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Large-scale high-throughput measurement technologies have allowed system-wide modeling and analysis of cells in health and disease. Each type of measurement data, be it transcript enumeration data, protein lysate array data, or microarray data from heterogeneous cell populations, requires appropriate statistical and computational methods.
Publications:
R. Vêncio, I. Shmulevich, "ProbCD: enrichment analysis accounting for categorization uncertainty," BMC Bioinformatics, Vol. 8, No. 383, 2007.
R. Vêncio, L. Varuzza, C. Pereira, H. Brentani, I. Shmulevich, "Simcluster: clustering enumeration gene expression data on the simplex space," BMC Bioinformatics, Vol. 8, No. 246, 2007.
M. Ahdesmäki , H. Lähdesmäki, A. Gracey , I. Shmulevich and O. Yli-Harja, "Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data," BMC Bioinformatics, Vol. 8, No. 233, 2007.
I. Tabus, A. Hategan, C. Mircean, J. Rissanen, I. Shmulevich, W. Zhang, J. Astola, “Nonlinear modeling of protein expressions in protein arrays,” IEEE Transactions on Signal Processing, Vol. 54, No. 6, pp. 2394-2407, 2006.
C. Mircean, I. Shmulevich, D. Cogdell, W. Choi, Y. Jia, I. Tabus, S. R. Hamilton, W. Zhang, "Robust estimation of protein expression ratios with lysate microarray technology," Bioinformatics, Vol. 21, No. 9, pp. 1935-1942, 2005.
H. Lähdesmäki, I. Shmulevich, V. Dunmire, O. Yli-Harja, W. Zhang, "In Silico Microdissection of Microarray Data from Heterogeneous Cell Populations," BMC Bioinformatics 6:54, 2005.
I. Shmulevich, J. Astola, D. Cogdell, S. R. Hamilton, and W. Zhang, "Data Extraction From Composite Oligonucleotide Microarrays," Nucleic Acids Research, Vol. 31, No. 7, e36, 2003.
I. Shmulevich, W. Zhang, "Binary Analysis and Optimization-Based Normalization of Gene Expression Data," Bioinformatics, Vol. 18, No. 4, pp. 555-565, 2002.
Software Links:
ProbCD
SimCluster
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