Crossref
book-chapter
Springer US
Fundamentals of Data Mining in Genomics and Proteomics (297)
References
39
Referenced
43
- Adam, B.L., Qu, Y., Davis, J.W., Ward, M.D., Clements, M.A., Cazares, L.H., Semmes, O.J., Schellhammer, P.F., Yasui, Y., Feng, Z., and Wright, G.L., Jr. (2002). Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res., 62(13):3609–3614. / Cancer Res. by B.L. Adam (2002)
-
Adam, P.J., Boyd, R., Tyson, K.L., Fletcher, G.C., Stamps, A., Hudson, L., Poyser, H.R., Redpath, N., Griffiths, M., Steers, G., Harris, A.L., Patel, S., Berry, J., Loader, J.A., Townsend, R.R., Daviet, L., Legrain, P., Parekh, R., and Terrett, J.A. (2003). Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer. J. Biol. Chem., 278(8):6482–6489.
(
10.1074/jbc.M210184200) / J. Biol. Chem. by P.J. Adam (2003) -
Baggerly, K.A., Edmonson, S.R., Morris, J.S., and Coombes, K.R. (2004a). High-resolution scrum proteomic patterns for ovarian cancer detection. Endocr. Relat. Cancer, 11(4):583–584; author reply 585–587.
(
10.1677/erc.1.00868) / Endocr. Relat. Cancer by K.A. Baggerly (2004) -
Baggerly, K.A., Morris, J.S., and Coombes, K.R. (2004b). Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics, 20(5):777–785.
(
10.1093/bioinformatics/btg484) / Bioinformatics by K.A. Baggerly (2004) -
Baggerly, K.A., Morris, J.S., Wang, J., Gold, D., Xiao, L.C., and Coombes, K.R. (2003). A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics, 3(9):1667–1672.
(
10.1002/pmic.200300522) / Proteomics by K.A. Baggerly (2003) -
Chaudhuri, P. and Marron, S. (1999). SiZer for exploration of structures of curves. JASA, 94:807–823.
(
10.1080/01621459.1999.10474186) / JASA by P. Chaudhuri (1999) -
Coombes, K.R., Fritsche, H.A., Jr., Clarke, C, Chen, J.N., Baggerly, K.A., Morris, J.S., Xiao, L.C., Hung, M.C., and Kuerer, H.M. (2003). Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin. Chem., 49(10):1615–1623.
(
10.1373/49.10.1615) / Clin. Chem. by K.R. Coombes (2003) -
Coombes, K.R., Koomen, J.M., Baggerly, K.A., Morris, J.S., and Kobayashi, R. (2005a). Understanding the characteristics of mass spectrometry data through the use of simulation. Cancer Informatics, 1:41–52.
(
10.1177/117693510500100103) / Cancer Informatics by K.R. Coombes (2005) -
Coombes, K.R., Tsavachidis, S., Morris, J.S., Baggerly, K.A., Hung, M.C., and Kuerer, H.M. (2005b). 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.
(
10.1002/pmic.200401261) / Proteomics by K.R. Coombes (2005) -
Clyde, M.A., House, L.L., and Wolpert, R.L. (2006). Nonparametric models for proteomic peak identification and quantification. ISDS Discussion Paper, 2006–2007.
(
10.1017/CBO9780511584589.016) -
Daubechies, I. (1992). Ten Lectures on Wavelets Philadelphia: Society for Industrial and Applied Mathematics.
(
10.1137/1.9781611970104) -
Fung, E.T. and Enderwick, C. (2002). Proteinchip clinical proteomics: computational challenges and solutions. Biotechniques, Suppl.32, S34–S41.
(
10.2144/mar0205) / Biotechniques by E.T. Fung (2002) -
Gyaourova, A., Kamath, C, and Fodor, I.K. (2002). Undecimated wavelet transforms for image de-noising. Technical Report UCRL-ID-150931, Lawrence Livermore National Laboratory, Livermore, CA.
(
10.2172/15002085) / Undecimated wavelet transforms for image de-noising / Technical Report by A. Gyaourova (2002) -
Hawkins, D.M., Wolfinger, R.D., Liu, L., and Young, S.S. (2003). Exploring blood spectra for signs of ovarian cancer. Chance, 16:19–23.
(
10.1080/09332480.2003.10554870) / Chance by D.M. Hawkins (2003) -
Kerr, M.K., Martin, M., and Churchill, G.A. (2000). Analysis of variance for gene expression microarray data. J. Comp. Biol., 7(6):819–837.
