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Volumn 12, Issue , 2011, Pages

Selection of organisms for the co-evolution-based study of protein interactions

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL RESOURCES; FUNCTIONAL RELATIONSHIP; OPTIMAL PERFORMANCE; OPTIMAL SETS; PHYLOGENETIC DISTRIBUTION; PHYLOGENETIC TREES; PROTEIN INTERACTION;

EID: 80052581482     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-363     Document Type: Article
Times cited : (12)

References (27)
  • 1
    • 34247586171 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    • 10.1371/journal.pcbi.0030043, 1857810, 17465672
    • Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 2007, 3(4):e43. 10.1371/journal.pcbi.0030043, 1857810, 17465672.
    • (2007) PLoS Comput Biol , vol.3 , Issue.4
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 2
    • 72549092384 scopus 로고    scopus 로고
    • Computational Methods to predict protein interaction partners
    • London: Springer-Verlag, Panchenko AR, Przytycka TM
    • Valencia A, Pazos F. Computational Methods to predict protein interaction partners. Protein-protein interactions and networks 2008, 67-81. London: Springer-Verlag, Panchenko AR, Przytycka TM.
    • (2008) Protein-protein interactions and networks , pp. 67-81
    • Valencia, A.1    Pazos, F.2
  • 3
    • 41149141724 scopus 로고    scopus 로고
    • Predicting biological networks from genomic data
    • 10.1016/j.febslet.2008.02.033, 18294967
    • Harrington ED, Jensen LJ, Bork P. Predicting biological networks from genomic data. FEBS Lett 2008, 582(8):1251-1258. 10.1016/j.febslet.2008.02.033, 18294967.
    • (2008) FEBS Lett , vol.582 , Issue.8 , pp. 1251-1258
    • Harrington, E.D.1    Jensen, L.J.2    Bork, P.3
  • 4
    • 54349091030 scopus 로고    scopus 로고
    • Protein co-evolution, co-adaptation and interactions
    • 10.1038/emboj.2008.189, 2556093, 18818697
    • Pazos F, Valencia A. Protein co-evolution, co-adaptation and interactions. EMBO J 2008, 27(20):2648-2655. 10.1038/emboj.2008.189, 2556093, 18818697.
    • (2008) EMBO J , vol.27 , Issue.20 , pp. 2648-2655
    • Pazos, F.1    Valencia, A.2
  • 5
    • 41149150650 scopus 로고    scopus 로고
    • Co-evolution and co-adaptation in protein networks
    • 10.1016/j.febslet.2008.02.017, 18282476
    • Juan D, Pazos F, Valencia A. Co-evolution and co-adaptation in protein networks. FEBS Lett 2008, 582(8):1225-1230. 10.1016/j.febslet.2008.02.017, 18282476.
    • (2008) FEBS Lett , vol.582 , Issue.8 , pp. 1225-1230
    • Juan, D.1    Pazos, F.2    Valencia, A.3
  • 6
    • 0033551248 scopus 로고    scopus 로고
    • Assigning protein functions by comparative genome analysis: Protein pylogenetic profiles
    • 10.1073/pnas.96.8.4285, 16324, 10200254
    • Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: Protein pylogenetic profiles. Proc Natl Acad Sci USA 1999, 96:4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 4285-4288
    • Pellegrini, M.1    Marcotte, E.M.2    Thompson, M.J.3    Eisenberg, D.4    Yeates, T.O.5
  • 7
    • 0041358614 scopus 로고    scopus 로고
    • Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages
    • 10.1038/nbt861, 12923548
    • Date SV, Marcotte EM. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 2003, 21(9):1055-1062. 10.1038/nbt861, 12923548.
    • (2003) Nat Biotechnol , vol.21 , Issue.9 , pp. 1055-1062
    • Date, S.V.1    Marcotte, E.M.2
  • 8
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • 10.1093/protein/14.9.609, 11707606
    • Pazos F, Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 2001, 14:609-614. 10.1093/protein/14.9.609, 11707606.
    • (2001) Protein Eng , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 9
    • 77952837458 scopus 로고    scopus 로고
    • Studying the co-evolution of protein families with the Mirrortree web server
    • 10.1093/bioinformatics/btq137, 20363731
    • Ochoa D, Pazos F. Studying the co-evolution of protein families with the Mirrortree web server. Bioinformatics 2010, 26(10):1370-1371. 10.1093/bioinformatics/btq137, 20363731.
    • (2010) Bioinformatics , vol.26 , Issue.10 , pp. 1370-1371
    • Ochoa, D.1    Pazos, F.2
  • 10
    • 24644502565 scopus 로고    scopus 로고
    • Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome
    • 10.1016/j.jmb.2005.07.005, 16139301
    • Pazos F, Ranea JAG, Juan D, Sternberg MJE. Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. J Mol Biol 2005, 352(4):1002-1015. 10.1016/j.jmb.2005.07.005, 16139301.
    • (2005) J Mol Biol , vol.352 , Issue.4 , pp. 1002-1015
    • Pazos, F.1    Ranea, J.A.G.2    Juan, D.3    Sternberg, M.J.E.4
  • 11
    • 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
    • 10.1093/bioinformatics/bti564, 15994190
    • Sato T, Yamanishi Y, Kanehisa M, Toh H. The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 2005, 21(17):3482-3489. 10.1093/bioinformatics/bti564, 15994190.
