Nathan Daniel Price - Publications

Affiliations: 
2005 University of California, San Diego, La Jolla, CA 

154 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Zubair N, Conomos MP, Hood L, Omenn GS, Price ND, Spring BJ, Magis AT, Lovejoy JC. Genetic Predisposition Impacts Clinical Changes in a Lifestyle Coaching Program. Scientific Reports. 9: 6805. PMID 31048771 DOI: 10.1038/s41598-019-43058-0  0.92
2019 Shen F, Sun R, Yao J, Li J, Liu Q, Price ND, Liu C, Wang Z. OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling. Plos Computational Biology. 15: e1006835. PMID 30849073 DOI: 10.1371/journal.pcbi.1006835  0.6
2019 Pearl JR, Colantuoni C, Bergey DE, Funk CC, Shannon P, Basu B, Casella AM, Oshone RT, Hood L, Price ND, Ament SA. Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders. Cell Systems. PMID 30772379 DOI: 10.1016/j.cels.2019.01.002  0.84
2018 Paquette AG, Chu T, Wu X, Wang K, Price ND, Sadovsky Y. Distinct communication patterns of trophoblastic miRNA among the maternal-placental-fetal compartments. Placenta. 72: 28-35. PMID 30501878 DOI: 10.1016/j.placenta.2018.10.004  0.6
2018 Chakrabarty P, Li A, Ladd TB, Strickland MR, Koller EJ, Burgess JD, Funk CC, Cruz PE, Allen M, Yaroshenko M, Wang X, Younkin C, Reddy J, Lohrer B, Mehrke L, ... ... Price ND, et al. TLR5 decoy receptor as a novel anti-amyloid therapeutic for Alzheimer's disease. The Journal of Experimental Medicine. PMID 30158114 DOI: 10.1084/jem.20180484  0.84
2018 Magis AT, Earls JC, Glusman G, Omenn GS, Lovejoy JC, Price ND, Hood L. Reply to "Precision medicine in the clouds". Nature Biotechnology. 36: 680-682. PMID 30080845 DOI: 10.1038/nbt.4211  0.92
2018 Readhead B, Haure-Mirande JV, Funk CC, Richards MA, Shannon P, Haroutunian V, Sano M, Liang WS, Beckmann ND, Price ND, Reiman EM, Schadt EE, Ehrlich ME, Gandy S, Dudley JT. Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus. Neuron. PMID 29937276 DOI: 10.1016/j.neuron.2018.05.023  0.84
2018 Mikheev AM, Mikheeva SA, Severs LJ, Funk CC, Huang L, McFaline-Figueroa JL, Schwensen J, Trapnell C, Price ND, Wong S, Rostomily RC. Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma. Molecular Oncology. PMID 29754406 DOI: 10.1002/1878-0261.12320  0.84
2018 Trachana K, Bargaje R, Glusman G, Price ND, Huang S, Hood LE. Taking Systems Medicine to Heart. Circulation Research. 122: 1276-1289. PMID 29700072 DOI: 10.1161/CIRCRESAHA.117.310999  0.6
2018 Dinalankara W, Ke Q, Xu Y, Ji L, Pagane N, Lien A, Matam T, Fertig EJ, Price ND, Younes L, Marchionni L, Geman D. Digitizing omics profiles by divergence from a baseline. Proceedings of the National Academy of Sciences of the United States of America. PMID 29666255 DOI: 10.1073/pnas.1721628115  0.92
2018 Ament SA, Pearl JR, Cantle JP, Bragg RM, Skene PJ, Coffey SR, Bergey DE, Wheeler VC, MacDonald ME, Baliga NS, Rosinski J, Hood LE, Carroll JB, Price ND. Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. Molecular Systems Biology. 14: e7435. PMID 29581148  0.68
2018 Kearney P, Boniface JJ, Price ND, Hood L. The building blocks of successful translation of proteomics to the clinic. Current Opinion in Biotechnology. 51: 123-129. PMID 29427919 DOI: 10.1016/j.copbio.2017.12.011  0.76
2018 Paquette AG, Shynlova O, Kibschull M, Price ND, Lye SJ. Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor. American Journal of Obstetrics and Gynecology. PMID 29305255 DOI: 10.1016/j.ajog.2017.12.234  0.36
2017 King B, Farrah T, Richards MA, Mundy M, Simeonidis E, Price ND. ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions. Bioinformatics (Oxford, England). PMID 29267848 DOI: 10.1093/bioinformatics/btx796  0.56
2017 Paquette AG, Brockway HM, Price ND, Muglia LJ. Comparative transcriptomic analysis of human placentae at term and preterm delivery. Biology of Reproduction. PMID 29228154 DOI: 10.1093/biolre/iox163  0.36
2017 Pearl JR, Heath LM, Bergey DE, Kelly JP, Smith C, Laurino MY, Weiss A, Price ND, LaSpada A, Bird TD, Jayadev S. Enhanced retinal responses in Huntington's disease patients. Journal of Huntington's Disease. 6: 237-247. PMID 28968243 DOI: 10.3233/JHD-170255  0.56
2017 Samal A, Craig JP, Coradetti ST, Benz JP, Eddy JA, Price ND, Glass NL. Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa. Biotechnology For Biofuels. 10: 225. PMID 28947916 DOI: 10.1186/s13068-017-0901-2  0.96
