Toward digital staining using imaging mass spectrometry and random forests

Journal of Proteome Research

Volumn 8, Issue 7, 2009, Pages 3558-3567

  Hanselmann, Michael ^a   Köthe, Ullrich ^a   Kirchner, Marc ^a   Renard, Bernhard Y ^a   Amstalden, Erika R ^b   Glunde, Kristine ^c   Heeren, Ron M A ^c   Hamprecht, Fred A ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b FOM INSTITUTE AMOLF   (Netherlands)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bioinformatics; Hyperspectral images; Imaging mass spectrometry; Markov Random Fields; Random Forest classification; Smoothing; Spectral images

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; DIGITAL IMAGING; HUMAN; HUMAN CELL; IMAGING MASS SPECTROMETRY; LABORATORY AUTOMATION; MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; RANDOM FOREST; SENSITIVITY ANALYSIS; STAINING; TISSUE TYPING;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MARKOV CHAINS; MASS SPECTROMETRY; MODELS, STATISTICAL; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; PROTEOMICS; SOFTWARE;

EID: 67650370012     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900253y     Document Type: Article

References (49)

1. Uhlen, M.; et al. Mol. Cell. Proteomics 2005, 4, 1920-32.
2. Caprioli, R. M.; Farmer, T. B.; Gile, J. Anal. Chem. 1997, 69, 4751-4760.
3. McDonnell, L. A.; Heeren, R. M. A. Mass Spectrom. Rev. 2006, 26, 606-643.
4. Seeley, E.; Caprioli, R. M. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 18126-18131.
5. Chaurand, P.; Schwartz, S. A.; Caprioli, R. M. Curr. Opin. Chem. Biol. 2002, 6, 676-681.
6. Simpkins, F.; Czechowicz, J. A.; Liotta, L.; Kohn, E. C. Pharmacogenomics 2005, 6, 647-653.
7. Yanagisawa, K.; Shyr, Y.; Xu, B.; Massion, P.; Larsen, P.; White, B.; Roberts, J.; Edgerton, M.; Gonzalez, A.; Nadaf, S.; Moore, J. H.; Caprioli, R. M.; Carbone, D. P. Lancet 2003, 362, 433-439.
8. Rohner, T. C.; Staab, D.; Stoeckli, M. Mech. Ageing Dev. 2005, 126, 177-185.
9. Belu, A. M.; Davies, M. C.; Newton, J. M.; Patel, N. Anal. Chem. 2000, 72, 5625-5638.
10. Cornett, D. S.; Frappier, S. L.; Caprioli, R. M. Anal. Chem. 2008, 80, 5648-5653.
11. Broersen, A.; van Liere, R.; Heeren, R. M. A. Proc. 5th IASTED Intern. Conf. Visualization, Imaging, Image Process. 2005, 540-545.
12. Hanselmann, M.; Kirchner, M.; Renard, B. Y.; Amstalden, E. R.; Glunde, K.; Heeren, R. M. A.; Hamprecht, F. A. Anal. Chem. 2008, 80, 9649-9658.
13. Deininger, S.-O.; Ebert, M.; Fütterer, A.; Gerhard, M.; Röcken, C. J. Proteome Res. 2008, 7, 5230-5236.
14. Schölkopf, B.; Smola, A. Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond; MIT Press: Cambridge, MA, 2002.
15. Breiman, L. Machine Learn. 2001, 45, 5-32.
16. Sanders, M. E.; Dias, E. C.; Xu, B. J.; Mobley, J. A.; Billheimer, D.; Roder, H.; Grigorieva, J.; Dowsett, M.; Arteaga, C. L.; Caprioli, R. M. J. Proteome Res. 2008, 7, 1500-1507.
17. Taguchi, F.; et al. J. Natl. Cancer Inst. 2007, 99, 838-846.
18. Schwamborn, K.; Krieg, R. C.; Reska, M.; Jakse, G.; Knuechel, R.; Wellmann, A. Int. J. Mol. Med. 2007, 20, 155-159.