(
10.1089/10665270050514954) / J. Comp. Biol. by M.K. Kerr (2000) -
Kuerer, H.M., Coombes, K.R., Chen, J.N., Xiao, L., Clarke, C, Fritsche, H., Krishnamurthy, S., Marcy, S., Hung, M.C., and Hunt, K.K. (2004). Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. Surgery, 136(5):1061–1069.
(
10.1016/j.surg.2004.04.011) / Surgery by H.M. Kuerer (2004) - Lang, M., Guo, H., Odegard, J. E., Burrus, C.S., and Well, R. O. Jr. (1995). Nonlinear processing of a shift invariant DWT for noise reduction. In Szu, H.H., editor, Proc. SPIE. Waveelet Applications II, volume 2491, pages 640–651, Bellingham, WA. SPIE.
-
Lang, M., Guo, H., Odegard, J.E., Burrus, C.S., and Well, R.O. Jr. (1996). Noise reduction using an undecimated discrete wavelet transform. IEEE Signal Processing Letters, 3:10–12.
(
10.1109/97.475823) / IEEE Signal Processing Letters by M. Lang (1996) -
Lee, K.R., Lin, X., and Park, D.C., and Eslava, S. (2003). Megavariate data analysis of mass spectrometric proteomics data using latent variable projection method. Proteomics, 3:1680–1686.
(
10.1002/pmic.200300515) / Proteomics by K.R. Lee (2003) -
Liggett, W., Cazares, L., and Semmes, O.J. (2003). A look at mass spectral measurement. Chance, 16:24–28.
(
10.1080/09332480.2003.10554871) / Chance by W. Liggett (2003) -
Mallat, S.G.(1989). A Theory for Multiresolution Signal Decompsition: The Wavelet Representation. IEEE Trans. Patter Analysis and Machine Intelligence, 11:674–693.
(
10.1109/34.192463) / IEEE Trans. Patter Analysis and Machine Intelligence by S.G. Mallat (1989) -
Malyarenko, D.I., Cooke, W.E., Adam, B.L., Malik, G., Chen, H., Tracy, E. R., Trosset, M.W., Sasinowski, M., Semmes, O.J., and Manos, D.M. (2005). Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques. Clin. Chem., 51(1):65–74.
(
10.1373/clinchem.2004.037283) / Clin. Chem. by D.I. Malyarenko (2005) -
Merchant, M. and Weinberger, S.R. (2000). Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis, 21(6):1164–1177.
(
10.1002/(SICI)1522-2683(20000401)21:6<1164::AID-ELPS1164>3.0.CO;2-0) / Electrophoresis by M. Merchant (2000) -
Morris, J.S., Coombes, K.R., Koomen, J., Baggerly, K.A., and Kobayashi, R. (2005). Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics, 21(9):1764–1775.
(
10.1093/bioinformatics/bti254) / Bioinformatics by J.S. Morris (2005) - Morris, J.S., Brown, P.J., Herrick, R.H., Baggerly, K.A., and Coombes, K.R. (2006). Bayesian analysis of mass spectrometry proteomics data using wavelet based functional mixed models. UT MD Anderson Cancer Center Department of Biostatistics and Applied Mathematics Working Papers Series, Working Paper 22:1–32. / UT MD Anderson Cancer Center Department of Biostatistics and Applied Mathematics Working Papers Series by J.S. Morris (2006)
-
Paweletz, C.P., Trock, B., Pennanen, M., Tsangaris, T., Magnant, C, Liotta, L.A., and Petricoin, E.F., 3rd (2001). Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: Potential for new biomarkers to aid in the diagnosis of breast cancer. Dis. Markers, 17(4):301–307.
(
10.1155/2001/674959) / Dis. Markers by C.P. Paweletz (2001) -
Pawlik, T.M., Fritsche, H., Coombes, K.R., Xiao, L., Krishnamurthy, S., Hunt, K.K., Pusztai, L., Chen, J.N., Clarke, C.H., Arun, B., Hung, M.C., and Kuerer, H.M. (2005). Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry. Breast Cancer Res. Treat., 89(2):149–157.
(
10.1007/s10549-004-1710-4) / Breast Cancer Res. Treat. by T.M. Pawlik (2005) -
Petricoin, E.F., 3rd, Ornstein, D.K., Paweletz, C.P., Ardekani, A., Hackett, P.S., Hitt, B.A., Velassco, A., Trucco, C, Wiegand, L., Wood, K., Simone, C.B., Levine, P.J., Linehan, W.M., Emmert-Buck, M.R., Steinberg, S.M., Kohn, E.C., and Liotta, L.A. (2002). Serum proteomic patterns for detection of prostate cancer. J. Natl. Cancer Inst., 94(20):1576–1578.