2017 Seo SO, Janssen H, Magis A, Wang Y, Lu T, Price ND, Jin YS, Blaschek HP. Genomic, transcriptional and phenotypic analysis of the glucose derepressed Clostridium beijerinckii mutant exhibiting acid crash phenotype. Biotechnology Journal. PMID 28762642 DOI: 10.1002/biot.201700182  1
2017 Price ND, Magis AT, Earls JC, Glusman G, Levy R, Lausted C, McDonald DT, Kusebauch U, Moss CL, Zhou Y, Qin S, Moritz RL, Brogaard K, Omenn GS, Lovejoy JC, et al. A wellness study of 108 individuals using personal, dense, dynamic data clouds. Nature Biotechnology. PMID 28714965 DOI: 10.1038/nbt.3870  0.92
2017 Marshall-Colon A, Long SP, Allen DK, Allen G, Beard DA, Benes B, von Caemmerer S, Christensen AJ, Cox DJ, Hart JC, Hirst PM, Kannan K, Katz DS, Lynch JP, Millar AJ, ... ... Price ND, et al. Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. Frontiers in Plant Science. 8: 786. PMID 28555150 DOI: 10.3389/fpls.2017.00786  1
2017 Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND. Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. Plos Computational Biology. 13: e1005489. PMID 28520713 DOI: 10.1371/journal.pcbi.1005489  1
2017 Coffey SR, Bragg RM, Minnig S, Ament SA, Cantle JP, Glickenhaus A, Shelnut D, Carrillo JM, Shuttleworth DD, Rodier JA, Noguchi K, Bennett CF, Price ND, Kordasiewicz HB, Carroll JB. Peripheral huntingtin silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington's disease. Plos One. 12: e0175968. PMID 28453524 DOI: 10.1371/journal.pone.0175968  0.68
2017 Ghosh D, Funk CC, Caballero J, Shah N, Rouleau K, Earls JC, Soroceanu L, Foltz G, Cobbs CS, Price ND, Hood L. A Cell-Surface Membrane Protein Signature for Glioblastoma. Cell Systems. PMID 28365151 DOI: 10.1016/j.cels.2017.03.004  0.92
2017 Bragg RM, Coffey SR, Weston RM, Ament SA, Cantle JP, Minnig S, Funk CC, Shuttleworth DD, Woods EL, Sullivan BR, Jones L, Glickenhaus A, Anderson JS, Anderson MD, Dunnett SB, ... ... Price ND, et al. Corrigendum: Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.Htt(Q111/+) model of Huntington's disease. Scientific Reports. 7: 44960. PMID 28350386 DOI: 10.1038/srep44960  0.84
2017 Ament SA, Pearl JR, Grindeland A, St Claire J, Earls JC, Kovalenko M, Gillis T, Mysore J, Gusella JF, Lee JM, Kwak S, Howland D, Lee MY, Baxter D, Scherler K, ... ... Price ND, et al. High resolution time-course mapping of early transcriptomic, molecular and cellular phenotypes in Huntington's disease CAG knock-in mice across multiple genetic backgrounds. Human Molecular Genetics. PMID 28334820 DOI: 10.1093/hmg/ddx006  0.92
2017 Pollak J, Rai KG, Funk CC, Arora S, Lee E, Zhu J, Price ND, Paddison PJ, Ramirez JM, Rostomily RC. Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy. Plos One. 12: e0172884. PMID 28264064 DOI: 10.1371/journal.pone.0172884  0.84
2017 Bragg RM, Coffey SR, Weston RM, Ament SA, Cantle JP, Minnig S, Funk CC, Shuttleworth DD, Woods EL, Sullivan BR, Jones L, Glickenhaus A, Anderson JS, Anderson MD, Dunnett SB, ... ... Price ND, et al. Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.Htt(Q111/+) model of Huntington's disease. Scientific Reports. 7: 41570. PMID 28176805 DOI: 10.1038/srep41570  0.84
2016 Carrasquillo MM, Allen M, Burgess JD, Wang X, Strickland SL, Aryal S, Siuda J, Kachadoorian ML, Medway C, Younkin CS, Nair A, Wang C, Chanana P, Serie D, Nguyen T, ... ... Price ND, et al. A candidate regulatory variant at the TREM gene cluster associates with decreased Alzheimer's disease risk and increased TREML1 and TREM2 brain gene expression. Alzheimer's & Dementia : the Journal of the Alzheimer's Association. PMID 27939925 DOI: 10.1016/j.jalz.2016.10.005  0.84
2016 Richards MA, Lie TJ, Zhang J, Ragsdale SW, Leigh JA, Price ND. Exploring Hydrogenotrophic Methanogenesis: A Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. Journal of Bacteriology. PMID 27736793 DOI: 10.1128/JB.00571-16  0.56
2016 Allen M, Carrasquillo MM, Funk C, Heavner BD, Zou F, Younkin CS, Burgess JD, Chai HS, Crook J, Eddy JA, Li H, Logsdon B, Peters MA, Dang KK, Wang X, ... ... Price ND, et al. Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases. Scientific Data. 3: 160089. PMID 27727239 DOI: 10.1038/sdata.2016.89  0.96
