Ashish Bhan and Eric Mjolsness,"Static and dynamic models of biological networks", to appear in Complexity, 2006.
 Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, G. Wesley Hatfield and Eric D. Mjolsness. Application of a Generalized MWC Model for the
Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes, Journal of Bioinformatics and Computational Biology, 2006.
 Roden, J., King, B.W., Trout, D., Mortazavi, A., Wold, B. J. Hart, C. E. Mining gene expression data by interpreting principal components. BMC Bioinformatics 7:194, Apr 7 2006.
 Cheong R, Bergmann A, Werner SL, Regal J, Hoffmann A, Levchenko A. Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. J Biol Chem. 2006 Feb 3;281(5):2945-50. Epub 2005 Dec 1.
 Komarova, NL, Zou, X, Nie, Q and Bardwell, L. A theoretical
framework for specificity in cell signaling. Molecular Systems Biology,
doi:10.1038/msb4100031 (online only journal), 18 October 2005.
 Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, G. Wesley Hatfield and Eric D. Mjolsness. The Generalized Monod, Wyman, Changeux model for mathematical modeling of metabolic enzymes with allosteric regulation, IEEE Computational Systems Bioinformatics Conference,Stanford University, August 8-12 2005.
 J. Cheng, L. Scharenbroich, P. Baldi, and E. Mjolsness,Sigmoid: Towards a Generative, Scalable, Software Infrastructure for Pathway Bioinformatics and Systems Biology, IEEE Intelligent Systems, May/June 2005 (Vol. 20, No. 3), pp. 68-75.
 Hart CE, Sharenbroich L, Bornstein BJ, Trout D. King B., Mjolsness E., and Wold BJ. "A mathematical and computational framework for quantitative comparison and integration of large scale gene expression data." Nucleic Acids Research, May 10;33(8):2580-94, 2005.
 Chin-Ran Yang, Bruce E. Shapiro, She-pin Hung, Eric D. Mjolsness, and G. Wesley Hatfield. A Mathematical Model for the Branched Chain Amino Acid Biosynthetic Pathways of Escherichia coli K12 , Journal of Biological Chemistry, 2005 Mar 25;280(12):11224-32.
 Yang, C-R., Shapiro, B.E., Mjolsness, E.D., and Hatfield, G.W. An enzyme mechanism language for the mathematical modeling of metabolic pathways, Bioinformatics, vol. 21 no. 6, pages 774-780, March 2005.
 Graumann J, Dunipace LA, Seol JH, McDonald WH, Yates JR, Wold BJ, Deshaies RJ. Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Molecular & Cellular Proteomics 3 (3): 226-237, 2004.
 BE. Shapiro, A. Levchenko, EM. Meyerowitz, BJ. Wold, and ED. Mjolsness, Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations, Bioinformatics, 19(5): 677-678, 2002.
 Mjolsness, E.D, "The Sigmoid Biological Pathway Modeling System".
The Seventh Annual BioPathways Meeting, Special Interest Group at , the Intelligent Systems in Molecular Biology conference,Detroit, June 24, 2005.
 Duff, Chudova, Wold, Smyth, & Mjolsness. Statistical inference of biologically-plausible dynamic regulatory networks with core-leaf topology, ICSB, 2005.