메뉴 건너뛰기




Volumn 25, Issue 2, 2010, Pages 327-343

Evolving trees for the retrieval of mass spectrometry-based bacteria fingerprints

Author keywords

Bacteria identification; Evolving tree; Mass spectrometry; Prototype learning; Sparse coding

Indexed keywords

BACTERIA; CLASSIFICATION (OF INFORMATION); CONFORMAL MAPPING; DATA VISUALIZATION; FORESTRY; HIERARCHICAL SYSTEMS; MASS SPECTROMETERS; MASS SPECTROMETRY; SELF ORGANIZING MAPS; TOPOGRAPHY;

EID: 78049433134     PISSN: 02191377     EISSN: 02193116     Source Type: Journal    
DOI: 10.1007/s10115-009-0249-4     Document Type: Article
Times cited : (7)

References (46)
  • 1
    • 50949123272 scopus 로고    scopus 로고
    • Rapid identification and typing of listeria species by matrix-assisted laser desorption ionization-time of flight mass spectrometry
    • Barbuddhe SB, Maier T, Schwarz G, Kostrzewa M, Hof H, Domann E, Chakraborty T, Hain T (2008) Rapid identification and typing of listeria species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 74(17): 5402-5407.
    • (2008) Appl Environ Microbiol , vol.74 , Issue.17 , pp. 5402-5407
    • Barbuddhe, S.B.1    Maier, T.2    Schwarz, G.3    Kostrzewa, M.4    Hof, H.5    Domann, E.6    Chakraborty, T.7    Hain, T.8
  • 2
    • 0032784636 scopus 로고    scopus 로고
    • Neural maps and topographic vector quantization
    • Bauer H-U, Herrmann M, Villmann T (1999) Neural maps and topographic vector quantization. Neural Netw 12(4-5): 659-676.
    • (1999) Neural Netw , vol.12 , Issue.4-5 , pp. 659-676
    • Bauer, H.-U.1    Herrmann, M.2    Villmann, T.3
  • 3
    • 0026898892 scopus 로고
    • Quantifying the neighborhood preservation of self-organizing feature maps
    • Bauer H-U, Pawelzik KR (1992) Quantifying the neighborhood preservation of self-organizing feature maps. IEEE Trans Neural Netw 3(4): 570-579.
    • (1992) IEEE Trans Neural Netw , vol.3 , Issue.4 , pp. 570-579
    • Bauer, H.-U.1    Pawelzik, K.R.2
  • 4
    • 0031101545 scopus 로고    scopus 로고
    • Growing a hypercubical output space in a self-organizing feature map
    • Bauer H-U, Villmann T (1997) Growing a hypercubical output space in a self-organizing feature map. IEEE Trans Neural Netw 8(2): 218-226.
    • (1997) IEEE Trans Neural Netw , vol.8 , Issue.2 , pp. 218-226
    • Bauer, H.-U.1    Villmann, T.2
  • 5
    • 78049417412 scopus 로고    scopus 로고
    • Bruker Daltonik GmbH, Available on
    • Bruker Daltonik GmbH (2008) Bruker BioTyper 2. 0. Available on http://www. bdal. de.
    • (2008) Bruker BioTyper 2.0
  • 6
    • 78049417412 scopus 로고    scopus 로고
    • Bruker Daltonik GmbH, User manual. Available on
    • Bruker Daltonik GmbH (2008) Bruker BioTyper 2. 0, User manual. Available on http://www. bdal. de.
    • (2008) Bruker BioTyper 2.0
  • 7
    • 78049415685 scopus 로고    scopus 로고
    • Bruker Daltonik GmbH, Available on, (Dr. Markus Kostrzewa), Personal Communication
    • Bruker Daltonik GmbH (2008) Bruker listeria and vibrio spectra. Available on http://www. bdal. de (Dr. Markus Kostrzewa), Personal Communication.
    • (2008) Bruker listeria and vibrio spectra
  • 8
    • 70350536514 scopus 로고    scopus 로고
    • Sparcl: an effective and efficient algorithm for mining arbitrary shape-based clusters
    • (in press)
    • Chaoji V, Al Hasan M, Salem S, Zaki MJ (2009) Sparcl: an effective and efficient algorithm for mining arbitrary shape-based clusters. Knowl Inf Syst (in press).
    • (2009) Knowl Inf Syst
    • Chaoji, V.1    Al Hasan, M.2    Salem, S.3    Zaki, M.J.4