2016 Sagner M, McNeil A, Puska P, Auffray C, Price ND, Hood L, Lavie CJ, Han ZG, Chen Z, Brahmachari SK, McEwen BS, Soares MB, Balling R, Epel E, Arena R. The P4 Health Spectrum - A Predictive, Preventive, Personalized and Participatory Continuum for Promoting Healthspan. Progress in Cardiovascular Diseases. PMID 27546358 DOI: 10.1016/j.pcad.2016.08.002  0.76
2016 Dinov ID, Heavner B, Tang M, Glusman G, Chard K, Darcy M, Madduri R, Pa J, Spino C, Kesselman C, Foster I, Deutsch EW, Price ND, Van Horn JD, Ames J, et al. Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations. Plos One. 11: e0157077. PMID 27494614 DOI: 10.1371/journal.pone.0157077  0.76
2016 Allen M, Burgess JD, Ballard T, Serie D, Wang X, Younkin CS, Sun Z, Kouri N, Baheti S, Wang C, Carrasquillo MM, Nguyen T, Lincoln S, Malphrus K, Murray M, ... ... Price ND, et al. Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci. Acta Neuropathologica. PMID 27115769 DOI: 10.1007/s00401-016-1576-7  0.84
2016 Zhou JX, Samal A, 'Hérouël AF, Price ND, Huang S. Relative Stability of Network States in Boolean Network Models of Gene Regulation in Development. Bio Systems. PMID 26965665 DOI: 10.1016/j.biosystems.2016.03.002  1
2016 McDonald D, Glusman G, Price ND. Personalized nutrition through big data. Nature Biotechnology. 34: 152-4. PMID 26849520 DOI: 10.1038/nbt.3476  1
2015 Magis AT, Funk CC, Price ND. SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis. Ieee Life Sciences Letters. 1: 22-25. PMID 29270443 DOI: 10.1109/LLS.2015.2465870  0.92
2015 López García de Lomana A, Schäuble S, Valenzuela J, Imam S, Carter W, Bilgin DD, Yohn CB, Turkarslan S, Reiss DJ, Orellana MV, Price ND, Baliga NS. Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii. Biotechnology For Biofuels. 8: 207. PMID 26633994 DOI: 10.1186/s13068-015-0391-z  1
2015 Ma S, Minch KJ, Rustad TR, Hobbs S, Zhou SL, Sherman DR, Price ND. Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis. Plos Computational Biology. 11: e1004543. PMID 26618656 DOI: 10.1371/journal.pcbi.1004543  1
2015 Pestal K, Funk CC, Snyder JM, Price ND, Treuting PM, Stetson DB. Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-organ Development. Immunity. 43: 933-944. PMID 26588779 DOI: 10.1016/j.immuni.2015.11.001  0.84
2015 Heavner BD, Price ND. Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. Plos Computational Biology. 11: e1004530. PMID 26566239 DOI: 10.1371/journal.pcbi.1004530  1
2015 Imam S, Schäuble S, Valenzuela J, López García de Lomana A, Carter W, Price ND, Baliga NS. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. The Plant Journal : For Cell and Molecular Biology. PMID 26485611 DOI: 10.1111/tpj.13059  1
2015 Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, ... ... Price ND, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284  1
2015 Tian Q, Sangar V, Price ND. Emerging proteomic technologies provide enormous and underutilized potential for brain cancer research. Molecular & Cellular Proteomics : McP. PMID 26407994 DOI: 10.1074/mcp.R115.053884  1
2015 Toga AW, Foster I, Kesselman C, Madduri R, Chard K, Deutsch EW, Price ND, Glusman G, Heavner BD, Dinov ID, Ames J, Van Horn J, Kramer R, Hood L. Big Biomedical data as the key resource for discovery science. Journal of the American Medical Informatics Association : Jamia. PMID 26198305 DOI: 10.1093/jamia/ocv077  0.76
2015 Eddy JA, Funk CC, Price ND. Fostering synergy between cell biology and systems biology. Trends in Cell Biology. PMID 26013981 DOI: 10.1016/j.tcb.2015.04.005  1
2015 Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga NS. A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Scientific Data. 2: 150010. PMID 25977815 DOI: 10.1038/sdata.2015.10  1
2015 Ament SA, Szelinger S, Glusman G, Ashworth J, Hou L, Akula N, Shekhtman T, Badner JA, Brunkow ME, Mauldin DE, Stittrich AB, Rouleau K, Detera-Wadleigh SD, Nurnberger JI, Edenberg HJ, ... ... Price ND, et al. 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. PMID 25730879 DOI: 10.1073/pnas.1424958112  0.76
2015 Chandrasekaran S, Rittschof CC, Djukovic D, Gu H, Raftery D, Price ND, Robinson GE. Aggression is associated with aerobic glycolysis in the honey bee brain(1). Genes, Brain, and Behavior. 14: 158-66. PMID 25640316 DOI: 10.1111/gbb.12201  1
