Publications 2007
2008 — 2007 — 2006 — 2005 — 2004 — 2003
Publications In Press
Recent Posters
Chen, Y., Blackwell, T.W., Chen, J., Gao, J., Lee, A.W. and States, D.J. (2007) Integration of Genome and Chromatin Structure with Gene Expression Profiles to Predict c-MYC Recognition Site Binding and Function. PLoS Computational Biology In press.
Culp, M. and Michailidis, G. (2007), An Iterative Algorithm for Extending Learners to a Semi-supervised Setting, to appear in Journal of Computational and Graphical Statistics
Culp, M., and Michailidis, G. (2007), Graph Based Semi-Supervised Learning, to appear in IEEE Transactions on Pattern Analysis and Machine Intelligence
Falkner JA, Falkner JW, Andrews PC. ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats. Bioinformatics. 2007 Jan 15;23(2):262-3.
Falkner JA, Kachman M, Veine DM, Walker A, Strahler JR, Andrews PC. Validated MALDI-TOF/TOF Mass Spectra for Protein Standards. J Am Soc Mass Spectrom. 2007 May;18(5):850-5.
Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Mol Syst Biol.; 3:105. Apr 17 (2007).
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, Sullivan SM, Walker AK, Strahler JR, Andrews PC, Maddock JR. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J Bacteriol. 2007 May;189(9):3434-44.
Kelley R, Feizi H, Ideker T. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics. Epub ahead of print Jul 10 (2007).
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).
Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R. SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics. 23(13):i359-i366. Jul 1 (2007).
Parrish, J.R., Liu, G., Hines, J.A., Yu, J., Chan, J.E., Mangiola, B.A., Zhang, H., Pacifico, S., Fotouhi, F., DiRita, V.J., Ideker, T., Andrews, P., and Finley, Jr., R.L. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biology, 8(7) R130.1-19, 2007.
Rajagopala, S.V., Titz, B., Goll, J., Parrish, J.R., Wohlbold, K., McKevitt, K.T., Palzkill, T., Mori, H., Finley, Jr., R.L., and Uetz, P. Functional Genomics of bacterial motility. Molecular Systems Biology, 3:128, 2007.
Tan K, Shlomi T, Feizi H, Ideker T, Sharan R. Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A. Jan 16 (2007).
Tian, Y., McEachin, R.C, Santos, C., States, D.J., Patel, J.M. (2007) SAGA: a subgraph matching tool for biological graphs. Bioinformatics. 23(2):232-9.