Nathan Price, PhD

Associate Director

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Nathan Price is the Associate Director of the Institute for Systems Biology. He is also Affiliate Faculty in the Departments of Bioengineering, Computer Science & Engineering, and Molecular & Cellular Biology at the University of Washington.  Prior to joining ISB in 2011, he was an assistant professor at the University of Illinois at Urbana-Champaign, where he maintains adjunct appointments.  Dr. Price has won numerous awards for his work, including an American Cancer Society Postdoctoral Fellowship, a Howard Temin Pathway to Independence Award from the National Institutes of Health (NIH), a National Science Foundation (NSF) CAREER award, a young investigator award from the Roy J. Carver Charitable Trust, being named as one of the inaugural “Tomorrow’s PIs” by Genome Technology, and, most recently, as a Camille Dreyfus Teacher-Scholar. Dr. Price served on the National Academies-Institute of Medicine (IOM) committee to review omics based tests to predict clinical outcome in clinical trials from 2010-2012. Dr. Price served on the scientific advisory board of TetraVitae Bioscience until it was acquired by Eastman Chemical in 2011. He now serves on the Scientific Advisory Boards of Trelys, Inc. and the Novo Nordisk Foundation Center for Biosustainability.  He is also a member of the Board of Directors of the P4 Medicine Institute. He serves on the editorial boards of several scientific journals, including Science Translational MedicineIEEE Life Science LettersBMC Systems Biology, Industrial Biotechnology, and Biotechnology Journal, and was previously a Deputy Editor of PLOS Computational Biology. For more information, please see the Price Lab Website.

PhD, Bioengineering University of California, San Diego, 2005

Computational biology, biological networks, genome-scale models, translational bioinformatics

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2015

Chandrasekaran S, Rittschof C.C, Djukovic D., Gu H., Raftery D., Price ND,Robinson GE.  2015.  Aggression is associated with aerobic glycolysis in the honey bee brain. Genes, brain, and behavior.

Simeonidis E, Price ND.  2015.  Genome-scale modeling for metabolic engineering.Journal of industrial microbiology & biotechnology. 42:327-38.

Chakrabarty P., Li A., Ceballos-Diaz C., Eddy JA, Funk C.C, Moore B., DiNunno N., Rosario A.M, Cruz P.E, Verbeeck C. et al..  2015.  IL-10 Alters Immunoproteostasis in APP Mice, Increasing Plaque Burden and Worsening Cognitive Behavior. Neuron. 85:519-33.

Hood L, Lovejoy J.C, Price ND.  2015.  Integrating big data and actionable health coaching to optimize wellness. BMC medicine. 13:4.

Ament SA, Szelinger S., Glusman G, Ashworth J, Hou L., Akula N., Shekhtman T., Badner J.A, Brunkow M.E, Mauldin DE et al..  2015.  Rare variants in neuronal excitability genes influence risk for bipolar disorder. Proceedings of the National Academy of Sciences of the United States of America. 112:3576-81.

Heavner B.D, Price ND.  2015.  Transparency in metabolic network reconstruction enables scalable biological discovery. Current opinion in biotechnology. 34C:105-109.

2014

Hood L, Price ND.  2014.  Demystifying disease, democratizing health care. Science translational medicine. 6:225ed5.

Benedict MN, Henriksen J.R, Metcalf WW, Whitaker R.J, Price ND.  2014.  ITEP: An integrated toolkit for exploration of microbial pan-genomes. BMC genomics. 15:8.

Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K.  2014.  Systems approach to neurodegenerative disease biomarker discovery. Annual review of pharmacology and toxicology. 54:457-81.

2013

Earls J.C, Eddy JA, Funk C.C, Ko Y., Magis AT, Price ND.  2013.  AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. BMC bioinformatics. 14:78.

Ko Y., Ament SA, Eddy JA, Caballero J, Earls J.C, Hood L, Price ND.  2013.  Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. 110:3095-100.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD et al..  2013.  A community-driven global reconstruction of human metabolism. Nature biotechnology.

Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.  2013.  Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnology journal.

Simeonidis E, Chandrasekaran S, Price ND.  2013.  A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism). Methods Mol Biol. 985:103-12.

Chandrasekaran S, Price ND.  2013.  Metabolic constraint-based refinement of transcriptional regulatory networks. PLoS Comput Biol. 9:e1003370.

Sung J, Kim P.J, Ma S, Funk C.C, Magis AT, Wang Y, Hood L, Geman D, Price ND.  2013.  Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures. PLoS Comput Biol. 9:e1003148.

Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K.  2013.  Systems Approach to Neurodegenerative Disease Biomarker Discovery. Annu Rev Pharmacol Toxicol.

