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Volumn 283, Issue 1, 2011, Pages 44-52

Adaptive compressive learning for prediction of protein-protein interactions from primary sequence

Author keywords

Compressed sensing; Nyquist sampling; Protein protein interactions prediction; Sequential discrete representation

Indexed keywords

ALGORITHM; BIOLOGICAL ANALYSIS; EXPERIMENTAL STUDY; GENETIC ANALYSIS; PROTEIN; SAMPLING; THEORETICAL STUDY; YEAST;

EID: 79958028560     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.05.023     Document Type: Article
Times cited : (51)

References (73)
  • 1
    • 0038825237 scopus 로고    scopus 로고
    • Stochastic proximity embedding
    • Agrafiotis D.K. Stochastic proximity embedding. J. Comput. Chem. 2003, 24:1215-1221.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1215-1221
    • Agrafiotis, D.K.1
  • 2
    • 33750095186 scopus 로고    scopus 로고
    • Rotation forest: a new classifier ensemble method
    • Alonso C. Rotation forest: a new classifier ensemble method. IEEE Trans. Pattern Anal. 2006, 28:1619-1630.
    • (2006) IEEE Trans. Pattern Anal. , vol.28 , pp. 1619-1630
    • Alonso, C.1
  • 3
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • Aloy P., Russell R.B. Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. USA 2002, 99:5896-5901.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 4
    • 0037250158 scopus 로고    scopus 로고
    • InterPreTS: protein interaction prediction through tertiary structure
    • Aloy P., Russell R.B. InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 2003, 19:161-162.
    • (2003) Bioinformatics , vol.19 , pp. 161-162
    • Aloy, P.1    Russell, R.B.2
  • 5
    • 55649115527 scopus 로고    scopus 로고
    • A simple proof of the restricted isometry property for random matrices
    • Baraniuk R., Davenport M., DeVore R., Wakin M. A simple proof of the restricted isometry property for random matrices. Constr. Approx. 2008, 28:253-263.
    • (2008) Constr. Approx. , vol.28 , pp. 253-263
    • Baraniuk, R.1    Davenport, M.2    DeVore, R.3    Wakin, M.4
  • 6
    • 24744435534 scopus 로고    scopus 로고
    • Kernel methods for predicting protein-protein interactions
    • Ben-Hur A., Noble W.S. Kernel methods for predicting protein-protein interactions. Bioinformatics 2005, 21(Suppl. 1):i38-i46.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Ben-Hur, A.1    Noble, W.S.2
  • 7
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • Bock J.R., Gough D.A. Predicting protein-protein interactions from primary structure. Bioinformatics 2001, 17:455-460.
    • (2001) Bioinformatics , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 9
    • 79960570900 scopus 로고    scopus 로고
    • Compressed learning: universal sparse dimensionality reduction and learning in the measurement domain
    • Calderbank, R., Jafarpour, S., Schapire, R., 2009. Compressed learning: universal sparse dimensionality reduction and learning in the measurement domain, http://dsp.rice.edu/files/cs/cl.pdf.
    • (2009)
    • Calderbank, R.1    Jafarpour, S.2    Schapire, R.3
  • 10
    • 42649140570 scopus 로고    scopus 로고
    • The restricted isometry property and its implications for compressed sensing
    • Candes E.J. The restricted isometry property and its implications for compressed sensing. C.R. Math. 2008, 346:589-592.
    • (2008) C.R. Math. , vol.346 , pp. 589-592
    • Candes, E.J.1
  • 11
    • 33947416035 scopus 로고    scopus 로고
    • Near-optimal signal recovery from random projections: universal encoding strategies?
    • Candes E.J., Tao T. Near-optimal signal recovery from random projections: universal encoding strategies?. IEEE Trans. Inform. Theory 2006, 52:5406-5425.
    • (2006) IEEE Trans. Inform. Theory , vol.52 , pp. 5406-5425
    • Candes, E.J.1    Tao, T.2
  • 12
    • 33745604236 scopus 로고    scopus 로고
    • Stable signal recovery from incomplete and inaccurate measurements
    • Candes E.J., Romberg J.K., Tao T. Stable signal recovery from incomplete and inaccurate measurements. Commun. Pur. Appl. Math 2006, 59:1207-1223.