2015 Chakrabarty P, Li A, Ceballos-Diaz C, Eddy JA, Funk CC, Moore B, DiNunno N, Rosario AM, Cruz PE, Verbeeck C, Sacino A, Nix S, Janus C, Price ND, Das P, et al. IL-10 alters immunoproteostasis in APP mice, increasing plaque burden and worsening cognitive behavior. Neuron. 85: 519-33. PMID 25619653 DOI: 10.1016/j.neuron.2014.11.020  1
2015 Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR. The DNA-binding network of Mycobacterium tuberculosis. Nature Communications. 6: 5829. PMID 25581030 DOI: 10.1038/ncomms6829  1
2015 Simeonidis E, Price ND. Genome-scale modeling for metabolic engineering. Journal of Industrial Microbiology & Biotechnology. 42: 327-38. PMID 25578304 DOI: 10.1007/s10295-014-1576-3  0.56
2015 Hood L, Lovejoy JC, Price ND. Integrating big data and actionable health coaching to optimize wellness. Bmc Medicine. 13: 4. PMID 25575752 DOI: 10.1186/s12916-014-0238-7  1
2015 Heavner BD, Price ND. Transparency in metabolic network reconstruction enables scalable biological discovery. Current Opinion in Biotechnology. 34: 105-9. PMID 25562137 DOI: 10.1016/j.copbio.2014.12.010  0.64
2015 Geman D, Ochs M, Price ND, Tomasetti C, Younes L. An argument for mechanism-based statistical inference in cancer Human Genetics. 134: 479-495. PMID 25381197 DOI: 10.1007/s00439-014-1501-x  1
2015 Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND. Data-driven integration of genome-scale regulatory and metabolic network models Frontiers in Microbiology. 6. DOI: 10.3389/fmicb.2015.00409  1
2015 Heavner BD, Price ND. Transparency in metabolic network reconstruction enables scalable biological discovery Current Opinion in Biotechnology. 34: 105-109. DOI: 10.1016/j.copbio.2014.12.010  1
2015 Simeonidis E, Price ND. Genome-scale modeling for metabolic engineering Journal of Industrial Microbiology and Biotechnology. 42: 327-338. DOI: 10.1007/s10295-014-1576-3  1
2014 Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS, Sherman DR. Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biology. 15: 502. PMID 25380655 DOI: 10.1186/PREACCEPT-1701638048134699  1
2014 Ma S, Sung J, Magis AT, Wang Y, Geman D, Price ND. Measuring the effect of inter-study variability on estimating prediction error. Plos One. 9: e110840. PMID 25330348 DOI: 10.1371/journal.pone.0110840  1
2014 Benedict MN, Mundy MB, Henry CS, Chia N, Price ND. Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models. Plos Computational Biology. 10: e1003882. PMID 25329157 DOI: 10.1371/journal.pcbi.1003882  1
2014 Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND. MediaDB: a database of microbial growth conditions in defined media. Plos One. 9: e103548. PMID 25098325 DOI: 10.1371/journal.pone.0103548  1
2014 Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND. Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells. Molecular & Cellular Proteomics : McP. 13: 2618-31. PMID 24997998 DOI: 10.1074/mcp.M114.040428  1
2014 Craig TA, Zhang Y, Magis AT, Funk CC, Price ND, Ekker SC, Kumar R. Detection of 1α,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing. Zebrafish. 11: 207-18. PMID 24650217 DOI: 10.1089/zeb.2013.0899  1
2014 Hood L, Price ND. Demystifying disease, democratizing health care. Science Translational Medicine. 6: 225ed5. PMID 24574336 DOI: 10.1126/scitranslmed.3008665  1
2014 Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND. ITEP: An integrated toolkit for exploration of microbial pan-genomes Bmc Genomics. 15. PMID 24387194 DOI: 10.1186/1471-2164-15-8  1
2014 Dong Y, Kumar CG, Chia N, Kim PJ, Miller PA, Price ND, Cann IK, Flynn TM, Sanford RA, Krapac IG, Locke RA, Hong PY, Tamaki H, Liu WT, Mackie RI, et al. Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir. Environmental Microbiology. 16: 1695-708. PMID 24238218 DOI: 10.1111/1462-2920.12325  0.32
2014 Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K. Systems approach to neurodegenerative disease biomarker discovery. Annual Review of Pharmacology and Toxicology. 54: 457-81. PMID 24160693 DOI: 10.1146/annurev-pharmtox-011613-135928  1