  • 10
    • 4644310754 scopus 로고    scopus 로고
    • Identification of tuberculosis bacteria based on shape and color
    • Forero MG, Sroubek F, Cristobal G (2004) Identification of tuberculosis bacteria based on shape and color. Real-time Imaging 10(4): 251-262.
    • (2004) Real-Time Imaging , vol.10 , Issue.4 , pp. 251-262
    • Forero, M.G.1    Sroubek, F.2    Cristobal, G.3
  • 12
    • 38149083538 scopus 로고    scopus 로고
    • Relational neural gas
    • Lecture Notes in Computer Science (LNAI), Springer, Heidelberg
    • Hammer B, Hasenfuss A (2007) Relational neural gas. In: Künstliche Intelligenz 2007, Lecture Notes in Computer Science (LNAI), Springer, Heidelberg, pp 190-204.
    • (2007) Künstliche Intelligenz 2007 , pp. 190-204
    • Hammer, B.1    Hasenfuss, A.2
  • 15
    • 53049098598 scopus 로고    scopus 로고
    • Species identification of oetzis clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests
    • Hollemeyer K, Altmeyer W, Heinzle E, Pitra C (2008) Species identification of oetzis clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests. Rapid Commun Mass Spectr 22: 2751-2767.
    • (2008) Rapid Commun Mass Spectr , vol.22 , pp. 2751-2767
    • Hollemeyer, K.1    Altmeyer, W.2    Heinzle, E.3    Pitra, C.4
  • 16
    • 39749093671 scopus 로고    scopus 로고
    • Highly efficient classification and identification of human pathogenic bacteria by MALDI-TOF-MS
    • Hsieh S-Y, Tseng C-L, Lee Y-S (2008) Highly efficient classification and identification of human pathogenic bacteria by MALDI-TOF-MS. Mol Cell Proteomics 7(2): 448-456.
    • (2008) Mol Cell Proteomics , vol.7 , Issue.2 , pp. 448-456
    • Hsieh, S.-Y.1    Tseng, C.-L.2    Lee, Y.-S.3
  • 17
    • 34248152305 scopus 로고    scopus 로고
    • Identifying bacterial species using CE-MS and SEQUEST with an empirical scoring function
    • Hu A, Lo AA, Chen CT, Lin KC, Ho YP (2007) Identifying bacterial species using CE-MS and SEQUEST with an empirical scoring function. Electrophoresis 28(9): 1387-1392.
    • (2007) Electrophoresis , vol.28 , Issue.9 , pp. 1387-1392
    • Hu, A.1    Lo, A.A.2    Chen, C.T.3    Lin, K.C.4    Ho, Y.P.5
  • 18
    • 34248647608 scopus 로고    scopus 로고
    • Stability of feature selection algorithms: a study on high-dimensional spaces
    • Kalousis A, Prados J, Hilario M (2007) Stability of feature selection algorithms: a study on high-dimensional spaces. Knowl Inf Syst 12(1): 95-116.
    • (2007) Knowl Inf Syst , vol.12 , Issue.1 , pp. 95-116
    • Kalousis, A.1    Prados, J.2    Hilario, M.3
  • 19
    • 4444357465 scopus 로고    scopus 로고
    • Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases
    • Keys CJ, Dare DJ, Sutton H, Wells G, Lunt M, McKenna T, McDowall M, Shah HN (2004) Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases. Infect Genet Evol 4(3): 221-242.
    • (2004) Infect Genet Evol , vol.4 , Issue.3 , pp. 221-242
    • Keys, C.J.1    Dare, D.J.2    Sutton, H.3    Wells, G.4    Lunt, M.5    McKenna, T.6    McDowall, M.7    Shah, H.N.8
  • 20
    • 40049086065 scopus 로고    scopus 로고
    • Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification
    • Khatun J, Hamlett E, Giddings MC (2008) Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. Bioinformatics 24(5): 674-681.
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 674-681
    • Khatun, J.1    Hamlett, E.2    Giddings, M.C.3
  • 21
    • 0000549293 scopus 로고    scopus 로고
    • Self-organizing maps
    • (2nd extended edn). Springer, Berlin
