Keck MS & Proteomics Resource Publications

2000-2009

133. Stone, K., and Williams, K. (2009) Reverse-Phase HPLC Separation of Enzymatic Digests of Proteins, in Protein Protocols Handbook, 937-946.

132. Stone, K., Gulcicek, E., and Williams, K. R. (2009) Enzymatic Digestion of Proteins in Solution and in SDS Polyacrylamide Gels, in Protein Protocols Handbook, 3rd ed., 901-913.

131. Rinehart, J., Maksimova, Y. D., Tanis, J. E., Stone, K. L., Hodson, C. A., Zhang, J., Risinger, M., Pan, W., Wu, D., Colangelo, C. M., Forbush, B., Joiner, C. H., Gulcicek, E. E., Gallagher, P. G., and Lifton, R. P. (2009) Sites of regulated phosphorylation that control K-Cl cotransporter activity. Cell 138, 525-536, (PMCID: PMC 2811214).

130. Rajagopal, C., Stone, K. L., Francone, V. P., Mains, R. E., and Eipper, B. A. (2009) Secretory granule to the nucleus: role of a multiply phosphorylated intrinsically unstructured domain. J. Biol. Chem. 284, 25723-25734, (PMCID: PMC 2757974).

129. Patel, J. C., Hueffer, K., Lam, T. T., and Galan, J. E. (2009) Diversification of a Salmonella virulence protein function by ubiquitin-dependent differential localization. Cell 137, 283-294, (PMCID: PMC 2673707).

128. Luo, R., Colangelo, C. M., Sessa, W. C., and Zhao, H. (2009) Bayesian Analysis of iTRAQ Data with Nonrandom Missingness: Identification of Differentially Expressed Proteins. Stat Biosci 1, 228-245, (PMCID: PMC 3172970).

127. Chong, R., Swiss, R., Briones, G., Stone, K. L., Gulcicek, E. E., and Agaisse, H. (2009) Regulatory mimicry in Listeria monocytogenes actin-based motility. Cell Host Microbe 6, 268-278, (PMCID: PMC 2752869).

126. Yi, T., Rao, D. A., Tang, P. C., Wang, Y., Cuchara, L. A., Bothwell, A. L., Colangelo, C. M., Tellides, G., Pober, J. S., and Lorber, M. I. (2008) Amelioration of human allograft arterial injury by atorvastatin or simvastatin correlates with reduction of interferon-gamma production by infiltrating T cells. Transplantation 86, 719-727, (PMCID: PMC 2650813).

125. Shaw, M. L., Stone, K. L., Colangelo, C. M., Gulcicek, E. E., and Palese, P. (2008) Cellular proteins in influenza virus particles. PLoS Pathog 4, e1000085, (PMCID: PMC 2390764).

124. Robles-Flores, M., Meléndez, L., García, W., Mendoza-Hernández, G., Lam, T.K., Castañeda-Patlán, C., and González-Aguilar, H. (2008) Posttranslational modifications on protein kinase C isozymes: Effects of epinephrine and phorbol esters, Biochimica et Biophysica Acta, 1783, 695–712.

123. Bjornson, R. D., Carriero, N. J., Colangelo, C., Shifman, M., Cheung, K. H., Miller, P. L., and Williams, K. (2008) X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers. J. Proteome Res 7, 293-299.

122. Yu, W., Liu, J., Colangelo, C., Gulcicek, E., and Zhao, H. (2007) A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry. Comput. Biol. Chem 31, 215-221.

121. Stone, K. L., Crawford, M., McMurray, W., Williams, N., and Williams, K. R. (2007) Identification of proteins based on MS/MS spectra and location of posttranslational modifications. Methods Mol. Biol. 386, 57-77.

120. Stone, K. L., Bjornson, R. D., Blasko, G. G., Bruce, C., Cofrancesco, R., Carriero, N. J., Colangelo, C. M., Crawford, J. K., Crawford, J. M., daSilva, N. C., Deluca, J. D., Elliott, J. I., Elliott, M. M., Flory, P. J., Folta-Stogniew, E. J., Gulcicek, E., Kong, Y., Lam, T. T., Lee, J. Y., Lin, A., LoPresti, M. B., Mane, S. M., McMurray, W. J., Tikhonova, I. R., Westman, S., Williams, N. A., Wu, T. L., Hongyu, Z., and Williams, K. R. (2007) Keck Foundation Biotechnology Resource Laboratory, Yale University. Yale J. Biol. Med. 80, 195-211 (PMCID: PMC 2347368).

119. Shifman, M. A., Li, Y., Colangelo, C. M., Stone, K. L., Wu, T. L., Cheung, K. H., Miller, P. L., and Williams, K. R. (2007) YPED: a web-accessible database system for protein expression analysis. J Proteome Res 6, 4019-4024.

118. Yu, W., Wu, B., Liu, J., Li, X., Stone, K., Williams, K. R., and Zhao, H. (2006) MALDI-MS data analysis for disease biomarker discovery. Methods Mol. Biol. 328, 199-216.

117. Yu, W., Wu, B., Lin, N., Stone, K., Williams, K., and Zhao, H. (2006) Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Comput Biol Chem 30, 27-38.