2014 Bai JP, Fontana RJ, Price ND, Sangar V. Systems pharmacology modeling: an approach to improving drug safety. Biopharmaceutics & Drug Disposition. 35: 1-14. PMID 24136298 DOI: 10.1002/bdd.1871  1
2014 Ma S, Sung J, Magis AT, Wang Y, Geman D, Price ND. Measuring the effect of inter-study variability on estimating prediction error Plos One. 9. DOI: 10.1371/journal.pone.0110840  1
2013 Flores M, Glusman G, Brogaard K, Price ND, Hood L. P4 medicine: how systems medicine will transform the healthcare sector and society. Personalized Medicine. 10: 565-576. PMID 25342952 DOI: 10.2217/PME.13.57  1
2013 Chandrasekaran S, Price ND. Metabolic constraint-based refinement of transcriptional regulatory networks. Plos Computational Biology. 9: e1003370. PMID 24348226 DOI: 10.1371/journal.pcbi.1003370  1
2013 Wang C, Funk CC, Eddy JA, Price ND. Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas. Plos One. 8: e76694. PMID 24146911 DOI: 10.1371/journal.pone.0076694  1
2013 Li XJ, Hayward C, Fong PY, Dominguez M, Hunsucker SW, Lee LW, McLean M, Law S, Butler H, Schirm M, Gingras O, Lamontagne J, Allard R, Chelsky D, Price ND, et al. A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Science Translational Medicine. 5: 207ra142. PMID 24132637 DOI: 10.1126/scitranslmed.3007013  1
2013 Sung J, Kim PJ, Ma S, Funk CC, Magis AT, Wang Y, Hood L, Geman D, Price ND. Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures. Plos Computational Biology. 9: e1003148. PMID 23935471 DOI: 10.1371/journal.pcbi.1003148  1
2013 Heavner BD, Smallbone K, Price ND, Walker LP. Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance Database. 2013. PMID 23935056 DOI: 10.1093/database/bat059  1
2013 Labhsetwar P, Cole JA, Roberts E, Price ND, Luthey-Schulten ZA. Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. Proceedings of the National Academy of Sciences of the United States of America. 110: 14006-11. PMID 23908403 DOI: 10.1073/pnas.1222569110  1
2013 Wang Y, Li X, Milne CB, Janssen H, Lin W, Phan G, Hu H, Jin YS, Price ND, Blaschek HP. Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii. Applied and Environmental Microbiology. 79: 5853-63. PMID 23872562 DOI: 10.1128/AEM.00971-13  1
2013 Earls JC, Eddy JA, Funk CC, Ko Y, Magis AT, Price ND. AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. Bmc Bioinformatics. 14: 78. PMID 23496976 DOI: 10.1186/1471-2105-14-78  1
2013 Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, ... ... Price ND, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/nbt.2488  1
2013 Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnology Journal. 8: 1070-9. PMID 23420771 DOI: 10.1002/biot.201200266  1
2013 Simeonidis E, Chandrasekaran S, Price ND. A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism). Methods in Molecular Biology (Clifton, N.J.). 985: 103-12. PMID 23417801 DOI: 10.1007/978-1-62703-299-5_6  1
2013 Ko Y, Ament SA, Eddy JA, Caballero J, Earls JC, Hood L, Price ND. 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. PMID 23386717 DOI: 10.1073/pnas.1222897110  1
2013 Price ND. Genome-scale models for microbial factories Industrial Biotechnology. 9: 177-178. DOI: 10.1089/ind.2013.1586  1
2013 Hood L, Flores MA, Brogaard KR, Price ND. Systems Medicine and the Emergence of Proactive P4 Medicine: Predictive, Preventive, Personalized and Participatory Handbook of Systems Biology. 445-467. DOI: 10.1016/B978-0-12-385944-0.00023-X  1
2013 Price ND, Edelman LB, Lee I, Yoo H, Hwang D, Carlson G, Galas DJ, Heath JR, Hood L. Systems Biology and Systems Medicine Genomic and Personalized Medicine. 1: 60-72. DOI: 10.1016/B978-0-12-382227-7.00005-7  1
2013 Georgatos F, Ballereau S, Pellet J, Ghanem M, Price N, Hood L, Guo YK, Boutigny D, Auffray C, Balling R, Schneider R. Computational infrastructures for data and knowledge management in systems biology Systems Biology. 1: 377-397. DOI: 10.1007/978-94-007-6803-1_13  1
2012 Wang Y, Eddy JA, Price ND. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. Bmc Systems Biology. 6: 153. PMID 23234303 DOI: 10.1186/1752-0509-6-153  1
2012 Simcha D, Price ND, Geman D. The limits of de novo DNA motif discovery. Plos One. 7: e47836. PMID 23144830 DOI: 10.1371/journal.pone.0047836  1
2012 Sangar V, Eddy JA, Simeonidis E, Price ND. Mechanistic modeling of aberrant energy metabolism in human disease. Frontiers in Physiology. 3: 404. PMID 23112774 DOI: 10.3389/fphys.2012.00404  1
