Journal Articles

Article titles link to NCBI abstract, where applicable.

2011

1. Li Q, Singh CR, Ma S, Price ND, Jagannath C., Label-free Proteomics and Systems Biology Analysis of Mycobacterial Phagosomes in Dendritic Cells and Macrophages. J Proteome Res. 10(5):2425-39.(2011)
2. Magis AT, Earls JC, Ko YH, Eddy JA, Price ND., Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics. 27(6):872-3.(2011)
3. Yan X, Ma L, Yi D, Yoon JG, Diercks A, Foltz G, Price ND, Hood LE, Tian Q., A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A. 108(4):1591-6.(2011)
4. Bebek G, Koyuturk M, Chance MR, Price ND., INTEGRATIVE -OMICS FOR TRANSLATIONAL SCIENCE - Session Introduction. Pac Symp Biocomput. 1-3.(2011)

2010

1. Ma S, Funk CC, Price ND., Systems approaches to molecular cancer diagnostics. Discov Med. 10(55):531-42.(2010)
2. Chandrasekaran S, Price ND., Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. [journal full text], Proc Natl Acad Sci U S A.107(41):17845-50.(2010)
3. Edelman LB, Eddy JA, Price ND., In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med. 2(4):438-5.(2010)
4. The MAQC Consortium (including Sung, J. and Price, N.D.), The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models [journal full text], Nature Biotechnology 28, 827-838 (2010)
5. Price, N.D. and Lee, S.Y., Editorial: Systems biology for biotech applications [journal full text], Biotechnology Journal, 5(7):636-637 (2010).
6. Yang, J., Eddy, J.A., Hategan, A., Tabus, I., Wang, Y., Cogdell, D., Price, N.D., Pollock, R.E., Lazar, A.J., Hunt, K.K., Trent, J.C., and Zhang, W., Integrated Proteomic and Genomic Analysis Reveals a Novel Mesenchymal to Epithelial Reverting Transition in Leiomyosarcoma through Regulation of Slug [journal full text], Molecular & Cellular Proteomics,9(11):2405-13 (2010).
7. Edelman, L.B., Eddy, J.A., and Price, N.D., In silico models of cancer [journal full text], Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2(4):438-459 (2010).
8. Eddy, J.A., Hood, L., Price, N.D., and Geman, D., Identifiying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC) [journal full text], PLoS Computational Biology, 6(5):e1000792 (2010).
9. Kim, P.J. and Price, N.D., Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions [journal full text], Physical Review Letters, 104(14):148103 (2010). Highlighted by ScienceNews.
10. Eddy, J.A., Sung, J., Geman, D., and Price, N.D., Relative expression analysis for molecular cancer diagnosis and prognosis [journal full text], Technology in Cancer Research & Treatment, 9(2):149-159 (2010).
11. Ezeji, T., Milne, C., Price, N.D., and Blaschek, H.P., Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms [journal full text], Applied Microbiology and Biotechnology, 85(6):1697-1712 (2010).
12. Galas, D.J., Nykter, M., Carter, G.W., Price, N.D., and Shmulevich, I., Biological information as set-based complexity [journal full text], IEEE Transactions on Information Theory, 56(2):667-677 (2010).
13. Edelman, L.B., Chandrasekaran, S., and Price, N.D., Systems biology of embryogenesis [journal full text], Reproduction, Fertility, and Development, 22(1):98-105 (2010).

2009

1. Eddy, J.A., Geman D., and Price, N.D., Relative expression analysis for identifying perturbed pathways [journal full text], Conference Proceedings of the IEEE Engineering in Medicine and Biology Society, 2009:5456-5459 (2009).
2. Edelman, L.B., Toia, G., Geman, D., Zhang, W., and Price, N.D., Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases [journal full text], BMC Genomics, 10:583 (2009). Highly Accessed.
3. Milne, C.B., Kim, P.J., Eddy, J.A., and Price, N.D., Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology [journal full text], Biotechnology Journal, 4(12):1653-1670 (2009).
4. Hwang, D., Lee, I.Y., Yoo, H., Gehlenborg, N., Cho, J.H., Petritis, B., Baxter, D., Pitstick, R., Young, R., Spicer, D., Price, N.D., Hohmann, J.G., Dearmond, S.J., Carlson, G.A., and Hood L.E., A systems approach to prion disease [journal full text], Molecular Systems Biology, 5:252 (2009).