    • (2006) Commun. Pur. Appl. Math , vol.59 , pp. 1207-1223
    • Candes, E.J.1    Romberg, J.K.2    Tao, T.3
  • 13
    • 79960571758 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines. Software available at:
    • Chang, C.C., Lin, C.J., 2001. LIBSVM: a library for support vector machines. Software available at: http://www.csie.ntu.edu.tw/cjlin/libsvm.
    • (2001)
    • Chang, C.C.1    Lin, C.J.2
  • 15
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein cellular attributes using pseudo-amino acid composition
    • Chou K.C. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins 2001, 43:246-255.
    • (2001) Proteins , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 16
    • 33748944288 scopus 로고    scopus 로고
    • Predicting protein subcellular location by fusing multiple classifiers
    • Chou K.C., Shen H.B. Predicting protein subcellular location by fusing multiple classifiers. J. Cell. Biochem. 2006, 99:517-527.
    • (2006) J. Cell. Biochem. , vol.99 , pp. 517-527
    • Chou, K.C.1    Shen, H.B.2
  • 17
    • 33745759451 scopus 로고    scopus 로고
    • Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization
    • Chou K.C., Shen H.B. Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization. Biochem. Biophys. Res. Commun. 2006, 347:150-157.
    • (2006) Biochem. Biophys. Res. Commun. , vol.347 , pp. 150-157
    • Chou, K.C.1    Shen, H.B.2
  • 18
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • Chou K.C., Shen H.B. Recent progress in protein subcellular location prediction. Anal. Biochem. 2007, 370:1-16.
    • (2007) Anal. Biochem. , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 19
    • 34249318001 scopus 로고    scopus 로고
    • Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites
    • Chou K.C., Shen H.B. Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J. Proteome Res. 2007, 6:1728-1734.
    • (2007) J. Proteome Res. , vol.6 , pp. 1728-1734
    • Chou, K.C.1    Shen, H.B.2
  • 20
    • 75149112324 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using an ensemble method
    • Deng L., Guan J., Dong Q., Zhou S. Prediction of protein-protein interaction sites using an ensemble method. BMC Bioinf. 2009, 10:426.
    • (2009) BMC Bioinf. , vol.10 , pp. 426
    • Deng, L.1    Guan, J.2    Dong, Q.3    Zhou, S.4
  • 21
    • 77951469170 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions from primary sequences
    • Dong Q.W., Zhou S.G., Liu X. Prediction of protein-protein interactions from primary sequences. Int. J. Data Min. Bioinf. 2010, 4:211-227.
    • (2010) Int. J. Data Min. Bioinf. , vol.4 , pp. 211-227
    • Dong, Q.W.1    Zhou, S.G.2    Liu, X.3
  • 23
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature 1989, 340:245-246.
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 24
    • 0033564491 scopus 로고    scopus 로고
    • Toward evidence-based medical statistics. 1: the P value fallacy
    • Goodman S.N. Toward evidence-based medical statistics. 1: the P value fallacy. Ann. Intern. Med. 1999, 130:995-1004.
    • (1999) Ann. Intern. Med. , vol.130 , pp. 995-1004
    • Goodman, S.N.1
  • 25
    • 0004125042 scopus 로고
    • L. Erlbaum Associates, Hillsdale, N.J.
    • Gorsuch R.L. Factor Analysis 1983, L. Erlbaum Associates, Hillsdale, N.J.
    • (1983) Factor Analysis
    • Gorsuch, R.L.1
  • 26
    • 44349159560 scopus 로고    scopus 로고
    • Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    • Guo Y., Yu L., Wen Z., Li M. Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucl. Acids Res. 2008, 36:3025-3030.