2012 Magis AT, Price ND. The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules. Bmc Bioinformatics. 13: 227. PMID 22966958 DOI: 10.1186/1471-2105-13-227  1
2012 Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, Magis AT, Funk C, Price ND, Ekker SC, Kumar R. Research resource: whole transcriptome RNA sequencing detects multiple 1α,25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish. Molecular Endocrinology (Baltimore, Md.). 26: 1630-42. PMID 22734042 DOI: 10.1210/me.2012-1113  1
2012 Sung J, Wang Y, Chandrasekaran S, Witten DM, Price ND. Molecular signatures from omics data: from chaos to consensus. Biotechnology Journal. 7: 946-57. PMID 22528809 DOI: 10.1002/biot.201100305  1
2012 Bebek G, Koyutürk M, Price ND, Chance MR. Network biology methods integrating biological data for translational science. Briefings in Bioinformatics. 13: 446-59. PMID 22390873 DOI: 10.1093/bib/bbr075  1
2012 Tian Q, Price ND, Hood L. Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. Journal of Internal Medicine. 271: 111-21. PMID 22142401 DOI: 10.1111/j.1365-2796.2011.02498.x  1
2012 Benedict MN, Gonnerman MC, Metcalf WW, Price ND. Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A. Journal of Bacteriology. 194: 855-65. PMID 22139506 DOI: 10.1128/JB.06040-11  1
2011 Kim PJ, Price ND. Genetic co-occurrence network across sequenced microbes. Plos Computational Biology. 7: e1002340. PMID 22219725 DOI: 10.1371/journal.pcbi.1002340  1
2011 Ghosh A, Zhao H, Price ND. Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. Plos One. 6: e27316. PMID 22076150 DOI: 10.1371/journal.pone.0027316  1
2011 Chandrasekaran S, Ament SA, Eddy JA, Rodriguez-Zas SL, Schatz BR, Price ND, Robinson GE. 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. PMID 21960440 DOI: 10.1073/pnas.1114093108  1
2011 Milne CB, Eddy JA, Raju R, Ardekani S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. Bmc Systems Biology. 5: 130. PMID 21846360 DOI: 10.1186/1752-0509-5-130  1
2011 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. Journal of Proteome Research. 10: 2425-39. PMID 21413810 DOI: 10.1021/pr101245u  1
2011 Magis AT, Earls JC, Ko YH, Eddy JA, Price ND. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup. Bioinformatics (Oxford, England). 27: 872-3. PMID 21257608 DOI: 10.1093/bioinformatics/btr033  1
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 1591-6. PMID 21220328 DOI: 10.1073/pnas.1018696108  1
2011 Bebek G, Chance M, Koyuturk M, Price ND, De La Vega FM, Bustamante CD, Leal SM, Foster J, Moore J, Bernauer J, Flores S, Huang X, Shin S, Zhou R, Alkan C, et al. Pacific symposium on biocomputing 2011 Pacific Symposium On Biocomputing 2011, Psb 2011. v.  1
2011 Quarterman JC, Jin YS, Price ND, Kim PJ. Optimal strain design of saccharomyces cerevisiae for bioethanol production 11aiche - 2011 Aiche Annual Meeting, Conference Proceedings 1
2011 Bebek G, Koyutürk M, Chance MR, Price ND. Integrative-omics for translational science-session introduction Pacific Symposium On Biocomputing 2011, Psb 2011. 1-3.  1
2010 Galas DJ, Nykter M, Carter GW, Price ND, Shmulevich I. Biological Information as Set-Based Complexity. Ieee Transactions On Information Theory. 56: 667-677. PMID 27857450 DOI: 10.1109/TIT.2009.2037046  0.4
2010 Ma S, Funk CC, Price ND. Systems approaches to molecular cancer diagnostics. Discovery Medicine. 10: 531-42. PMID 21189224  1
2010 Chandrasekaran S, Price ND. 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. PMID 20876091 DOI: 10.1073/pnas.1005139107  1
2010 Edelman LB, Eddy JA, Price ND. In silico models of cancer. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 438-59. PMID 20836040 DOI: 10.1002/wsbm.75  1
2010 Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, ... ... Price ND, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/nbt.1665  1
2010 Price ND, Lee SY. Editorial: Systems biology for biotech applications. Biotechnology Journal. 5: 636-7. PMID 20665637 DOI: 10.1002/biot.201000216  1
2010 Yang J, Eddy JA, Pan Y, Hategan A, Tabus I, Wang Y, Cogdell D, Price ND, Pollock RE, Lazar AJ, Hunt KK, Trent JC, Zhang W. 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. PMID 20651304 DOI: 10.1074/mcp.M110.000240  1