2008

1. Nykter, M., Price, N.D., Larjo, A., Aho, T., Aldana, M., Kauffman, S.A., Hood, L., Yli-Harja, O., and Shmulevich, I., Critical networks exhibit maximal information diversity in structure-dynamics relationships [journal full text], Physical Review Letters, 100(5):058702 (2008).
2. 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 [journal full text], Proceedings of the National Academy of Sciences USA, 105(6):1897-1900 (2008). Highlighted by Nature Reviews Genetics.
3. Price, N.D., Foltz, G., Madan, A., Hood, L., and Tian, Q., Systems biology and cancer stem cells [journal full text], Journal of Cellular and Molecular Medicine, 12(1):97-110 (2008).

2007

1. Price, N.D., and Shmulevich, I., Biochemical and statistical network models for systems biology [journal full text], Current Opinion in Biotechnology, 18:365-370 (2007).
2. 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 [journal full text], Proceedings of the National Academy of Sciences USA, 104:3414-3419 (2007).

2006

1. 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 [journal full text], PLoS Computational Biology, 2:e101 (2006). Cover Article
2. 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 [journal full text], Biophysical Journal, 90:3919-3928 (2006).
3. Becker, S.A., Price, N.D., and Palsson, B.O., Metabolite coupling in genome-scale metabolic networks [journal full text], BMC Bioinformatics, 7:111 (2006).
4. Barrett, C., Price, N.D., and Palsson, B.O., Network-based analysis of metabolic regulation using uniform random sampling and singular value decomposition [journal full text], BMC Bioinformatics, 7:132 (2006).
5. Allen, T.E., Price, N.D., Joyce, A., and Palsson, B.O., Long-range patterns in prokaryotic genome sequences indicate significant chromosomal organization [journal full text], PLoS Computational Biology, 2(1): e2 (2006). Cover Article

2005

1. Thiele, I., Vo, T., Price, N.D., and Palsson, B.O., Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single and double deletion mutants [journal full text], Journal of Bacteriology, 187:5818-5830 (2005).
2. 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 full text], Journal of Biological Chemistry, 280:11683-11695 (2005).

2004

1. Price, N.D., Reed, J.L. and Palsson, B.O., Genome-scale models of microbial cells:evaluating the consequences of constraints [journal full text], Nature Reviews Microbiology, 2:886-897(2004).
2. Price, N.D., Schellenberger, J., and Palsson, B.O., Uniform sampling of steady state flux spaces: means to design experiments and to interpret enzymopathies [journal full text], Biophysical Journal, 87:2172-2186(2004).
3. Raghunathan, A.^*, Price, N.D.^* and Kolker,E., In silico metabolic model and protein expression of Haemophilus influenzae strain Rd KW20 in rich medium [journal full text], OMICS: A Journal of Integrative Biology, 8(1):25-42 (2004).

2003

1. 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 full text], Journal of Theoretical Biology, 225(2):1985-194 (2003).
2. Palsson, B.O., Price, N.D., Papin, J.A., Development of network-based pathway definitions: the need to analyze real metabolic networks [journal full text], Trends in Biotechnology, 21(5):195-198 (2003).
3. Papin, J.A., Price, N.D., Wiback, S.J., Fell, D.A., and Palsson, B.O., Metabolic pathways in the post-genome era [journal full text], Trends in Biochemical Sciences, 28:250-258 (2003).
4. Price, N.D., Papin, J.A., Schilling, C.H., and Palsson, B.O., Genome-scale microbial in silico models: the constraints-based approach [journal full text], Trends in Biotechnology, 21(4):162-169 (2003).
5. 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 [journal full text], Biophysical Journal, 84:794-804 (2003).

2002

1. Papin, J.A.^*, Price, N.D.^*, and Palsson, B.O., Extreme pathway lengths and reaction participation in genome-scale metabolic networks [journal full text], Genome Research, 12:1889-1900 (2002).
2. Price, N.D., Famili, I., Beard, D.A. and Palsson, B.O., Extreme pathways and Kirchhoff's second law [journal full text], Biophysical Journal, 83(1):2879-2882 (2002).
3. 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 full text], Journal of Theoretical Biology, 215(1):67-82 (2002).
4. 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 [journal full text], Genome Research, 12:760-769 (2002).

* These authors contributed equally to these works.

Book Chapters

1. Blaschek, H.P., Ezeji, T., and Price, N.D., Present and future possibilities for the deconstruction and utilization of lignocellulosic biomass [publisher full text], Handbook of Bioenergy Economics and Policy, (Khanna, M., Scheffran, J., and Zilberman, D., editors), Springer (2010).
2. 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 (2009).
3. Eddy, J.A. and Price, N.D., Biological data integration and model building, Encyclopedia of Complexity and Systems Science, (Meyers, R.A., editor), Springer (2009).
4. 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).