19. Gerhard, M.; Deininger, S.-O.; Schleif, F.-M. Symp. Comput.-Based Med. Syst. 2007, 403-405.
20. Groseclose, M. R.; Massion, P. P.; Chaurand, P.; Caprioli, R. M. Proteomics 2008, 8, 3715-3724.
21. Schwartz, S. A.; Weil, R. J.; Thompson, R. C.; Shyr, Y.; Moore, J. H.; Toms, S. A.; Johnson, M.; Caprioli, R. Cancer Res. 2005, 65, 7674.
22. Barrett, J. H.; Cairns, D. A. Stat. Appl. Genet. Mol. Biol. 2008, 7, article 4.
23. Ge, G.; Wong, G. W. BMC Bioinform. 2008, 9, 275-287.
24. Ulintz, P. J.; Zhu, J.; Qin, Z. S.; Andrews, P. C. Mol. Cell. Proteomics 2006, 5, 497-509.
25. Datta, S.; DePadilla, L. M. Stat. Methodol. 2006, 3, 79-92.
26. Hand, D. J. Stat. Appl. Genet. Mol. Biol. 2008, 7, article 15.
27. Geurts, P.; Fillet, M.; de Seny, D.; Meuwis, M.-A.; Malaise, M.; Merville, M.-P.; Wehenkel, L. Bioinformatics 2005, 21, 3138-3145.
28. Izmirlian, G. Ann. N.Y. Acad. Sci. 2005, 1020, 154-174.
29. Gislason, P. O.; Benediktsson, J. A.; Sveinsson, J. R. Pattern Recognition Lett. 2006, 27, 294-300.
30. Gao, D.; Zhang, Y.-X.; Zhao, Y.-H. Res. Astron. Astrophys. 2009, 9, 220-226.
31. Menze, B. H.; Kelm, B. M.; Weber, M. A.; Bachert, P.; Hamprecht, F. A. Magn. Reson. Med. 2008, 59, 1457-66.
32. Diaz-Uriate, R.; Alvarez de Andrs, S. BMC Bioinform. 2006, 7, 1-13.
33. Abu-Nimeh, S.; Nappa, D.; Wang, X.; Nair, S. ACM Proc. Antiphishing Work. Groups 2nd Annu. eCrime Researchers Summit 2007, 8, 60-69.
34. Pal, M. Int. J. Remote Sensing 2005, 26, 217-222.
35. Geman, S.; Geman, D. IEEE Trans. Pattern Anal. Machine Intell. 1984, 6, 721-741.
36. Bishop, C. M. Pattern Recognition and Machine Learning; Springer: New York, 2007.
37. Welk, M.; Feddern, C.; Burgeth, B.; Weickert, J. Pattern Recognit. Lecture Notes Comput. Sci. 2003, 2781, 1724.
38. Hastie, T.; Tibshirani, R.; Friedman, J. The Elements of Statistical Learning; Springer: New York, 2001.
39. Winkler, G. Image Analysis, Random Fields and Markov Chain Monte Carlo Methods: A Mathematical Introduction; Springer: New York, 2003.
40. Pearl, J. Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference; Morgan Kaufmann: San Mateo, CA, 1988.
41. Komodakis, N.; Tziritas, G. IEEE Trans. Image Process. 2007, 16, 2649-2661.
42. Jähne, B. Digital image processing: concepts, algorithms, and scientific applications, 3rd ed.; Springer: New York, 1995.
43. Lerch, K. M. Sc. thesis, University of Heidelberg, Germany, 2006.
44. Chen, C.; Liaw, A.; Breiman, L. Using Random Forest to Learn Imbalanced Data; Technical Report, 2004; pp 1-12.
45. Morris, J. S.; Coombes, K. R.; Koomen, J.; Baggerly, K. A.; Kobayashi, R. Bioinformatics 2005, 21, 1764-1775.
46. Tibshirani, R.; Hastie, T.; Narasimhan, B.; Soltys, S.; Shi, G.; Koong, A.; Le, Q.-T. Bioinformatics 2004, 20, 3034-3044.
47. Murphy, K. Bayes Net Toolbox for MATLAB, http://www.cs.ubc.ca/murphyk/ Software/BNT/bnt.html, 1997-2002, accessed October 2008.
48. Glunde, K.; Jie, C.; Bhujwalla, Z. M. Neoplasia 2006, 8, 758-771.
49. Glunde, K.; Ackerstaff, E.; Natarajan, K.; Artemov, D.; Bhujwalla, Z. M. Magn. Reson. Med. 2002, 48, 819-825.