    • (2008) Nucl. Acids Res. , vol.36 , pp. 3025-3030
    • Guo, Y.1    Yu, L.2    Wen, Z.3    Li, M.4
  • 27
    • 24944442468 scopus 로고    scopus 로고
    • Effect of sampling on topology predictions of protein-protein interaction networks
    • Han J.-D.J., Dupuy D., Bertin N., Cusick M.E., Vidal M. Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol. 2005, 23:839-844.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 839-844
    • Han, J.-D.J.1    Dupuy, D.2    Bertin, N.3    Cusick, M.E.4    Vidal, M.5
  • 30
    • 68249127556 scopus 로고    scopus 로고
    • Improving protein localization prediction using amino acid group based physichemical encoding
    • Hu J.J., Zhang F. Improving protein localization prediction using amino acid group based physichemical encoding. Bioinf. Comput. Biol. Proc. 2009, 5462:248-258.
    • (2009) Bioinf. Comput. Biol. Proc. , vol.5462 , pp. 248-258
    • Hu, J.J.1    Zhang, F.2
  • 34
    • 0031381525 scopus 로고    scopus 로고
    • Wrappers for feature subset selection
    • Kohavi R., John G.H. Wrappers for feature subset selection. Artif. Intell. 1997, 97:273-324.
    • (1997) Artif. Intell. , vol.97 , pp. 273-324
    • Kohavi, R.1    John, G.H.2
  • 35
    • 33646852452 scopus 로고    scopus 로고
    • Prediction of mitochondrial proteins using support vector machine and hidden Markov model
    • Kumar M., Verma R., Raghava G.P. Prediction of mitochondrial proteins using support vector machine and hidden Markov model. J. Biol. Chem. 2006, 281:5357-5363.
    • (2006) J. Biol. Chem. , vol.281 , pp. 5357-5363
    • Kumar, M.1    Verma, R.2    Raghava, G.P.3
  • 36
    • 38649127567 scopus 로고    scopus 로고
    • Identification of DNA-binding proteins using support vector machines and evolutionary profiles
    • Kumar M., Gromiha M.M., Raghava G.P. Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinf. 2007, 8:463.
    • (2007) BMC Bioinf. , vol.8 , pp. 463
    • Kumar, M.1    Gromiha, M.M.2    Raghava, G.P.3
  • 38
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 39
    • 13244265581 scopus 로고    scopus 로고
    • Information assessment on predicting protein-protein interactions
    • Lin N., Wu B., Jansen R., Gerstein M., Zhao H. Information assessment on predicting protein-protein interactions. BMC Bioinf. 2004, 5:154.
    • (2004) BMC Bioinf. , vol.5 , pp. 154
    • Lin, N.1    Wu, B.2    Jansen, R.3    Gerstein, M.4    Zhao, H.5
  • 40
    • 60349114820 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions based on PseAA composition and hybrid feature selection
    • Liu L., Cai Y., Lu W., Feng K., Peng C., Niu B. Prediction of protein-protein interactions based on PseAA composition and hybrid feature selection. Biochem. Biophys. Res. Commun. 2009, 380:318-322.
    • (2009) Biochem. Biophys. Res. Commun. , vol.380 , pp. 318-322
    • Liu, L.1    Cai, Y.2    Lu, W.3    Feng, K.4    Peng, C.5    Niu, B.6
  • 41
    • 13444262436 scopus 로고    scopus 로고
    • Predicting protein-protein interactions using signature products
    • Martin S., Roe D., Faulon J.L. Predicting protein-protein interactions using signature products. Bioinformatics 2005, 21:218-226.
    • (2005) Bioinformatics , vol.21 , pp. 218-226
    • Martin, S.1    Roe, D.2    Faulon, J.L.3
  • 42
    • 27844440887 scopus 로고    scopus 로고
    • Hyperplanes for predicting protein-protein interactions
    • Nanni L. Hyperplanes for predicting protein-protein interactions. Neurocomputing 2005, 69:257-263.
    • (2005) Neurocomputing , vol.69 , pp. 257-263
    • Nanni, L.1
  • 43
    • 32544454675 scopus 로고    scopus 로고
    • Experimental comparison of one-class classifiers for online signature verification
    • Nanni L. Experimental comparison of one-class classifiers for online signature verification. Neurocomputing 2006, 69:869-873.