2010 Eddy JA, Hood L, Price ND, Geman D. Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). Plos Computational Biology. 6: e1000792. PMID 20523739 DOI: 10.1371/journal.pcbi.1000792  1
2010 Kim PJ, Price ND. Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions. Physical Review Letters. 104: 148103. PMID 20481966 DOI: 10.1103/PhysRevLett.104.148103  1
2010 Eddy JA, Sung J, Geman D, Price ND. Relative expression analysis for molecular cancer diagnosis and prognosis. Technology in Cancer Research & Treatment. 9: 149-59. PMID 20218737 DOI: c4306/Relative-Expression-Analysis-for-Molecular-Cancer-Diagnosis-and-Prognosis-149-160-p17776.html  1
2010 Ezeji T, Milne C, Price ND, Blaschek HP. Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms. Applied Microbiology and Biotechnology. 85: 1697-712. PMID 20033401 DOI: 10.1007/s00253-009-2390-0  1
2010 Edelman LB, Chandrasekaran S, Price ND. Systems biology of embryogenesis. Reproduction, Fertility, and Development. 22: 98-105. PMID 20003850 DOI: 10.1071/RD09215  1
2010 Galas DJ, Nykter M, Carter GW, Price ND, Shmulevich I. Biological information as set-based complexity Ieee Transactions On Information Theory. 56: 667-677. DOI: 10.1109/TIT.2009.2037046  1
2010 Milenkovic O, Alterovitz G, Battail G, Coleman TP, Hagenauer J, Meyn SP, Price N, Ramoni MF, Shmulevich I, Szpankowski W. Introduction to the special issue on information theory in molecular biology and neuroscience Ieee Transactions On Information Theory. 56: 649-652. DOI: 10.1109/TIT.2009.2036971  1
2010 Ma S, Sung J, Wang Y, Price ND. Lung disease diagnosis from gene expression profiles Aiche Annual Meeting, Conference Proceedings 1
2009 Eddy JA, Geman D, Price ND. 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. Annual Conference. 2009: 5456-9. PMID 19964680 DOI: 10.1109/IEMBS.2009.5334063  1
2009 Edelman LB, Toia G, Geman D, Zhang W, Price ND. Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. Bmc Genomics. 10: 583. PMID 19961616 DOI: 10.1186/1471-2164-10-583  1
2009 Milne CB, Kim PJ, Eddy JA, Price ND. Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnology Journal. 4: 1653-70. PMID 19946878 DOI: 10.1002/biot.200900234  1
2009 Hwang D, Lee IY, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R, Young R, Spicer D, Price ND, Hohmann JG, Dearmond SJ, Carlson GA, Hood LE. A systems approach to prion disease. Molecular Systems Biology. 5: 252. PMID 19308092 DOI: 10.1038/msb.2009.10  1
2009 Price ND, Edelman LB, Lee I, Yoo H, Hwang D, Carlson G, Galas DJ, Heath JR, Hood L. Systems Biology and the Emergence of Systems Medicine Genomic and Personalized Medicine, Two-Vol Set. 74-85. DOI: 10.1016/B978-0-12-369420-1.00006-8  1
2009 Milne CB, Raju R, Kim PJ, Price ND. Metabolic reconstruction and analysis of butanol producing strain Clostridium beijerinckii NCIMB 8052 Conference Proceedings - 2009 Aiche Annual Meeting, 09aiche 0.76
2008 Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I. Critical networks exhibit maximal information diversity in structure-dynamics relationships. Physical Review Letters. 100: 058702. PMID 18352443 DOI: 10.1103/PhysRevLett.100.058702  1
2008 Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O, Shmulevich I. Gene expression dynamics in the macrophage exhibit criticality. Proceedings of the National Academy of Sciences of the United States of America. 105: 1897-900. PMID 18250330 DOI: 10.1073/pnas.0711525105  1
2008 Price ND, Foltz G, Madan A, Hood L, Tian Q. Systems biology and cancer stem cells. Journal of Cellular and Molecular Medicine. 12: 97-110. PMID 18031300 DOI: 10.1111/j.1582-4934.2007.00151.x  1
2008 Raju R, Milne CB, Price ND. Metabolic network reconstruction and analysis of butanol producing strain clostridium beijerinckii Aiche Annual Meeting, Conference Proceedings 1
2008 Sung J, Price ND. Panel of gene-pair relative expression classifiers for stratifying various cancer and non-cancer diseases of the human brain Aiche Annual Meeting, Conference Proceedings 1
2008 Eddy JA, Geman D, Price ND. Pathway expression rank analysis (p-xray): A novel tool for gene set expression analysis Aiche Annual Meeting, Conference Proceedings 1
