A computational approach through protein-protein interaction and gene regulatory networks analysis. Virus Genes 46:242-544
    • (2013) Virus Genes , vol.46 , pp. 242-544
    • Zaman, A.1    Rahaman, M.H.2    Razzaque, S.3
  • 192
    • 79953654633 scopus 로고    scopus 로고
    • CAERUS: Predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data
    • Zhang KX, Ouellette BFF. 2011. CAERUS: predicting CAncER oUtcomeS using relationship between protein structural information, protein networks, gene expression data, and mutation data. PLoS Comput. Biol. 7:e10011144
    • (2011) PLoS Comput. Biol. , vol.7
    • Zhang, K.X.1    Ouellette, B.F.F.2
  • 193
    • 84880710519 scopus 로고    scopus 로고
    • Extracting a few functionally reproducible biomarkers to build robust subnetwork-based classifiers for the diagnosis of cancer
    • Zhang L, Li S,Hao C, Hong G, Zou J, et al. 2013. Extracting a few functionally reproducible biomarkers to build robust subnetwork-based classifiers for the diagnosis of cancer. Gene 526:232-388
    • (2013) Gene , vol.526 , pp. 232-388
    • Zhang, L.1    Li, S.2    Hao, C.3    Hong, G.4    Zou, J.5
  • 194
    • 84867881743 scopus 로고    scopus 로고
    • Structure-based prediction of protein-protein interactions on a genome-wide scale
    • ZhangQC, Petrey D, Deng L, Qiang L, Shi Y, et al. 2012. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490:556-600
    • (2012) Nature , vol.490 , pp. 556-600
    • Zhang, Q.C.1    Petrey, D.2    Deng, L.3    Qiang, L.4    Shi, Y.5
  • 198
    • 45149106353 scopus 로고    scopus 로고
    • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
    • Zhu J, Zhang B, Smith EN, Drees B, Brem RB, et al. 2008. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat. Genet. 40:854-611
    • (2008) Nat. Genet. , vol.40 , pp. 854-611
    • Zhu, J.1    Zhang, B.2    Smith, E.N.3    Drees, B.4    Brem, R.B.5
  • 199
    • 33845762340 scopus 로고    scopus 로고
    • Multi-target therapeutics: When the whole is greater than the sum of the parts
    • Zimmermann GR, Lehár J, Keith CT. 2007. Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov. Today 12:34-422
    • (2007) Drug Discov. Today , vol.12 , pp. 34-422
    • Zimmermann, G.R.1


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