    • (2005) Bioinformatics , vol.21 , Issue.17 , pp. 3482-3489
    • Sato, T.1    Yamanishi, Y.2    Kanehisa, M.3    Toh, H.4
  • 12
    • 34248513211 scopus 로고    scopus 로고
    • Predicting protein domain interactions from coevolution of conserved regions
    • 10.1002/prot.21347, 17357158
    • Kann MG, Jothi R, Cherukuri PF, Przytycka TM. Predicting protein domain interactions from coevolution of conserved regions. Proteins 2007, 67(4):811-820. 10.1002/prot.21347, 17357158.
    • (2007) Proteins , vol.67 , Issue.4 , pp. 811-820
    • Kann, M.G.1    Jothi, R.2    Cherukuri, P.F.3    Przytycka, T.M.4
  • 13
    • 38949168935 scopus 로고    scopus 로고
    • High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
    • 10.1073/pnas.0709671105, 2242690, 18199838
    • Juan D, Pazos F, Valencia A. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA 2008, 105(3):934-939. 10.1073/pnas.0709671105, 2242690, 18199838.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.3 , pp. 934-939
    • Juan, D.1    Pazos, F.2    Valencia, A.3
  • 14
    • 24044546509 scopus 로고    scopus 로고
    • Refined phylogenetic profiles method for predicting protein-protein interactions
    • 10.1093/bioinformatics/bti532, 15947018
    • Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y. Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics 2005, 21(16):3409-3415. 10.1093/bioinformatics/bti532, 15947018.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3409-3415
    • Sun, J.1    Xu, J.2    Liu, Z.3    Liu, Q.4    Zhao, A.5    Shi, T.6    Li, Y.7
  • 15
    • 34347374679 scopus 로고    scopus 로고
    • Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
    • 10.1186/1471-2105-8-173, 1904249, 17521444
    • Jothi R, Przytycka TM, Aravind L. Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 2007, 8:173. 10.1186/1471-2105-8-173, 1904249, 17521444.
    • (2007) BMC Bioinformatics , vol.8 , pp. 173
    • Jothi, R.1    Przytycka, T.M.2    Aravind, L.3
  • 19
    • 48249112175 scopus 로고    scopus 로고
    • MPIDB: the microbial protein interaction database
    • 10.1093/bioinformatics/btn285, 2638870, 18556668
    • Goll J, Rajagopala SV, Shiau SC, Wu H, Lamb BT, Uetz P. MPIDB: the microbial protein interaction database. Bioinformatics 2008, 24(15):1743-1744. 10.1093/bioinformatics/btn285, 2638870, 18556668.
    • (2008) Bioinformatics , vol.24 , Issue.15 , pp. 1743-1744
    • Goll, J.1    Rajagopala, S.V.2    Shiau, S.C.3    Wu, H.4    Lamb, B.T.5    Uetz, P.6
  • 20
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • 10.1093/nar/gkh340, 390337, 15034147
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
    • (2004) Nucleic Acids Res , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 21
  • 22
    • 0038437326 scopus 로고    scopus 로고
    • Wikipedia
    • Wikipedia ROC analysis Wikipedia., http://en.wikipedia.org/wiki/Receiver_operating_characteristic
    • ROC analysis
  • 23
    • 0032743092 scopus 로고    scopus 로고
    • MinDE-dependent pole-to-pole oscillation of division inhibitor MinC in Escherichia coli
    • 103778, 10515933
    • Raskin DM, de Boer PA. MinDE-dependent pole-to-pole oscillation of division inhibitor MinC in Escherichia coli. J Bacteriol 1999, 181(20):6419-6424. 103778, 10515933.
    • (1999) J Bacteriol , vol.181 , Issue.20 , pp. 6419-6424
    • Raskin, D.M.1    de Boer, P.A.2
  • 24
    • 84874759493 scopus 로고    scopus 로고
    • Wikipedia
    • Wikipedia ATP-binding cassette transporter Wikipedia., http://en.wikipedia.org/wiki/ATP-binding_cassette_transporter
    • ATP-binding cassette transporter
  • 25
    • 79551521494 scopus 로고    scopus 로고
    • Measuring the evolutionary rewiring of biological networks
    • 10.1371/journal.pcbi.1001050, 3017101, 21253555
    • Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol 2011, 7(1):e1001050. 10.1371/journal.pcbi.1001050, 3017101, 21253555.
    • (2011) PLoS Comput Biol , vol.7 , Issue.1
    • Shou, C.1    Bhardwaj, N.2    Lam, H.Y.3    Yan, K.K.4    Kim, P.M.5    Snyder, M.6    Gerstein, M.B.7
  • 26
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • 10.1016/j.jmb.2003.07.006, 14499603
    • Aloy P, Ceulemans H, Stark A, Russell RB. The relationship between sequence and interaction divergence in proteins. J Mol Biol 2003, 332(5):989-998. 10.1016/j.jmb.2003.07.006, 14499603.
    • (2003) J Mol Biol , vol.332 , Issue.5 , pp. 989-998
    • Aloy, P.1    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 27
    • 33746622998 scopus 로고    scopus 로고
    • Protein-protein interactions more conserved within species than across species
    • 10.1371/journal.pcbi.0020079, 1513270, 16854211
    • Mika S, Rost B. Protein-protein interactions more conserved within species than across species. PLoS Comput Biol 2006, 2(7):e79. 10.1371/journal.pcbi.0020079, 1513270, 16854211.
    • (2006) PLoS Comput Biol , vol.2 , Issue.7
    • Mika, S.1    Rost, B.2


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