2007 Price ND, Shmulevich I. Biochemical and statistical network models for systems biology. Current Opinion in Biotechnology. 18: 365-70. PMID 17681779 DOI: 10.1016/j.copbio.2007.07.009  1
2007 Price ND, Trent J, El-Naggar AK, Cogdell D, Taylor E, Hunt KK, Pollock RE, Hood L, Shmulevich I, Zhang W. Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proceedings of the National Academy of Sciences of the United States of America. 104: 3414-9. PMID 17360660 DOI: 10.1073/pnas.0611373104  1
2006 Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. Matrix formalism to describe functional states of transcriptional regulatory systems. Plos Computational Biology. 2: e101. PMID 16895435 DOI: 10.1371/journal.pcbi.0020101  1
2006 Price ND, Thiele I, Palsson BØ. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophysical Journal. 90: 3919-28. PMID 16533855 DOI: 10.1529/biophysj.105.072645  1
2006 Barrett CL, Price ND, Palsson BO. Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition. Bmc Bioinformatics. 7: 132. PMID 16533395 DOI: 10.1186/1471-2105-7-132  1
2006 Becker SA, Price ND, Palsson BØ. Metabolite coupling in genome-scale metabolic networks. Bmc Bioinformatics. 7: 111. PMID 16519800 DOI: 10.1186/1471-2105-7-111  1
2006 Allen TE, Price ND, Joyce AR, Palsson BØ. Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. Plos Computational Biology. 2: e2. PMID 16410829 DOI: 10.1371/journal.pcbi.0020002  1
2005 Thiele I, Vo TD, Price ND, Palsson BØ. 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. PMID 16077130 DOI: 10.1128/JB.187.16.5818-5830.2005  1
2005 Thiele I, Price ND, Vo TD, Palsson BØ. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. The Journal of Biological Chemistry. 280: 11683-95. PMID 15572364 DOI: 10.1074/jbc.M409072200  1
2004 Price ND, Reed JL, Palsson BØ. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Reviews. Microbiology. 2: 886-97. PMID 15494745 DOI: 10.1038/nrmicro1023  1
2004 Price ND, Schellenberger J, Palsson BO. Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophysical Journal. 87: 2172-86. PMID 15454420 DOI: 10.1529/biophysj.104.043000  1
2004 Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BO. Comparison of network-based pathway analysis methods. Trends in Biotechnology. 22: 400-5. PMID 15283984 DOI: 10.1016/j.tibtech.2004.06.010  1
2004 Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R, Tyler RE, Akerley BJ, Smith AL, Palsson BO, 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: 25-41. PMID 15107235 DOI: 10.1089/153623104773547471  1
2003 Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BO. Network-based analysis of metabolic regulation in the human red blood cell. Journal of Theoretical Biology. 225: 185-94. PMID 14575652 DOI: 10.1016/S0022-5193(03)00237-6  1
2003 Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO. Metabolic pathways in the post-genome era. Trends in Biochemical Sciences. 28: 250-8. PMID 12765837 DOI: 10.1016/S0968-0004(03)00064-1  1
2003 Palsson BO, Price ND, Papin JA. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends in Biotechnology. 21: 195-8. PMID 12727379 DOI: 10.1016/S0167-7799(03)00080-5  1
2003 Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends in Biotechnology. 21: 162-9. PMID 12679064 DOI: 10.1016/S0167-7799(03)00030-1  1
2003 Price ND, Reed JL, Papin JA, Famili I, Palsson BO. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophysical Journal. 84: 794-804. PMID 12547764 DOI: 10.1016/S0006-3495(03)74899-1  1
2002 Papin JA, Price ND, Palsson BØ. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Research. 12: 1889-900. PMID 12466293 DOI: 10.1101/gr.327702  1
2002 Price ND, Famili I, Beard DA, Palsson BØ. Extreme pathways and Kirchhoff's second law. Biophysical Journal. 83: 2879-82. PMID 12425318 DOI: 10.1016/S0006-3495(02)75297-1  1
2002 Papin JA, Price ND, Edwards JS, Palsson B BØ. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. Journal of Theoretical Biology. 215: 67-82. PMID 12051985 DOI: 10.1006/jtbi.2001.2499  1
2002 Price ND, Papin JA, Palsson BØ. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Research. 12: 760-9. PMID 11997342 DOI: 10.1101/gr.218002. Article published online before print in April 2002  1
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