Publications

2008

E. Balleza, E. Alvarez-Buylla, A. Chaos, S. A. Kauffman, I. Shmulevich, M. Aldana, “Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms,” PLoS ONE, Vol. 3, No. 6, e2456, 2008.

W.W. Lee, D. Cui, M. Czesnikiewicz-Guzik, R.Z. Vencio, I. Shmulevich, A. Aderem, C.M. Weyand, J.J. Goronzy,” Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling,” Rejuvenation Research, Vol. 11, No. 6, pp. 1001-1011, 2008.

A. Aderem, I. Shmulevich, “Taming data,” Cell Host & Microbe, Vol. 4, No. 4, pp. 312-313, 2008.

J. Boyle, C. Cavnor, S. Killcoyne, I. Shmulevich, “Systems biology driven software design for the research enterprise,” BMC Bioinformatics, Vol. 9, No. 295, 2008.

W. Liu, H. Lähdesmäki, E. R. Dougherty, I. Shmulevich, “Inference of Boolean Networks using Sensitivity Regularization,” EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541, 12 pages, 2008.

H. Lähdesmäki, I. Shmulevich, “Learning the Structure of Dynamic Bayesian Networks from Time Series and Steady State Measurements,” Machine Learning, Vol. 71, pp.185-217, 2008.

M. Korb, A. G. Rust, V. Thorsson, C. Battail, B. Li, D. Hwang, K. Kennedy, J. C. Roach, C. M. Rosenberger, M. Gilchrist, D. Zak, C. Johnson, B. Marzolf, A. Aderem, I. Shmulevich, H. Bolouri, “The Innate Immune Database (IIDB) ,” BMC Immunology, Vol. 9, No. 7, 2008.

H. Lähdesmäki, A. G. Rust, I. Shmulevich, “Probabilistic inference of transcription factor binding from multiple data sources,” PLoS ONE, Vol. 3, No. 3, e1820, 2008.

S. A. Ramsey, S. L. Klemm, D. E. Zak, K. A. Kennedy, V. Thorsson, B. Li, M. Gilchrist, E. Gold, C. D. Johnson, V. Litvak, G. Navarro, J. C. Roach, C. M. Rosenberger, A. G. Rust, N. Yudkovsky, A. Aderem, I. Shmulevich, “Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics,” PLoS Computational Biology, Vol. 4, No. 3, e1000021, 2008.

M. Nykter, N. D. Price, A. Larjo, T. Aho, S. A. Kauffman, O. Yli-Harja, I. Shmulevich, “Critical networks exhibit maximal information diversity in structure-dynamics relationships,” Physical Review Letters, Vol. 100, 058702, 2008.

M. Nykter, N. D. Price , M. Aldana, S. A. Ramsey, S. A. Kauffman, L. Hood, O. Yli-Harja, I. Shmulevich, “Gene Expression Dynamics in the Macrophage Exhibit Criticality,” Proceedings of the National Academy of Sciences of the USA, Vol. 105, No. 6, pp. 1897-1900, 2008.