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Items: 1 to 20 of 28

1.

Clinical proteomics: A need to define the field and to begin to set adequate standards.

Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, Neusuess C, Novak J, Peter K, Rossing K, Schanstra J, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T.

Proteomics Clin Appl. 2007 Feb;1(2):148-56. doi: 10.1002/prca.200600771. Epub 2007 Jan 22.

PMID:
21136664
2.
3.

Benchmarking currently available SELDI-TOF MS preprocessing techniques.

Emanuele VA 2nd, Gurbaxani BM.

Proteomics. 2009 Apr;9(7):1754-62. doi: 10.1002/pmic.200701171.

PMID:
19294696
4.

Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data.

Cruz-Marcelo A, Guerra R, Vannucci M, Li Y, Lau CC, Man TK.

Bioinformatics. 2008 Oct 1;24(19):2129-36. doi: 10.1093/bioinformatics/btn398. Epub 2008 Aug 11.

5.

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data.

Meuleman W, Engwegen JY, Gast MC, Beijnen JH, Reinders MJ, Wessels LF.

BMC Bioinformatics. 2008 Feb 7;9:88. doi: 10.1186/1471-2105-9-88.

6.

How to distinguish healthy from diseased? Classification strategy for mass spectrometry-based clinical proteomics.

Hendriks MM, Smit S, Akkermans WL, Reijmers TH, Eilers PH, Hoefsloot HC, Rubingh CM, de Koster CG, Aerts JM, Smilde AK.

Proteomics. 2007 Oct;7(20):3672-80.

PMID:
17880000
7.

Mass spectrometry: uncovering the cancer proteome for diagnostics.

van der Merwe DE, Oikonomopoulou K, Marshall J, Diamandis EP.

Adv Cancer Res. 2007;96:23-50. Review.

PMID:
17161675
8.

Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.

Du P, Kibbe WA, Lin SM.

Bioinformatics. 2006 Sep 1;22(17):2059-65. Epub 2006 Jul 4.

PMID:
16820428
9.

A compendium to ensure computational reproducibility in high-dimensional classification tasks.

Ruschhaupt M, Huber W, Poustka A, Mansmann U.

Stat Appl Genet Mol Biol. 2004;3:Article37. Epub 2004 Dec 19.

PMID:
16646817
10.

Bias in error estimation when using cross-validation for model selection.

Varma S, Simon R.

BMC Bioinformatics. 2006 Feb 23;7:91.

11.

Comparison of software tools to improve the detection of carcinogen induced changes in the rat liver proteome by analyzing SELDI-TOF-MS spectra.

Beyer S, Walter Y, Hellmann J, Kramer PJ, Kopp-Schneider A, Kroeger M, Ittrich C.

J Proteome Res. 2006 Feb;5(2):254-61.

PMID:
16457590
12.

Guidelines for the next 10 years of proteomics.

Wilkins MR, Appel RD, Van Eyk JE, Chung MC, Görg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ.

Proteomics. 2006 Jan;6(1):4-8.

14.

HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples.

Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, Mehigh RJ, Cockrill SL, Scott GB, Tammen H, Schulz-Knappe P, Speicher DW, Vitzthum F, Haab BB, Siest G, Chan DW.

Proteomics. 2005 Aug;5(13):3262-77.

PMID:
16052621
15.

Prediction of cancer outcome with microarrays: a multiple random validation strategy.

Michiels S, Koscielny S, Hill C.

Lancet. 2005 Feb 5-11;365(9458):488-92.

PMID:
15705458
16.

Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.

Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R.

Bioinformatics. 2005 May 1;21(9):1764-75. Epub 2005 Jan 26.

PMID:
15673564
17.

Bioconductor: open software development for computational biology and bioinformatics.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J.

Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.

18.
19.

Sample classification from protein mass spectrometry, by 'peak probability contrasts'.

Tibshirani R, Hastie T, Narasimhan B, Soltys S, Shi G, Koong A, Le QT.

Bioinformatics. 2004 Nov 22;20(17):3034-44. Epub 2004 Jun 29.

PMID:
15226172
20.

Computational protein biomarker prediction: a case study for prostate cancer.

Wagner M, Naik DN, Pothen A, Kasukurti S, Devineni RR, Adam BL, Semmes OJ, Wright GL Jr.

BMC Bioinformatics. 2004 Mar 11;5:26.

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