    • (2006) Neurocomputing , vol.69 , pp. 869-873
    • Nanni, L.1
  • 44
    • 33745190057 scopus 로고    scopus 로고
    • MppS: an ensemble of support vector machine based on multiple physicochemical properties of amino acids
    • Nanni L., Lumini A. MppS: an ensemble of support vector machine based on multiple physicochemical properties of amino acids. Neurocomputing 2006, 69:1688-1690.
    • (2006) Neurocomputing , vol.69 , pp. 1688-1690
    • Nanni, L.1    Lumini, A.2
  • 45
    • 33646871614 scopus 로고    scopus 로고
    • An ensemble of K-local hyperplanes for predicting protein-protein interactions
    • Nanni L., Lumini A. An ensemble of K-local hyperplanes for predicting protein-protein interactions. Bioinformatics 2006, 22:1207-1210.
    • (2006) Bioinformatics , vol.22 , pp. 1207-1210
    • Nanni, L.1    Lumini, A.2
  • 46
    • 77953934865 scopus 로고    scopus 로고
    • High performance set of PseAAC and sequence based descriptors for protein classification
    • Nanni L., Brahnam S., Lumini A. High performance set of PseAAC and sequence based descriptors for protein classification. J. Theor. Biol. 2010, 266:1-10.
    • (2010) J. Theor. Biol. , vol.266 , pp. 1-10
    • Nanni, L.1    Brahnam, S.2    Lumini, A.3
  • 48
    • 77951225212 scopus 로고    scopus 로고
    • Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties
    • Ou Y.Y., Chen S.A., Gromiha M.M. Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties. Proteins 2010, 78:1789-1797.
    • (2010) Proteins , vol.78 , pp. 1789-1797
    • Ou, Y.Y.1    Chen, S.A.2    Gromiha, M.M.3
  • 50
    • 1642513708 scopus 로고    scopus 로고
    • Conservation of protein-protein interactions-lessons from ascomycota
    • Pagel P., Mewes H.W., Frishman D. Conservation of protein-protein interactions-lessons from ascomycota. Trends Genet. 2004, 20:72-76.
    • (2004) Trends Genet. , vol.20 , pp. 72-76
    • Pagel, P.1    Mewes, H.W.2    Frishman, D.3
  • 51
    • 9244239761 scopus 로고    scopus 로고
    • A domain interaction map based on phylogenetic profiling
    • Pagel P., Wong P., Frishman D. A domain interaction map based on phylogenetic profiling. J. Mol. Biol. 2004, 344:1331-1346.
    • (2004) J. Mol. Biol. , vol.344 , pp. 1331-1346
    • Pagel, P.1    Wong, P.2    Frishman, D.3
  • 52
  • 54
    • 77957356489 scopus 로고    scopus 로고
    • Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features
    • Pan X.Y., Zhang Y.N., Shen H.B. Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features. J. Proteome Res. 2010, 9:4992-5001.
    • (2010) J. Proteome Res. , vol.9 , pp. 4992-5001
    • Pan, X.Y.1    Zhang, Y.N.2    Shen, H.B.3
  • 55
    • 77950514410 scopus 로고    scopus 로고
    • Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences
    • Park Y. Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences. BMC Bioinf. 2009, 10:419.
    • (2009) BMC Bioinf. , vol.10 , pp. 419
    • Park, Y.1
  • 56
    • 48349125978 scopus 로고    scopus 로고
    • Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences
    • Pitre S., North C., Alamgir M., Jessulat M., Chan A., Luo X., Green J.R., Dumontier M., Dehne F., Golshani A. Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucl. Acids Res. 2008, 36:4286-4294.