    • Kohonen T (1995) Self-organizing maps. Springer Series in Information Sciences, vol 30 (2nd extended edn). Springer, Berlin (1997).
    • (1997) Springer Series in Information Sciences , vol.30
    • Kohonen, T.1
  • 22
    • 78049440928 scopus 로고    scopus 로고
    • Efficieny of MS + BioTyper based bacteria identification for the clinical market
    • Kostrzewa M (2009) Efficieny of MS + BioTyper based bacteria identification for the clinical market. Personal Communication.
    • (2009) Personal Communication
    • Kostrzewa, M.1
  • 25
    • 61849103486 scopus 로고    scopus 로고
    • Sparse coding neural gas: learning of overcomplete data representations
    • Labusch K, Barth E, Martinetz T (2009) Sparse coding neural gas: learning of overcomplete data representations. Neurocomputing 72: 1547-1555.
    • (2009) Neurocomputing , vol.72 , pp. 1547-1555
    • Labusch, K.1    Barth, E.2    Martinetz, T.3
  • 27
    • 0027632248 scopus 로고
    • Neural-gas' network for vector quantization and its application to time-series prediction
    • Martinetz TM, Berkovich SG, Schulten KJ (1993) 'Neural-gas' network for vector quantization and its application to time-series prediction. IEEE Trans Neural Netw 4(4): 558-569.
    • (1993) IEEE Trans Neural Netw , vol.4 , Issue.4 , pp. 558-569
    • Martinetz, T.M.1    Berkovich, S.G.2    Schulten, K.J.3
  • 28
    • 77956867857 scopus 로고    scopus 로고
    • Mathworks, Accessed on
    • Mathworks (2008) MATLAB statistics-toolbox. Accessed on http://www. mathworks. com.
    • (2008) MATLAB statistics-toolbox
  • 30
    • 0002399288 scopus 로고
    • Neural networks, principle components and subspaces
    • Oja E (1989) Neural networks, principle components and subspaces. Int J Neural Syst 1: 61-68.
    • (1989) Int J Neural Syst , vol.1 , pp. 61-68
    • Oja, E.1
  • 31
    • 0029938380 scopus 로고    scopus 로고
    • Emergence of simple-cell receptive field properties by learning a sparse code for natural images
    • Olshausen BA, Finch DJ (1996) Emergence of simple-cell receptive field properties by learning a sparse code for natural images. Nature 381: 607-609.
    • (1996) Nature , vol.381 , pp. 607-609
    • Olshausen, B.A.1    Finch, D.J.2
  • 32
    • 10844255636 scopus 로고    scopus 로고
    • The evolving tree-a novel self-organizing network for data analysis
    • Pakkanen J, Iivarinen J, Oja E (2004) The evolving tree-a novel self-organizing network for data analysis. Neural Process Lett 20(3): 199-211.
    • (2004) Neural Process Lett , vol.20 , Issue.3 , pp. 199-211
    • Pakkanen, J.1    Iivarinen, J.2    Oja, E.3
  • 33
    • 67349143735 scopus 로고    scopus 로고
    • Characterization and evaluation of similarity measures for pairs of clusterings
    • Pfitzner D, Leibbrandt R, Powers R (2009) Characterization and evaluation of similarity measures for pairs of clusterings. Knowl Inf Syst 19(3): 361-394.
    • (2009) Knowl Inf Syst , vol.19 , Issue.3 , pp. 361-394
    • Pfitzner, D.1    Leibbrandt, R.2    Powers, R.3
  • 34
    • 78049438130 scopus 로고    scopus 로고
    • A new multiobjective clustering technique based on the concepts of stability and symmetry
    • (in press)
    • Saha S, Bandyopadhyay S (2009) A new multiobjective clustering technique based on the concepts of stability and symmetry. Knowl Inf Syst (in press).
    • (2009) Knowl Inf Syst
    • Saha, S.1    Bandyopadhyay, S.2
  • 35
    • 67650242666 scopus 로고    scopus 로고
    • Support vector classification of proteomic profile spectra based on feature extraction with the bi-orthogonal discrete wavelet transform
