Publications 2006
2008 — 2007 — 2006 — 2005 — 2004 — 2003
Publications In Press
Recent Posters
Bandyopadhyay S, Sharan R, Ideker T. Cover Article: Systematic identification of functional orthologs based on protein network comparison. Genome Res. 16(3):428-35. (2006).
Beyer, A., Workman, CT., Hollunder, J., Radke, D., Möller, U., Wilhelm, T., Ideker, T. Integrated Assessment and Prediction of Transcription Factor Binding. PLoS Computational Biology 103(25):9464-9 (2006).
Carayol, N., Chen, J., Yang, F., Jin, T., Jin, L., States, D.J., Wang, C.Y. (2006) A dominant function of IKK/NF-kappaB signaling in global lipopolysaccharide-induced gene expression. J Biol Chem 281(41):31142-51.
Falkner JA, Falkner JW, Andrews PC. ProteomeCommons.org JAF: reference information and tools for proteomics. Bioinformatics. 2006 Mar 1;22(5):632-3. Epub 2006 Jan 24.
Feist, A.M., Scholten, J.C.M., Palsson, B.Ø., Brockman, F.J., and Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Molecular Systems Biology 2:2006.0004 (2006).
Fermin, D., Allen, B.B., Blackwell, T.W., Menon, R., Adamski, M., Xu, Y., Ulintz, P., Omenn, G.S. and States, D.J. (2006) Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biology, 7, R35.
Garcia BA, Joshi S, Thomas CE, Chitta RK, Diaz RL, Busby SA, Andrews PC, Ogorzalek Loo RR, Shabanowitz J, Kelleher NL, Mizzen CA, Allis CD, Hunt DF. Comprehensive Phosphoprotein Analysis of Linker Histone H1 from Tetrahymena thermophila.Mol Cell Proteomics. 2006 Sep;5(9):1593-1609. Epub 2006 Jul 10.
Huo, J.S., McEachin, R.C., Cui, T.X., Duggal, N.K., Hai, T., States, D.J. and Schwartz, J. (2006) Profiles of growth hormone (GH)-regulated genes reveal time-dependent responses and identify a mechanism for regulation of activating transcription factor 3 by GH. J Biol Chem, 281, 4132-4141.
Ideker, T., Valencia, A. Bioinformatics in the human interactome project. Bioinformatics. 22(24):2973-4. Dec 15 (2006).
Jagtap P, Michailidis G, Zielke R, Walker AK, Patel N, Strahler JR, Driks A, Andrews PC, Maddock JR. Early events of Bacillus anthracis germination identified by time-course quantitative proteomics.
Proteomics. 2006 Aug 23; [Epub ahead of print]
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27.
Jiang M, Datta K, Walker A, Strahler J, Bagamasbad P, Andrews PC, Maddock JR. The Escherichia coli GTPase CgtAE Is Involved in Late Steps of Large Ribosome Assembly. J Bacteriol. 2006 Oct;188(19):6757-70.
Keshamouni, V.G., Michailidi, G., Grasso, C.S., Anthwal, S., Strahler, J.R., Walker, A., Arenberg, D.A.,Reddy, R.C., Akulapalli, S., Thannickal, V.J., Standiford, T. J., Andrews, P.C. and Omenn, G.S.: Differential Protein Expression Profiling by iTRAQ-2DLC-MS/MS Reveals a Metastatic Phenotype in TGF-induced Epithelial-Mesenchymal Transitions in Human Lung Cancer Cells. Journal of Proteome Research. J Proteome Res. 2006 May;5(5):1143-54.
Kozarova A, Sliskovic I, Mutus B, Vacratsis PO, Simon ES, Andrews PC. Identification of Redox Sensitive Thiols of Protein Disulfide Isomerase Using Isotope Coded Affinity Technology and Mass Spectrometry. J Am Soc Mass Spectrom. 2006 Oct 27; [Epub ahead of print]
Lee, A.W. and States, D.J. (2006) Colony-stimulating factor-1 requires PI3-kinase-mediated metabolism for proliferation and survival in myeloid cells. Cell Death and Differentiation. Advance online publication, 3 March 2006; doi:10.1038/sj.cdd.4401884
Mak HC, Daly M, Gruebel B, Ideker T. CellCircuits: a database of protein network models. Nucleic Acids Res. Jan (2007) ;35(Database issue):D538-45. Nov 29 (2006).
Pacifico, S., Liu, G., Guest, S., Parrish, J.R., Fotouhi, F., and Finley, Jr., R.L. A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. BMC Bioinformatics 7, 195, 2006.
Parrish, J.R., Gulyas, K.D., and Finley, Jr., R.L. Yeast two-hybrid contributions to interactome mapping. Current Opin. Biotechnol. 17, 387-393, 2006.
Ranjan, P., Bingham, D.R. and Michailidis, G. (2006), Sequential Experiment Design for Contour Estimation from Complex Computer Codes, to appear in Technometrics
Culp, M., Johnson, K. and Michailidis, G. (2006), ada: an R package for Stochastic Boosting, Journal of Statistical Software, vol 17, issue 2 Haab, B., Geierstanger, B.H, Michailidis, G., Vitzhum, F., Forrester, S., Okon, R., Saviranta, P., Brinker, A., Sorette, M., Perlee, L., Suresh, S., Drwal, G., Adkins, J.N. and Omenn, G. (2005), Immunoassay and antibody microarray analysis of the HUPO PPP reference specimens: systematic variation between sample types and calibration of mass spectrometry data, Proteomics, 13, 3278-3291.
Rauch, A., Bellew, M., Eng, J., Fitzgibbon, M., Holzman, T., Hussey, P., Igra, M., Maclean, B., Lin, C.W., Detter, A., States, D.J., McIntosh, M (2006) Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. Journal of Proteome Research, 5, 112-121.
Reguly T., Breitkreutz A., Boucher L., Breitkreutz BJ., Hon GC., Myers CL., Parsons A., Friesen H., Oughtred R., Tong A., Stark C., Ho Y., Botstein D., Andrews B., Boone C., Troyanskya OG., Ideker T., Dolinski K., Batada NN., Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 5(4):11 (2006).
States, D.J., Omenn, G.S., Blackwell, T.W., Fermin, D., Eng, J., Speicher, D.W. and Hanash, S.M. (2006) Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nature Biotechnology, 24, 333-338.
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics. 7(1):360 (2006).
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.
Workman, CT., Mak, HC., McCuine, S., Tagne, JB., Agarwal, M., Ozier, O., Begley, TJ., Samson, LD., Ideker, T. A Systems Approach to Mapping DNA Damage Response Pathways. Science. 312 (5776):1054-1059 (2006).