Publications

 

Journal Articles

2008

Galas, D.J., Nykter, M., Carter, G.W., Price, N.D., and Shmulevich, I., Biological information and the complexity of sets: Information measures and metrics for complex systems, Submitted (2008).

Nykter, M., Price, N.D., Larjo, A., Aho, T., Aldana, M., Kauffman, S.A., Hood, L., Yli-Harja, O., and Shmulevich, I., Critical Boolean networks exhibit maximal information diversity in structure-dynamics relationships, Physical Review Letters, 100(5):058702 (2008).

Nykter, M., Price, N.D., Aldana, M., Ramsey, S., Kauffman, S.A., Hood, L., Yli-Harja, O., and Shmulevich, I., Gene expression dynamics in the macrophage exhibit criticality, Proceedings of the National Academy of Sciences USA, 105(6):1897-1900 (2008). Highlighted by Nature Reviews Genetics.

Price, N.D., Foltz, G., Madan, A., Hood, L., and Tian, Q., Systems biology and cancer stem cells,
Journal of Cellular and Molecular Medicine, 12(1):97-110 (2008).

2007

Price, N.D., and Shmulevich, I., Biochemical and statistical network models for systems biology,
Current Opinion in Biotechnology, 18:365-370 (2007).

Price, N.D., Trent, J., El-Naggar, A.K., Cogdell, D., Taylor, E., Hunt, K.K., Pollock, R.E., Hood, L., Shmulevich, I., and Zhang, W., Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas, Proceedings of the National Academy of Sciences USA, 104:3414-3419 (2007).

2006

Gianchandani, E.J.^*, Papin, J.A.^*, Price, N.D., Joyce, A., and Palsson, B.O., Matrix formalism for describing functional states of transcriptional regulatory networks, PLoS Computational Biology, 2:e101 (2006). Cover Article

Price, N.D., Thiele, I., and Palsson, B.O., Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of loop law thermodynamic constraints, Biophysical Journal, 90:3919-3928 (2006).

Becker, S.A., Price, N.D., and Palsson, B.O., Metabolite coupling in genome-scale metabolic networks, BMC Bioinformatics, 7:111 (2006).

Barrett, C., Price, N.D., and Palsson, B.O., Network-based analysis of metabolic regulation using uniform random sampling and singular value decomposition, BMC Bioinformatics, 7:132 (2006).

Allen, T.E., Price, N.D., Joyce, A., and Palsson, B.O., Long-range patterns in prokaryotic genome sequences indicate significant chromosomal organization, PLoS Computational Biology, 2(1): e2 (2006). Cover Article

2005

Thiele, I., Vo, T., Price, N.D., and Palsson, B.O., Genome-scale metabolic model of Helicobacter pylori, iIT338: an in silico genome-scale characterization of single and double deletion mutants, Journal of Bacteriology, 187:5818-5830 (2005).

Thiele, I., Price, N.D., Vo, T., and Palsson, B.O., Candidate metabolic network states in human mitochondria: impact of diabetes, ischemia, and diet, Journal of Biological Chemistry, 280:11683-11695 (2005).

2004

Price, N.D., Reed, J.L. and Palsson, B.O., Genome-scale models of microbial cells:evaluating the consequences of constraints, Nature Reviews Microbiology, 2:886-897(2004).

Price, N.D., Schellenberger, J., and Palsson, B.O., Uniform sampling of steady state flux spaces: means to design experiments and to interpret enzymopathies, Biophysical Journal, 87:2172-2186(2004).

Raghunathan, A.^*, Price, N.D.^* and Kolker,E., In silico metabolic model and protein expression of Haemophilus influenzae strain Rd KW20 in rich medium, OMICS: A Journal of Integrative Biology, 8(1):25-42 (2004).

2003

Price, N.D.^*, Reed, J.L.^*, Papin, J.A.^*, Wiback, S.J., and Palsson, B.O., Network-based analysis of regulation in the human red blood cell,” Journal of Theoretical Biology, 225(2):1985-194 (2003).

Palsson, B.O., Price, N.D., Papin, J.A., Development of network-based pathway definitions: the need to analyze real metabolic networks, Trends in Biotechnology, 21(5):195-198 (2003).

Papin, J.A., Price, N.D., Wiback, S.J., Fell, D.A., and Palsson, B.O., Metabolic pathways in the post-genome era, Trends in Biochemical Sciences, 28:250-258 (2003).

Price, N.D., Papin, J.A., Schilling, C.H., and Palsson, B.O., Genome-scale microbial in silico models: the constraints-based approach, Trends in Biotechnology, 21(4):162-169 (2003).

Price, N.D.^*, Reed, J.L.^*, Papin, J.A.^*, Famili, I. and Palsson, B.O., Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices, Biophysical Journal, 84:794-804 (2003).

2002

Papin, J.A.^*, Price, N.D.^*, and Palsson, B.O., Extreme pathway lengths and reaction participation in genome-scale metabolic networks, Genome Research, 12:1889-1900 (2002).

Price, N.D., Famili, I., Beard, D.A. and Palsson, B.O., Extreme pathways and Kirchhoff's second law, Biophysical Journal, 83(1):2879-2882 (2002).

Papin, J.A.^*, Price, N.D.^*, Edwards, J.S., and Palsson, B.O., The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy, Journal of Theoretical Biology, 215(1):67-82 (2002).

Price, N.D.^*, Papin, J.A.^*, Palsson, B.O., Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis, Genome Research, 12:760-769 (2002).

* These authors contributed equally to these works.

Book Chapters

Price, N.D., Edelman, L.B., Lee, I., Yoo, H., Hwang, D., Galas, D.J., Heath, J.R., and Hood, L., Systems biology and the emergence of systems medicine, Genomic and Personalized Medicine: From Principles to Practice, (Ginsburg, G. and Heath, W., editors), Elservier, to appear in 2009.

Eddy, J.A. and Price, N.D., Biological data integration and model building, Encyclopedia of Complexity and Systems Science, (Meyers, R.A., editor), Springer, In press (2009).

Papin, J.A., N.D. Price, and B.O. Palsson., In silico cells: studying genotype-phenotype relationships using constraints-based models, Metabolic Engineering in the Post-Genomic Era, (Westerhoff, H. and Kholodenko, B., editors) (2004).