Bibliography

1

Z. B. Alfassi.
On the normalization of a mass spectrum for comparison of two spectra.
Journal of The American Society for Mass Spectrometry, 15(3):385-387, 2004.

2

A. Barla, G. Jurman, S. Riccadonna, S. Merler, M. Chierici, and C. Furlanello.
Machine learning methods for predictive proteomics.
Briefings in Bioinformatics, 9(2):119-128, 2008.

3

J. B. Breen, F. G. Hopwood, K. L. Williams, and M. R. Wilkins.
Automatic Poisson peak harvesting for high throughput protein identification.
Electrophoresis, 21:2243-2251, 2000.

4

Y. Chen, V. Kamat, E. R. Dougherty, M. L. Bittner, P. S. Meltzer, and J. M. Trent.
Ratio statistics of gene expression levels and applications to microarray data analysis.
Bioinformatics, 18(9):1207-1215, 2002.

5

K. R. Coombes, K. A. Baggerly, and J. S. Morris.
Pre-processing mass spectrometry data.
In W. Dubitzky, M. Granzow, and D. Berrar, editors, Fundamentals of Data Mining in Genomics and Proteomics, pages 79-102. Springer, 2007.

6

K. R. Coombes, S. Tsavachidis, J. S. Morris, K. A. Baggerly, M-C. Hung, and H. M. Kuerer.
Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform.
Proteomics, 5(16):4107-4117, 2005.

7

A. Cruz-Marcelo, R. Guerra, M. Vannucci, Y. Li, C. C. Lau, and T. Man.
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data.
Bioinformatics, 24(19):2129-2136, 2008.

8

M. E. de Noo, R. A.E.M. Tollenaar, A. Özalp, P. J.K. Kuppen, M. R. Bladergroen, P. H.C. Eilers, and A. M. Deelder.
Reliability of human serum protein profiles generated with C8 magnetic beads assisted MALDI-TOF mass spectrometry.
Analytical Chemistry, 77(22):7232-7241, 2005.

9

Y. Liu, X. Si, and S. Jiao.
Optimized design of top-hat filter based on algorithms of support vector machine.
In Proceedings of the 7th World Congress on Intelligent Control and Automation WCICA, pages 1773-1776, 2008.

10

W. Meuleman, J. Y.M.N. Engwegen, M. W. Gast, J. H. Beijnen, M. J.T. Reinders, and L. F.A. Wessels.
Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data.
BMC Bioinformatics, 9(88), 2008.

11

K. Noy and D. Fasulo.
Improved model-based, platform-independent feature extraction for mass spectrometry.
Bioinformatics, 23(19):2528-2535, 2007.

12

M. Pelikan and H. Mühlenbein.
The bivariate marginal distribution algorithm.
In R. Roy, T. Furuhashi, and P. K. Chawdhry, editors, Advances in Soft Computing - Engineering Design and Manufacturing, pages 521-535, London, 1999. Springer-Verlag.

13

J. Prados, A. Kalousis, and M. Hilario.
On preprocessing of SELDI-MS data and its evaluation.
In Proceedings of the 19th IEEE Symposium on Computer-Based Medical Systems, pages 953-958, 2006.

14

H. W. Ressom, R. S. Varghese, M. Abdel-Hamid, S. A-L. Eissa, D. Saha, L. Goldman, E. F. Petricoin, T. P. Conrads, T. D. Veenstra, C. A. Loffredo, and R. Goldman.
Analysis of mass spectral serum profiles for biomarker selection.
Bioinformatics, 21(21):4039-4045, 2005.

15

H. W. Ressom, R. S. Varghese, S. K. Drake, G. L. Hortin, M. Abdel-Hamid, C. A. Loffredo, and R. Goldman.
Peak selection from MALDI-TOF mass spectra using ant colony optimization.
Bioinformatics, 23(5):619-626, 2007.

16

J. Reunanen.
Overfitting in making comparisons between variable selection methods.
Journal of Machine Learning Research, 3:1371-1382, 2003.

17

R. Santana, A. Ochoa, and M. R. Soto.
The mixture of trees factorized distribution algorithm.
In L. Spector, E. Goodman, A. Wu, W.B. Langdon, H.M. Voigt, M. Gen, S. Sen, M. Dorigo, S. Pezeshk, M. Garzon, and E. Burke, editors, Proceedings of the Genetic and Evolutionary Computation Conference GECCO-2001, pages 543-550, San Francisco, CA, 2001. Morgan Kaufmann Publishers.

18

A. C. Sauve and T. P. Speed.
Normalization, baseline correction and alignment of high-throughput mass spectrometry data.
In Proceedings of the Workshop on Genomic Siganl Processing and Statistics, 2004.

19

H. Shin and M. K. Markey.
A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples.
Journal of Biomedical Informatics, 39(2):227-248, 2006.

20

H. Shin, B. Sheub, M. Joseph, and M. K. Markey.
Guilt-by-association feature selection: Identifying biomarkers from proteomic profiles.
Journal of Biomedical Informatics, 41(1):124-136, 2008.

21

D. J. Slotta, L. S. Heath, N. Ramakrishnan, R. Helm, and M. Potts.
Clustering mass spectrometry data using order statistics.
Proteomics, 95:1687-1691, 2003.

22

P. Soille.
Morphological Image Analysis.
Springer, 1999.

23

A. Statnikov, C. F. Aliferis, I. Tsamardinos, D. Hardin, and S. Levy.
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis.
Bioinformatics, 21(5):631-643, 2005.

24

R. Tibshirani, T. Hastie, B. Narasimhan, S. Soltys, G. Shi, A. Koong, and Q-T. Le.
Sample classification from protein mass spectrometry, by 'peak probability contrasts'.
Bioinformatics, 20(17):3034-3044, 2004.

25

E. Wit and J. McClure.
Statistics for Microarrays. Design, Analysis and Inference.
John Wiley & Sons, 2004.

26

M. Zeng, J. Li, and Z. Peng.
The design of top-hat morphological filter and application to infrared target detection.
Infrared Physics & Technology, 48(1):67-76, 2006.