(
10.1093/jnci/94.20.1576) / J. Natl. Cancer Inst. by E.F. Petricoin 3rd (2002) -
Rai, A.J., Zhang, Z., Rosenzweig, J., Shih, I.M., Pham, T., Fung, E.T., Sokoll, L.J., and Chan, D.W. (2002). Proteomic approaches to tumor marker discovery. Arch. Pathol. Lab. Med., 126(12):1518–1526.
(
10.5858/2002-126-1518-PATTMD) / Arch. Pathol. Lab. Med. by A.J. Rai (2002) -
Schaub, S., Wilkins, J., Weiler, T., Sangster, K., Rush, D., and Nickerson, P. (2004). Urine protein profiling with surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry. Kidney Int., 65(1):323–332.
(
10.1111/j.1523-1755.2004.00352.x) / Kidney Int. by S. Schaub (2004) -
Sorace, J.M. and Zhan, M. (2003). A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics, 4:24.
(
10.1186/1471-2105-4-24) / BMC Bioinformatics by J.M. Sorace (2003) -
Tang, N., Tornatore, P., and Weinberger, S.R. (2004). Current developments in SELDI affinity technology. Moss Spectrom. Rev., 23(1):34–44.
(
10.1002/mas.10066) / Moss Spectrom. Rev. by N. Tang (2004) -
Wagner, M., Naik, D., and Pothen, A. (2003). Protocols for disease classification from mass spectrometry data. Proteomics, 3(9):1692–1698.
(
10.1002/pmic.200300519) / Proteomics by M. Wagner (2003) - Wellmann, A., Wollscheid, V., Lu, H., Ma, Z.L., Albers, P., Schutze, K., Rohde, V., Behrens, P., Dreschers, S., Ko, Y., and Wernert, N. (2002). Analysis of microdissected prostate tissue with proteinchip arrays-a way to new insights into carcinogenesis and to diagnostic tools. Int. J. Mol. Med., 9(4):341–347. / Int. J. Mol. Med. by A. Wellmann (2002)
-
Wolfinger, R.D., Gibson, G., Wolfinger, E.D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C, and Paules, R.S. (2001). Assessing gene significance from cDNA microarray expression data via mixed models. J. Comp. Biol., 8(6):625–637.
(
10.1089/106652701753307520) / J. Comp. Biol. by R.D. Wolfinger (2001) -
Yasui, Y., McLerran, D., Adam, B. L., Winget, M., Thornquist, M., and Feng, Z. (2003a). An automated peak identification/calibration procedure for high-dimensional protein measures from mass spectrometers. J. Biomed. Biotechnol., 2003(4):242–248.
(
10.1155/S111072430320927X) / J. Biomed. Biotechnol. by Y. Yasui (2003) -
Yasui, Y., Pepe, M., Thompson, M.L., Adam, B.L., Wright, G.L., Jr., Qu, Y., Potter, J.D., Winget, M., Thornquist, M., and Feng, Z. (2003b). A data-analytic strategy for protein biomarker discovery: profiling of highdimensional proteomic data for cancer detection. Biostatistics, 4(3):449–463.
(
10.1093/biostatistics/4.3.449) / Biostatistics by Y. Yasui (2003) -
Zhu, W., Wang, X., Ma, Y., Rao, M., Glimm, J., and Kovach, J.S. (2003). Detection of cancer-specific markers amid massive mass spectral data. Proc. Natl. Acad. Sci. USA, 100(25):14666–14671.
(
10.1073/pnas.2532248100) / Proc. Natl. Acad. Sci. USA by W. Zhu (2003) -
Zhukov, T.A., Johanson, R.A., Cantor, A.B., Clark, R.A., and Tockman, M.S. (2003). Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry. Lung Cancer, 40(3):267–279.
(
10.1016/S0169-5002(03)00082-5) / Lung Cancer by T.A. Zhukov (2003)
@inbook{Coombes, title={Pre-Processing Mass Spectrometry Data}, ISBN={9780387475080}, url={http://dx.doi.org/10.1007/978-0-387-47509-7_4}, DOI={10.1007/978-0-387-47509-7_4}, booktitle={Fundamentals of Data Mining in Genomics and Proteomics}, publisher={Springer US}, author={Coombes, Kevin R. and Baggerly, Keith A. and Morris, Jeffrey S.}, pages={79–102} }