116. Yu, W., Wu, B., Huang, T., Li, X., Williams, K., and Zhao, H. (2006) Statistical methods in proteomics, in Springer Handbook of Engineering Statistics, 11-20.

115. Yu, W., Li, X., Liu, J., Wu, B., Williams, K. R., and Zhao, H. (2006) Multiple peak alignment in sequential data analysis: a scale-space-based approach. IEEE/ACM Trans Comput Biol. Bioinform. 3, 208-219.

114. Wu, T. (2006) Two-Dimensional Difference Gel Electrophoresis, in New and Emerging Proteomics Techniques, Humana Press, 71-96.

113. Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K., and Zhao, H. (2006) Ovarian cancer classification based on mass spectrometry analysis of sera. Cancer Inform. 2, 123-132, (PMCID: PMC 2675484).

112. Stone, K. L., and Williams, K. R. (2006) Enzymatic Digestion of Proteins in Gels for Mass Spectrometric Identification and Structural Analysis, in Current Protocols in Protein Science (Coligan, J. E., Dunn, B. M., Ploegh, H. L., Speicher, D. W., and Wingfield, P. T. ed), John Wiley & Sons, New York, 11.3.1-11.3.10.

111. Colangelo, C. M., and Williams, K. R. (2006) Isotope-coded affinity tags for protein quantification. Methods Mol. Biol. 328, 151-158.

110. Bruce, C., Shifman, M. A., Miller, P., and Gulcicek, E. E. (2006) Probabilistic enrichment of phosphopeptides by their mass defect. Anal Chem 78, 4374-4382, (PMCID: PMC 2547851).

109. Shifman, M. A., Sun, K., Colangelo, C. M., Cheung, K. H., Miller, P., and Williams, K. (2005) YPED: a proteomics database for protein expression analysis. AMIA Annu Symp Proc, 1111, (PMCID: PMC 1560545).

108. Seo, J., Crawford, J.M., Stone, K.L. and Noga, E.J. (2005) Purification of a novel arthropod defensin from the American oyster, Crassostrea virginica. Biochemical and Biophysical Research Communications, 338, 1998-2004.

107. Gulcicek, E. E., Colangelo, C. M., McMurray, W., Stone, K., Williams, K., Wu, T., Zhao, H., Spratt, H., Kurosky, A., and Wu, B. (2005) Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. Technologies In Current Protocols in Bioinformatics (A. D. Baxevanis, D. B. Davison, R. D. M. Page, G. A. Petsko, L. D. Stein and G. D. Stormo, eds). John Wiley & Sons Inc, Hoboken, NJ. pp 13.1.1 - 13.1.31.

106. Carriero, N., Osier, M. V., Cheung, K. H., Miller, P. L., Gerstein, M., Zhao, H., Wu, B., Rifkin, S., Chang, J., Zhang, H., White, K., Williams, K., and Schultz, M. (2005) A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. J. Am. Med. Inform. Assoc. 12, 90-98, (PMCID: PMC 543832).

105. Williams, K., Wu, T., Colangelo, C., and Nairn, A. C. (2004) Recent advances in neuroproteomics and potential application to studies of drug addiction. Neuropharmacology 47 Suppl 1, 148-166.

104. Stone, K. L., and Williams, K. R. (2004) Enzymatic digestion of proteins in gels for mass spectrometric identification and structural analysis. (J.E. Coligan, B.M. Dunn, H.L. Ploegh, D.W. Speicher, P.T. Wingfield, eds.) . John Wiley & Sons, New York, pp. 11.3.1-11.3.10.

103. Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K., and Zhao, H. (2003) Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 19, 1636-1643.

102. Greenbaum, D., Colangelo, C., Williams, K., and Gerstein, M. (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 4, 117, (PMCID: PMC 193646).

101. Dillon, D. A., Stone, K., and Williams, K. R. (2003) Potential Application for Proteomics in Oncology, in Progress in Oncology 2002, (DeVita, V. T., Jr, Hellman, S., and Rosenberg, S. A. ed), Jones and Bartlett, Sudbury, MA, 1-22.

100. Arnott, D., Gawinowicz,M., Grant,R.A., Neubert, T.A., Packman,L.C., Speicher, K.D., Stone, K. and Turck, C.W. (2003) ABRF-PRG03: Phosphorylation Site Determination. J. Biomolecular Techniques 14(3), 205-215.

99. Arnott,D.P., Gawinowicz,M., Grant, R., Lane, W., Packman, L.C., Speicher, K. and Stone,K (2002) Proteomics in Mixtures: Study Results of ABRF-PRG02, Journal of Biomolecular Techniques 13, 179-186.

98. Tang, J., Frankel, A., Cook, R. J., Kim, S., Paik, W. K., Williams, K. R., Clarke, S., and Herschman, H. R. (2000) PRMT1 is the predominant type I protein arginine methyltransferase in mammalian cells. J. Biol. Chem. 275, 7723-7730.

97. Huszar, G. Stone, K. Dix, D. and Vigue, L. (2000) Putative creatine kinase M-isoform in human sperm is identified as the 70-kilodalton heat shock protein HspA2.  Biol. Reprod. 63(3), pp.925-932.