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Volumn 15, Issue 1, 2014, Pages

Peak picking NMR spectral data using non-negative matrix factorization

Author keywords

NMR spectrum; Non negative matrix factorization; Peak overlap; Peak picking

Indexed keywords

PROTEIN;

EID: 84893698083     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-46     Document Type: Article
Times cited : (23)

References (35)
  • 1
    • 4344698912 scopus 로고    scopus 로고
    • Automated NMR protein structure calculation
    • Güntert P. Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc 2003, 43:105-125.
    • (2003) Prog Nucl Magn Reson Spectrosc , vol.43 , pp. 105-125
    • Güntert, P.1
  • 2
    • 0028561099 scopus 로고
    • Positive matrix factorization - a nonnegative factor model with optimal utilization of error-estimates of data values
    • Paatero P, Tapper U. Positive matrix factorization - a nonnegative factor model with optimal utilization of error-estimates of data values. Environmetrics 1994, 5:111-126.
    • (1994) Environmetrics , vol.5 , pp. 111-126
    • Paatero, P.1    Tapper, U.2
  • 3
    • 0030954231 scopus 로고    scopus 로고
    • Least squares formulation of robust non-negative factor analysis
    • Paatero P. Least squares formulation of robust non-negative factor analysis. Chemometrics Intellig Lab Syst 1997, 37:23-35.
    • (1997) Chemometrics Intellig Lab Syst , vol.37 , pp. 23-35
    • Paatero, P.1
  • 4
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by non-negative matrix factorization
    • 10.1038/44565, 10548103
    • Lee DD, Seung HS. Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401:788-791. 10.1038/44565, 10548103.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 5
    • 84898964201 scopus 로고    scopus 로고
    • Algorithms for non-negative matrix factorization
    • Lee DD, Seung HS. Algorithms for non-negative matrix factorization. Adv Neur In 2001, 13:556-562.
    • (2001) Adv Neur In , vol.13 , pp. 556-562
    • Lee, D.D.1    Seung, H.S.2
  • 6
    • 84897584251 scopus 로고    scopus 로고
    • Nonnegative matrix factorization: a comprehensive review
    • Wang YX, Zhang YJ. Nonnegative matrix factorization: a comprehensive review. IEEE Trans Knowl Data Eng 2013, 25:1336-1353.
    • (2013) IEEE Trans Knowl Data Eng , vol.25 , pp. 1336-1353
    • Wang, Y.X.1    Zhang, Y.J.2
  • 7
    • 84900510076 scopus 로고    scopus 로고
    • Non-negative matrix factorization with sparseness constraints
    • Hoyer PO. Non-negative matrix factorization with sparseness constraints. J Mach Learn Res 2004, 5:1457-1469.
    • (2004) J Mach Learn Res , vol.5 , pp. 1457-1469
    • Hoyer, P.O.1
  • 9
    • 77950301212 scopus 로고    scopus 로고
    • Non-negative matrix factorization, a new tool for feature extraction: theory and applications
    • Buciu I. Non-negative matrix factorization, a new tool for feature extraction: theory and applications. Int J Comput Commun 2008, 3:67-74.
    • (2008) Int J Comput Commun , vol.3 , pp. 67-74
    • Buciu, I.1
  • 10
    • 33646682646 scopus 로고    scopus 로고
    • Nonnegative matrix factorization for spectral data analysis
    • Pauca VP, Piper J, Plemmons RJ. Nonnegative matrix factorization for spectral data analysis. Linear Algebra Appl 2006, 416:29-47.
    • (2006) Linear Algebra Appl , vol.416 , pp. 29-47
    • Pauca, V.P.1    Piper, J.2    Plemmons, R.J.3
  • 12
    • 43249131130 scopus 로고    scopus 로고
    • Non-negative matrix factorization with alpha-divergence
    • Cichocki A, Lee H, Kim YD, Choi S. Non-negative matrix factorization with alpha-divergence. Pattern Recog Lett 2008, 29:1433-1440.
    • (2008) Pattern Recog Lett , vol.29 , pp. 1433-1440