    • (2008) Nucl. Acids Res. , vol.36 , pp. 4286-4294
    • Pitre, S.1    North, C.2    Alamgir, M.3    Jessulat, M.4    Chan, A.5    Luo, X.6    Green, J.R.7    Dumontier, M.8    Dehne, F.9    Golshani, A.10
  • 58
    • 70449347879 scopus 로고    scopus 로고
    • Amino-acid residue association models for large scale protein-protein interaction prediction
    • Rao R., Tun K., Lakshminarayanan S., Dhar P.K. Amino-acid residue association models for large scale protein-protein interaction prediction. In Silico Biol. 2009, 9:179-194.
    • (2009) In Silico Biol. , vol.9 , pp. 179-194
    • Rao, R.1    Tun, K.2    Lakshminarayanan, S.3    Dhar, P.K.4
  • 59
    • 0033669189 scopus 로고    scopus 로고
    • A network of protein-protein interactions in yeast
    • Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 2000, 18:1257-1261.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1257-1261
    • Schwikowski, B.1    Uetz, P.2    Fields, S.3
  • 60
    • 33847668306 scopus 로고    scopus 로고
    • Hum-mPLoc: an ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites
    • Shen H.B., Chou K.C. Hum-mPLoc: an ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites. Biochem. Biophys. Res. Commun. 2007, 355:1006-1011.
    • (2007) Biochem. Biophys. Res. Commun. , vol.355 , pp. 1006-1011
    • Shen, H.B.1    Chou, K.C.2
  • 61
    • 37549004451 scopus 로고    scopus 로고
    • PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition
    • Shen H.B., Chou K.C. PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition. Anal. Biochem. 2008, 373:386-388.
    • (2008) Anal. Biochem. , vol.373 , pp. 386-388
    • Shen, H.B.1    Chou, K.C.2
  • 67
    • 46249133956 scopus 로고    scopus 로고
    • HSEpred: predict half-sphere exposure from protein sequences
    • Song J., Tan H., Takemoto K., Akutsu T. HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics 2008, 24:1489-1497.
    • (2008) Bioinformatics , vol.24 , pp. 1489-1497
    • Song, J.1    Tan, H.2    Takemoto, K.3    Akutsu, T.4
  • 68
    • 70449707137 scopus 로고    scopus 로고
    • Evaluation of different domain-based methods in protein interaction prediction
    • Ta H.X., Holm L. Evaluation of different domain-based methods in protein interaction prediction. Biochem. Biophys. Res. Commun. 2009, 390:357-362.
    • (2009) Biochem. Biophys. Res. Commun. , vol.390 , pp. 357-362
    • Ta, H.X.1    Holm, L.2
  • 69
    • 64649083745 scopus 로고    scopus 로고
    • Signal recovery from random measurements via orthogonal matching pursuit
    • Tropp J.A., Gilbert A.C. Signal recovery from random measurements via orthogonal matching pursuit. IEEE Trans. Inform. Theory 2007, 53:4655-4666.
    • (2007) IEEE Trans. Inform. Theory , vol.53 , pp. 4655-4666
    • Tropp, J.A.1    Gilbert, A.C.2
  • 70
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    • Xenarios I., Salwinski L., Duan X.J., Higney P., Kim S.M., Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 2002, 30:303-305.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.M.5    Eisenberg, D.6
  • 71
    • 78650128404 scopus 로고    scopus 로고
    • Computational methods for the prediction of protein-protein interactions
    • Xia J.F., Wang S.L., Lei Y.K. Computational methods for the prediction of protein-protein interactions. Protein Pept. Lett. 2010, 17:1069-1078.
    • (2010) Protein Pept. Lett. , vol.17 , pp. 1069-1078
    • Xia, J.F.1    Wang, S.L.2    Lei, Y.K.3
  • 72
    • 54049091165 scopus 로고    scopus 로고
    • Sequence based residue depth prediction using evolutionary information and predicted secondary structure
    • Zhang H., Zhang T., Chen K., Shen S., Ruan J., Kurgan L. Sequence based residue depth prediction using evolutionary information and predicted secondary structure. BMC Bioinf. 2008, 9:388.
    • (2008) BMC Bioinf. , vol.9 , pp. 388
    • Zhang, H.1    Zhang, T.2    Chen, K.3    Shen, S.4    Ruan, J.5    Kurgan, L.6


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