    • doi: 10. 1007/s00791-008-0087-z
    • Schleif F-M, Lindemann M, Maass P, Diaz M, Decker J, Elssner T, Kuhn M, Thiele H (2008) Support vector classification of proteomic profile spectra based on feature extraction with the bi-orthogonal discrete wavelet transform. Comput Vis Sci. doi: 10. 1007/s00791-008-0087-z.
    • (2008) Comput Vis Sci
    • Schleif, F.-M.1    Lindemann, M.2    Maass, P.3    Diaz, M.4    Decker, J.5    Elssner, T.6    Kuhn, M.7    Thiele, H.8
  • 37
    • 28944441291 scopus 로고    scopus 로고
    • New approaches to identification of bacterial pathogens by surface enhanced laser desorption/ionization time of flight mass spectrometry in concert with artificial neural networks, with special reference to Neisseria gonorrhoeae
    • Schmid O, Ball G, Lancashire L, Culak R, Shah H (2005) New approaches to identification of bacterial pathogens by surface enhanced laser desorption/ionization time of flight mass spectrometry in concert with artificial neural networks, with special reference to Neisseria gonorrhoeae. J Med Microbiol 54: 1205-1211.
    • (2005) J Med Microbiol , vol.54 , pp. 1205-1211
    • Schmid, O.1    Ball, G.2    Lancashire, L.3    Culak, R.4    Shah, H.5
  • 41
    • 12244306238 scopus 로고    scopus 로고
    • Effect of culture conditions on microorganism identification by matrix-assisted laser desorption ionization mass spectrometry
    • Valentine N, Wunschel S, Wunschel D, Petersen C, Wahl K (2005) Effect of culture conditions on microorganism identification by matrix-assisted laser desorption ionization mass spectrometry. Appl Environ Microbiol 71(1): 58-64.
    • (2005) Appl Environ Microbiol , vol.71 , Issue.1 , pp. 58-64
    • Valentine, N.1    Wunschel, S.2    Wunschel, D.3    Petersen, C.4    Wahl, K.5
  • 42
    • 33644899424 scopus 로고    scopus 로고
    • Magnification control in self-organizing maps and neural gas
    • Villmann T, Claussen J-C (2006) Magnification control in self-organizing maps and neural gas. Neural Comput 18(2): 446-469.
    • (2006) Neural Comput , vol.18 , Issue.2 , pp. 446-469
    • Villmann, T.1    Claussen, J.-C.2
  • 43
    • 0031097231 scopus 로고    scopus 로고
    • Topology preservation in self-organizing feature maps: exact definition and measurement
    • Villmann T, Der R, Herrmann M, Martinetz T (1997) Topology preservation in self-organizing feature maps: exact definition and measurement. IEEE Trans Neural Netw 8(2): 256-266.
    • (1997) IEEE Trans Neural Netw , vol.8 , Issue.2 , pp. 256-266
    • Villmann, T.1    Der, R.2    Herrmann, M.3    Martinetz, T.4
  • 44
    • 42049122152 scopus 로고    scopus 로고
    • Exploration of mass-spectrometric data in clinical proteomics using learning vector quantization methods
    • Villmann T, Schleif F-M, Hammer B, Kostrzewa M (2008) Exploration of mass-spectrometric data in clinical proteomics using learning vector quantization methods. Briefing Bioinf 9(2): 129-143.
    • (2008) Briefing Bioinf , vol.9 , Issue.2 , pp. 129-143
    • Villmann, T.1    Schleif, F.-M.2    Hammer, B.3    Kostrzewa, M.4
  • 45
    • 0036631742 scopus 로고    scopus 로고
    • Defining and using microbial spectral databases
    • Wilkes JG, Glover KL, Holcomb M (2002) Defining and using microbial spectral databases. J Am Soc Mass Spectr 13(7): 875-887.
    • (2002) J Am Soc Mass Spectr , vol.13 , Issue.7 , pp. 875-887
    • Wilkes, J.G.1    Glover, K.L.2    Holcomb, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.