Wang C., Funk C.C, Eddy JA, Price ND.  2013.  Transcriptional Analysis of Aggressiveness and Heterogeneity across Grades of Astrocytomas. PLoS One. 8:e76694.

Heavner B.D, Smallbone K, Price ND, Walker L.P.  2013.  Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford). 2013:bat059.

2012

Benedict MN, Gonnerman MC, Metcalf WW, Price ND.  2012.  Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A. Journal of bacteriology. 194:855-65.

Simcha D., Price ND, Geman D.  2012.  The limits of de novo DNA motif discovery.PloS one. 7:e47836.

Sangar V, Eddy JA, Simeonidis E, Price ND.  2012.  Mechanistic modeling of aberrant energy metabolism in human disease. Frontiers in physiology. 3:404.

Sung J, Wang Y, Chandrasekaran S, Witten DM, Price ND.  2012.  Molecular signatures from omics data: From chaos to consensus. Biotechnology journal.

Bebek G, Koyuturk M, Price ND, Chance MR.  2012.  Network biology methods integrating biological data for translational science. Briefings in bioinformatics.

Wang Y, Eddy JA, Price ND.  2012.  Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC systems biology. 6:153.

Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, Magis AT, Funk C,Price ND, Ekker SC et al..  2012.  Research resource: whole transcriptome RNA sequencing detects multiple 1alpha,25-dihydroxyvitamin d3-sensitive metabolic pathways in developing zebrafish. Molecular endocrinology. 26:1630-42.

Magis AT, Price ND.  2012.  The top-scoring ‘N’ algorithm: a generalized relative expression classification method from small numbers of biomolecules. BMC bioinformatics. 13:227.

2011

Chandrasekaran S, Ament SA, Eddy JA, Rodriguez-Zas SL, Schatz BR, Price ND,Robinson GE.  2011.  Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states. Proceedings of the National Academy of Sciences of the United States of America. 108:18020-5.

Yan X, Ma L, Yi D, Yoon JG, Diercks A, Foltz G, Price ND, Hood LE, Tian Q.  2011.  A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A. 108:1591-6.

Kim P.J, Price ND.  2011.  Genetic co-occurrence network across sequenced microbes.PLoS computational biology. 7:e1002340.

Magis AT, Earls J.C, Ko Y.H, Eddy JA, Price ND.  2011.  Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics. 27:872-3.

Bebek G, Koyuturk M, Chance MR, Price ND.  2011.  INTEGRATIVE -OMICS FOR TRANSLATIONAL SCIENCE – Session Introduction. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. :1-3.

Li Q., Singh C.R, Ma S, Price ND, Jagannath C..  2011.  Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages.Journal of proteome research. 10:2425-39.

Milne C.B, Eddy JA, Raju R., Ardekani S., Kim P.J, Senger R.S, Jin Y.S, Blaschek H.P, Price ND.  2011.  Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC systems biology. 5:130.

Tian Q, Price ND, Hood L.  2011.  Systems Cancer Medicine: Towards Realization of Predictive, Preventive, Personalized, and Participatory (P4) Medicine. Journal of internal medicine.

2010

Ezeji T., Milne C., Price ND, Blaschek H.P.  2010.  Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms.Applied microbiology and biotechnology. 85:1697-712.

Galas DJ, Nykter M, Carter GW, Price ND, Shmulevich I.  2010.  Biological Information as Set-Based Complexity. IEEE transactions on information theory. 56:667-677.

Price ND, Lee S.Y.  2010.  Editorial: Systems biology for biotech applications.Biotechnology journal. 5:636-7.

Eddy JA, Hood L, Price ND, Geman D.  2010.  Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol. 6:e1000792.

Edelman L.B, Eddy JA, Price ND.  2010.  In silico models of cancer. Wiley interdisciplinary reviews. Systems biology and medicine. 2:438-59.

Yang J, Eddy JA, Pan Y., Hategan A., Tabus I, Wang Y, Cogdell D, Price ND,Pollock RE, Lazar A.J et al..  2010.  Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug. Molecular & cellular proteomics : MCP. 9:2405-13.

Kim P.J, Price ND.  2010.  Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions. Physical review letters. 104:148103.

Chandrasekaran S, Price ND.  2010.  Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 107:17845-50.

Eddy JA, Sung J, Geman D, Price ND.  2010.  Relative expression analysis for molecular cancer diagnosis and prognosis. Technology in cancer research & treatment. 9:149-59.

Ma S, Funk C.C, Price ND.  2010.  Systems approaches to molecular cancer diagnostics. Discovery medicine. 10:531-42.

