Publications 2005
2008 — 2007 — 2006 — 2005 — 2004 — 2003
Publications In Press
Recent Posters
Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States D. J. (2005), “Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.” Proteomics. 5(13):3246-3261.
Falkner J, Andrews P. Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined. Bioinformatics. 2005 May 15; 21(10):2177-84. Ulintz PJ, Zhu J, Qin ZS, Andrews PC. Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol Cell Proteomics. 2006 Mar;5(3):497-509. Epub 2005 Nov 30.
Hsiao, A., Ideker, T. Olesfky, J. and Subramaniam, S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data Nucleic Acids Research. 33(Web Server issue):W627-32. (2005).
Kelley, R.., and Ideker, T., Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5): 561 - 566 (2005).
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D. J. (2005), “PRIDE: the proteomics identifications database.” Proteomics. 5(13):3537-3545.
Misek DE, Kuick R, Wang H, Galchev V, Deng B, Zhao R, Tra J, Pisano MR, Amunugama R, Allen D, Walker AK, Strahler JR, Andrews PC, Omenn GS, Hanash SM: A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. Proteomics. 5: 3343-3352, 2005.
Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 2005 Aug;5(13):3226-45.
Parrish, J.R., and Finley, Jr., R.L., Protein networks, in 2005 Yearbook of Science & Technology, McGraw Hill, New York, NY, pp 276-278, 2005.
Santos, C., Blake, J. and States, D.J. (2005) Supplementary data need to be kept in public repositories. Nature, 438, 738.
Santos, C., Eggle, D., States D. J. (2005), “Wnt Pathway Curation Using Automated Natural Language Processing: Combining Statistical Methods with Partial and Full Parse for Knowledge Extraction.” Bioinformatics. 21(8):1653-1658.
Sharan R., Ideker, T., Kelley, B., Shamir, R., Karp, RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol. 12(6):835-46. (2005).
Sharan, R. Suthram, S., Kelley, R. M., Sittler, T., Karp, R. M., Ideker, T. Cover Article: Conserved patterns of protein interaction in multiple species Proc Natl Acad Sci USA. 102(6):1974-9 (2005).
Soans, A.H., Stanyon, C.A., Zhang, H., and Finley, Jr., R.L., Using peptide aptamers to study proteins and protein networks; in Protein-Protein Interactions: A Molecular Cloning Manual, second edition (ed. Golemis, E.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Chapter 30, 2005.
Suthram, S., Sittler, T., and Ideker, T. The Plasmodium protein network diverges from those of other eukaryotes. Nature. 438(7064):108-12. (2005).
Uetz, P., and Finley, JR., R.L. From protein networks to systems biology. FEBS Letters 579, 1821-1827, 2005.
Workman, CT., Yin, Y.., Corcoran, DL., Ideker, T., Stormo, GD., and Benos, PV. enoLOGOS: a versatile web tool for energy normalized sequence logos Nucleic Acids Research. 33(Web Server issue):W389-92. (2005).
Yamada K, Strahler JR, Andrews PC, Matthews RG. Regulation of human methylenetetrahydrofolate reductase by phosphorylation. Proc Natl Acad Sci U S A. 102: 10454-10459, 2005.
Yeang, CH., Mak, HC., McCuine, S., Workman, C., Jaakkola, T. and T. Ideker. Validation and refinement of gene regulatory pathways on a network of physical interactions. Genome Biology. 6(7):R62. Epub 2005 (2005).
Yin, S., Li, X., Meng, Y., Finley, R.L. Jr., Sakr, W., Yang, H., Reddy, N., Sheng, S. Tumor-suppressive maspin regulates cell response to oxidative stress by direct interaction with glutathione S-transferase. J Biol Chem. 280, 34985-34996, 2005.