    • Cichocki, A.1    Lee, H.2    Kim, Y.D.3    Choi, S.4
  • 13
    • 33646528853 scopus 로고    scopus 로고
    • Exploiting discriminant information in nonnegative matrix factorization with application to frontal face verification
    • Zafeiriou S, Tefas A, Buciu I, Pitas I. Exploiting discriminant information in nonnegative matrix factorization with application to frontal face verification. IEEE Trans Neural Networks 2006, 17:683-695.
    • (2006) IEEE Trans Neural Networks , vol.17 , pp. 683-695
    • Zafeiriou, S.1    Tefas, A.2    Buciu, I.3    Pitas, I.4
  • 15
    • 34547844077 scopus 로고    scopus 로고
    • Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis
    • 10.1093/bioinformatics/btm134, 17483501
    • Kim H, Park H. Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis. Bioinformatics 2007, 23:1495-1502. 10.1093/bioinformatics/btm134, 17483501.
    • (2007) Bioinformatics , vol.23 , pp. 1495-1502
    • Kim, H.1    Park, H.2
  • 16
    • 41449100162 scopus 로고    scopus 로고
    • Non-negative matrix factorization of two-dimensional NMR spectra: application to complex mixture analysis
    • 10.1063/1.2816782, 18266430
    • Snyder DA, Zhang F, Robinette SL, Bruschweiler-Li L, Brüschweiler R. Non-negative matrix factorization of two-dimensional NMR spectra: application to complex mixture analysis. J Chem Phys 2008, 128:052313. 10.1063/1.2816782, 18266430.
    • (2008) J Chem Phys , vol.128 , pp. 052313
    • Snyder, D.A.1    Zhang, F.2    Robinette, S.L.3    Bruschweiler-Li, L.4    Brüschweiler, R.5
  • 17
    • 0001442123 scopus 로고
    • A versatile approach toward the partially automatic recognition of cross peaks in 2D 1H NMR spectra
    • Kleywegt GJ, Boelens R, Kaptein R. A versatile approach toward the partially automatic recognition of cross peaks in 2D 1H NMR spectra. J Magn Reson 1990, 88:601-608.
    • (1990) J Magn Reson , vol.88 , pp. 601-608
    • Kleywegt, G.J.1    Boelens, R.2    Kaptein, R.3
  • 18
    • 34249765651 scopus 로고
    • NMR View - a computer program for the visualization and analysis of NMR data
    • 10.1007/BF00404272, 22911360
    • Johnson BA, Blevins RA. NMR View - a computer program for the visualization and analysis of NMR data. J Biomol NMR 1994, 4:603-614. 10.1007/BF00404272, 22911360.
    • (1994) J Biomol NMR , vol.4 , pp. 603-614
    • Johnson, B.A.1    Blevins, R.A.2
  • 20
    • 0032247126 scopus 로고    scopus 로고
    • Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY
    • 10.1006/jmre.1998.1570, 9878459
    • Koradi R, Billeter M, Engeli M, Güntert P, Wüthrich K. Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J Magn Reson 1998, 135:288-297. 10.1006/jmre.1998.1570, 9878459.
    • (1998) J Magn Reson , vol.135 , pp. 288-297
    • Koradi, R.1    Billeter, M.2    Engeli, M.3    Güntert, P.4    Wüthrich, K.5
  • 21
  • 22
    • 66349110095 scopus 로고    scopus 로고
    • PICKY: a novel SVD-based NMR spectra peak picking method
    • 10.1093/bioinformatics/btp225, 2687979, 19477998
    • Alipanahi B, Gao X, Karakoc E, Donaldson L, Li M. PICKY: a novel SVD-based NMR spectra peak picking method. Bioinformatics 2009, 25:i268-i275. 10.1093/bioinformatics/btp225, 2687979, 19477998.
    • (2009) Bioinformatics , vol.25
    • Alipanahi, B.1    Gao, X.2    Karakoc, E.3    Donaldson, L.4    Li, M.5
  • 23
    • 41149124394 scopus 로고    scopus 로고
    • Hyperdimensional NMR spectroscopy with nonlinear sampling
    • 10.1021/ja077282o, 18311971
    • Jaravine VA, Zhuravleva AV, Permi P, Ibraghimov I, Orekhov VY. Hyperdimensional NMR spectroscopy with nonlinear sampling. J Am Chem Soc 2008, 130:3927-3936. 10.1021/ja077282o, 18311971.
    • (2008) J Am Chem Soc , vol.130 , pp. 3927-3936
