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Publications from the Yale/NIDA Neuroproteomics Center

Patent Applications:

1. Zhao, H., Williams, K., Wu, B., Stone, K., McMurray, W., and Abbott, T. (2005) Classification of Disease States Using Mass Spectrometry Data.

2. Gulcicek, E., Bruce, C., Shifman, M., and Williams, K. (2005) Use of Fractional Mass for Mass Spectrometric Detection of Phosphopeptides (provisional US patent application).

3. Pevsner, P. (NYU), Naftolin,F., Fadiel,A.,and Gulcicek, E. (2005) Transthoracic cardiac perfusion impregnation of organs in live experimental animals for subsequent study by biochemical methods. (provisional US patent application)

Publications:

1. Jin, M., Bateup, H., Padovan, J.C., Greengard, P., Nairn, A.C., Chait, B.T. (2005) Quantitative analysis of protein phosphorylation in mouse brain by hypothesis-driven multistage mass spectrometry. Anal Chem. 77, 7845-51.

2. Lee, S.Y., Voronov, S., Letinic, K., Nairn, A.C., Di Paolo, G. and De Camilli, P. (2005) Regulation of the interaction between phosphatidylinositol(4)phosphate 5-kinase type I and talin by proline-directed protein kinases. J. Cell Biol. 168, 789-79.

3. Bruce, C, Mark Shifman, Perry Miller, and Erol E. Gulcicek, (2006). Probabilistic Enrichment of Phosphopeptides by their Mass Defect, Anal. Chem., 78, 4374-82.

4. Colangelo, C. and Williams, K.R. (2006) Isotope Coded Affinity Tag for Protein Quantification in Methods in Molecular Biology: New and Emerging Proteomics Techniques (Nedelkov, D., and Nelson, R. eds), Vol. 328, Chapter 10, pp 151-158, Humana Press, Totowa, NJ.

5. Folta-Stogniew, E. (2006) Oligomeric States of Proteins Determined by Size-Exclusion Chromatography Coupled with Light Scattering, Absorbance and Refractive Index Detectors in Methods in Molecular Biology: New and Emerging Proteomics Techniques (Nedelkov, D., and Nelson, R. eds), Vol. 328, Chapter 6, pp 97-112, Humana Press, Totowa, NJ.

6. Gulcicek, E. E., Colangelo, C. M., McMurray, W., Stone, K., Wu, T., Zhao, H., Spratt, H., Kurosky, A., Wu, B. and Williams, K. (2006). Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein-Profiling 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) pp 13.1.1 - 13.1.31. John Wiley & Sons Inc, Hoboken, NJ.

7. 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 Informatics 2, 123-132. (This publication reports on the use of ovarian cancer as a commonly-used model system for development of a biomarker discovery algorithm which is now being applied to NIDA Neuroproteomics Center supported research.)

8. Wu, T. (2006) Two-Dimensional Difference Gel Electrophoresis in Methods in Molecular Biology: New and Emerging Proteomics Techniques (Nedelkov, D., and Nelson, R. eds), Vol. 328, Chapter 5, pp 71-96, Humana Press, Totowa, NJ.

9. Yu W, Li X, Liu J, Wu B, Williams K, Zhao H. (2006) Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space Based Approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3, 208-219.

10. Yu W, Wu B, Lin N, Stone K, Williams K, Zhao H. (2006) Detecting and Aligning Peaks in Mass Spectrometry Data with Applications to MALDI. Computational Biology and Chemistry 30, 27-38.

11. Yu, W., Wu, B., Huang, T., Li, X., Williams, K., and Zhao H. (2006) Statistical methods in proteomics. Springer Handbook of Engineering Statistics. (Pham, H. ed.) 623-638.

12. Yu, W., Wu, B., Liu, J., Li, X., Stone, K., Williams, K., and Zhao, H. (2006) MALDI-MS Data Analysis for Disease Biomarker Discovery in Methods in Molecular Biology: New and Emerging Proteomics Techniques (Nedelkov, D., and Nelson, R. eds), Vol. 328, Chapter 14, pp 199-216, Humana Press, Totowa, NJ.

