I. Shmulevich, J. D. Aitchison, “Deterministic and stochastic models of genetic regulatory networks,” Methods in Enzymology, Vol. 467, pp. 335-356, 2009.

J. Selinummi, P. Ruusuvuori, I. Podolsky, A. Ozinsky, E. Gold, O. Yli-Harja, A. Aderem, I. Shmulevich, “Bright Field Microscopy as an Alternative to Whole Cell Fluorescence in Automated Analysis of Macrophage Images,” PLoS ONE, Vol. 4, No. 10, 2009.

V. Litvak, S. Ramsey, A. Rust, D. Zak, K. Kennedy, A. Lampano, M. Nykter, I. Shmulevich, A. Aderem, “Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals ,” Nature Immunology, Vol. 10, No. 4, pp. 437-43, 2009.

T. A. Knijnenburg, L. F. A. Wessels, M. J. T. Reinders, I. Shmulevich, Fewer permutations, more accurate P-values,” Bioinformatics Vol. 25, No. 12, pp. i161-i168, 2009.

R. J. Taylor, D. Falconnet, A. Niemistö, S. A. Ramsey, S. Prinz, I. Shmulevich, T. Galitski, C. L. Hansen, “Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform,” Proceedings of the National Academy of Sciences of the USA, Vol. 106, No. 10, pp. 3758-3763, 2009.

L. Hu, W. Hittelman, T. Lu, P. Ji, R. Arlinghaus, I. Shmulevich, S. R. Hamilton, W. Zhang, “NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells,” Laboratory Investigation, Vol. 89, pp. 531–548, 2009.

M. Nykter, H. Lähdesmäki, A. Rust, V. Thorsson, I. Shmulevich, “ A data integration framework for prediction of transcription factor targets: a BCL6 case study,” Annals of the New York Academy of Sciences, Vol. 1158, pp. 205-214, 2009.

J. Boyle, H. Rovira, C. Cavnor, D. Burdick, S. Killcoyne, I. Shmulevich, “Adaptable Data Management for Systems Biology Investigations,” BMC Bioinformatics, Vol. 10, No. 79, 2009.

A.C. Huang, L. Hu, S.A. Kauffman, W. Zhang, I. Shmulevich, “Using Cell Fate Attractors to Uncover Transcriptional Regulation of HL60 Neutrophil Differentiation,” BMC Systems Biology, Vol. 3, No. 20, 2009.