    • Jaravine, V.A.1    Zhuravleva, A.V.2    Permi, P.3    Ibraghimov, I.4    Orekhov, V.Y.5
  • 25
    • 0031675604 scopus 로고    scopus 로고
    • Accelerating the EMML algorithm and related iterative algorithms by rescaled block-iterative methods
    • Byrne CL. Accelerating the EMML algorithm and related iterative algorithms by rescaled block-iterative methods. Ieee T Image Process 1998, 7:100-109.
    • (1998) Ieee T Image Process , vol.7 , pp. 100-109
    • Byrne, C.L.1
  • 26
    • 0022736170 scopus 로고
    • An iterative image space reconstruction algorithm suitable for volume ECT
    • Daube-Witherspoon ME, Muehllehner G. An iterative image space reconstruction algorithm suitable for volume ECT. IEEE Trans Med Imaging 1986, 5:61-66.
    • (1986) IEEE Trans Med Imaging , vol.5 , pp. 61-66
    • Daube-Witherspoon, M.E.1    Muehllehner, G.2
  • 27
    • 0023364564 scopus 로고
    • On the convergence of the iterative image space reconstruction algorithm for volume ECT
    • De Pierro AR. On the convergence of the iterative image space reconstruction algorithm for volume ECT. IEEE Trans Med Imaging 1987, 6:174-175.
    • (1987) IEEE Trans Med Imaging , vol.6 , pp. 174-175
    • De Pierro, A.R.1
  • 28
    • 0038685059 scopus 로고    scopus 로고
    • A new efficient method for determining the number of components in PARAFAC models
    • Bro R, Kiers HAL. A new efficient method for determining the number of components in PARAFAC models. J Chemometrics 2003, 17:274-286.
    • (2003) J Chemometrics , vol.17 , pp. 274-286
    • Bro, R.1    Kiers, H.A.L.2
  • 29
    • 0034183641 scopus 로고    scopus 로고
    • Three-mode principal components analysis: choosing the numbers of components and sensitivity to local optima
    • 10.1348/000711000159132, 10895519
    • Timmerman ME, Kiers HAL. Three-mode principal components analysis: choosing the numbers of components and sensitivity to local optima. Br J Math Stat Psychol 2000, 53:1-16. 10.1348/000711000159132, 10895519.
    • (2000) Br J Math Stat Psychol , vol.53 , pp. 1-16
    • Timmerman, M.E.1    Kiers, H.A.L.2
  • 30
    • 33745135758 scopus 로고    scopus 로고
    • Selecting among three-mode principal component models of different types and complexities: a numerical convex hull based method
    • Ceulemans E, Kiers HAL. Selecting among three-mode principal component models of different types and complexities: a numerical convex hull based method. Brit J Math Stat Psy 2006, 59:133-150.
    • (2006) Brit J Math Stat Psy , vol.59 , pp. 133-150
    • Ceulemans, E.1    Kiers, H.A.L.2
  • 34
    • 79953871014 scopus 로고    scopus 로고
    • Structural insights into Rcs phosphotransfer: the newly identified RcsD-ABL domain enhances interaction with the response regulator RcsB
    • 10.1016/j.str.2011.01.012, 21481780
    • Schmöe K, Rogov VV, Rogova NY, Löhr F, Güntert P, Bernhard F, Dötsch V. Structural insights into Rcs phosphotransfer: the newly identified RcsD-ABL domain enhances interaction with the response regulator RcsB. Structure 2011, 19:577-587. 10.1016/j.str.2011.01.012, 21481780.
    • (2011) Structure , vol.19 , pp. 577-587
    • Schmöe, K.1    Rogov, V.V.2    Rogova, N.Y.3    Löhr, F.4    Güntert, P.5    Bernhard, F.6    Dötsch, V.7
  • 35
    • 84864484147 scopus 로고    scopus 로고
    • A new algorithm for reliable and general NMR resonance assignment
    • 10.1021/ja305091n, 22794163
    • Schmidt E, Güntert P. A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc 2012, 134:12817-12829. 10.1021/ja305091n, 22794163.
    • (2012) J Am Chem Soc , vol.134 , pp. 12817-12829
    • Schmidt, E.1    Güntert, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.