13. Di Paolo, G. and De Camilli, P. (2006) Phosphoinositides in Cell Regulation and Membrane Dynamics, Nature 443, 651-657

14. Itoh T, and De Camilli P. (2006). BAR, F-BAR and ENTH/ANTH domains in the regulation of membrane-cytosol interfaces and membrane curvature. Biochim. Biophys. Acta. 1761, 897-912.

Abstracts:

1. Andrade, E.C., Wu, T., Colangelo, C., Lam, T., Berberich, M., Stone, K., Allen, P.B., Taylor, J.R., Williams. K.R., Nairn, A.C. (2005) Identification of alterations in synaptic protein composition following chronic cocaine exposure in mice. Program # 1030.5. Society for Neuroscience. Online.

2. Gulcicek, E., Berberich, M., Colangelo, C., Lam, TuKiet, McMurray, W., Stone, K., and Williams, K.R. (2005) Mass Spectrometric Integration of Robust Phosphoprotein Profiling Strategies. 53rd ASMS Conference on Mass Spectrometry, June 5 - 9, 2005, San Antonio, TX.

3. Hager, J., Tikhonova, I., Clarke, L., Voss, E., Lui, J., Zhao, H., Strittmatter, S., Nairn, A., and Williams, K. (2005) Establishing protocols for making and using protein arrays in an academic core facility. Chips-to-Hits Meeting, September 11-15, 2005, Boston, MA.

4. Krueger, D.D., Olausson, P., Wu, T., Williams, K.R., Taylor, J.R., Nairn, A.C., (2005) Proteomic analysis of persistent cortico-limbic-striatal neuroadaptations following repeated cocaine exposure in vervet monkeys. Program # 1030.6. 2005 Abstract viewer, Society for Neuroscience. Online.

5. Yu, W., Li, X., Liu, J., Wu, B., Williams, K., and Zhao, H. (2005) Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach. IEEE Computational Systems Bioinformatics Conference (CSB 2005), August 8-11, 2005, Stanford, CA.

6. Zimolo, Z, D'Souza, D.C., Perry, E., Krystal, J.H., Wu, T., Stone, K., Williams, K.. (2005) Proteomic analysis of antipsychotic response. International Congress on Schizophrenia Research 2005. Savannah, GA

7. Collin-Hansen, Christian; Erol E. Gulcicek; Terence Wu; Kenneth R. Williams; Angus C. Nairn (2006) Development of a robust strategy for the enrichment of phosphorylated proteins and peptides from complex mixtures, 54th ASMS Conference on Mass Spectrometry, May28 - June1, 2006.

8. Gulcicek, Erol E.; Mark A. Shifman; Perry Miller; Christopher M. Colangelo; Kathryn L. Stone; TuKiet T. Lam; Can Bruce (2006) High Probability MS Identification of Phosphopeptides by their Mass Defect. 54th ASMS Conference on Mass Spectrometry, May28 - June1, 2006.

9. Collin-Hansen, Christian, E. E. Gulcicek, T. Wu, K. R. Williams, A. C. Nairn; (2006), Comparison of methods for enrichment of phosphoproteins and phosphopeptides from complex samples, Poster # 99.11/OO91, Atlanta, GA: Society for Neuroscience, Oct. 14, 2006.

10. Gulcicek, Erol E., (2006) Protein and Phosphoprotein Profiling Strategies, The 4th International Forum on Post-Genome Technologies, September 25-26, 2006, Hongzhou, China, Invited Keynote speaker.

11. Andrade, E., Colangelo, C., Berberich, M., Allen, P., Taylor, J.R., Williams, K.R., Nairn, A.C. (2006) Identification of alterations in synaptic protein composition in cortico-limbic-striatal brain regions after chronic cocaine exposure in mice. Society for Neuroscience. Online.

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Comments or suggestions to Greg Blasko.

Last modified: 30-Aug-2006 (GB)