Edelman L.B, Chandrasekaran S, Price ND.  2010.  Systems biology of embryogenesis. Reproduction, fertility, and development. 22:98-105.

2009

Milne C.B, Kim P.J, Eddy JA, Price ND.  2009.  Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnology journal. 4:1653-70.

Eddy JA, Geman D, Price ND.  2009.  Relative expression analysis for identifying perturbed pathways. Conference proceedings : … Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2009:5456-9.

Hwang D, Lee I, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R,Young R, Spicer D et al..  2009.  A systems approach to prion disease. Molecular systems biology. 5:252.

Price ND, Edelman LB, Lee I, Yoo H, Hwang D, Carlson G, Galas DJ, Heath JR,Hood L.  2009.  Systems biology and the emergence of systems medicine. Genomic and Personalized Medicine: From Principles to Practice.

Edelman L.B, Toia G., Geman D, Zhang W, Price ND.  2009.  Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. BMC genomics. 10:583.

2008

Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I.  2008.  Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett. 100:058702.

Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O,Shmulevich I.  2008.  Gene expression dynamics in the macrophage exhibit criticality.Proc Natl Acad Sci U S A. 105:1897-900.

Price ND, Foltz G, Madan A, Hood L, Tian Q.  2008.  Systems biology and cancer stem cells. J Cell Mol Med. 12:97-110.

2007

Price ND, Shmulevich I.  2007.  Biochemical and statistical network models for systems biology. Curr Opin Biotechnol. 18:365-70.

Price ND, Trent J, El-Naggar AK, Cogdell D, Taylor E, Hunt KK, Pollock RE, Hood L, Shmulevich I, Zhang W.  2007.  Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A. 104:3414-9.

2006

Price ND, Thiele I, Palsson BO.  2006.  Candidate states of Helicobacter pylori’s genome-scale metabolic network upon application of “loop law” thermodynamic constraints.Biophysical journal. 90:3919-28.

Allen T.E, Price ND, Joyce A.R, Palsson BO.  2006.  Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS computational biology. 2:e2.

Gianchandani E.P, Papin JA, Price ND, Joyce A.R, Palsson BO.  2006.  Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS computational biology. 2:e101.

Becker S.A, Price ND, Palsson BO.  2006.  Metabolite coupling in genome-scale metabolic networks. BMC bioinformatics. 7:111.

Barrett C.L, Price ND, Palsson BO.  2006.  Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. BMC bioinformatics. 7:132.

2005

Thiele I, Price ND, Vo T.D, Palsson BO.  2005.  Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. The Journal of biological chemistry. 280:11683-95.

Thiele I, Vo T.D, Price ND, Palsson BO.  2005.  Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. Journal of bacteriology. 187:5818-30.

2004

Papin JA, Stelling J., Price ND, Klamt S., Schuster S., Palsson BO.  2004.  Comparison of network-based pathway analysis methods. Trends in biotechnology. 22:400-5.

Price ND, Reed J.L, Palsson BO.  2004.  Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature reviews. Microbiology. 2:886-97.

Raghunathan A., Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF,Cherny T, Xie T, Reilly TJ, Munson, Jr. R. et al..  2004.  In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.Omics : a journal of integrative biology. 8:25-41.

Price ND, Schellenberger J., Palsson BO.  2004.  Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophysical journal. 87:2172-86.

2003

Price ND, Reed J.L, Papin JA, Famili I., Palsson BO.  2003.  Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophysical journal. 84:794-804.

Palsson BO, Price ND, Papin JA.  2003.  Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends in biotechnology. 21:195-8.

Price ND, Papin JA, Schilling C.H, Palsson BO.  2003.  Genome-scale microbial in silico models: the constraints-based approach. Trends in biotechnology. 21:162-9.

Papin JA, Price ND, Wiback S.J, Fell D.A, Palsson BO.  2003.  Metabolic pathways in the post-genome era. Trends in biochemical sciences. 28:250-8.

Price ND, Reed J.L, Papin JA, Wiback S.J, Palsson BO.  2003.  Network-based analysis of metabolic regulation in the human red blood cell. Journal of theoretical biology. 225:185-94.

2002

Price ND, Papin JA, Palsson BO.  2002.  Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome research. 12:760-9.

Papin JA, Price ND, Palsson BO.  2002.  Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome research. 12:1889-900.

Price ND, Famili I., Beard D.A, Palsson BO.  2002.  Extreme pathways and Kirchhoff’s second law. Biophysical journal. 83:2879-82.

Papin JA, Price ND, Edwards J.S, B. Palsson B.  2002.  The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. Journal of theoretical biology. 215:67-82.