Publications & Thought Leadership

h-index = 82 (Google Scholar)

Ellis, D., Watanabe, K., Wilmanski, T., Lustgarten, M.S., Korat, A.V.A., Glusman, G., Hadlock, J.J., Fiehn, O., Sebastiani, P., Price, N.D., Hood, L., Magis, A.T., Evans, S.J., Pflieger, L., Lovejoy, J.C., Gibbons, S.M., Funk, C.C., Baloni, P., Rappaport, N., APOE Genotype and Biological Age Impact Inter-Omic Associations Related to Bioenergetics, Aging, 3;17 (2025) PMID: 39605362

Pearl JR, Shetty AC, Cantle JP, Bergey DE, Bragg RM, Coffey SR, Kordasiewicz HB, Hood LE, Price ND, Ament SA, Carroll JB., Altered Huntingtin-Chromatin Interactions Predict Transcriptional and Epigenetic Changes in Huntington’s Disease Mouse Model, Disease Models & Mechanisms, 10:dmm.052282 (2025) PMID: 40205980

Kornilov, S.A., Price, N.D., Gelina,s R., Acosta, J., Brunkow, M.E., Gervasi-Follmar, T., Winger, R.C., Aldershoff, D., Lausted, C., Troisch, P., Smith, B., Heath, J.R., Repovic, P., Cohan, S., Magis, A.T., Multi-Omic characterization of the effects of Ocrelizumab in patients with relapsing-remitting multiple sclerosis, Journal of the Neurological Sciences, 15;467:123303 (2024) PMID: 39561535

Hwang, Y.M., Piekos, S.N., Paquette, A.G., Wei, Q., Price, N.D., Hood, L., Hadlock, J.J.., Accelerating adverse pregnancy outcomes research amidst rising medication use: parallel retrospective cohort analyses for signal prioritization, BMC Medicine, 22(1):495 (2024) PMID: 39456023

Bauer, B.A., Schmidt, C.M., Ruddy, K.J., Olson, J.E., Meydan, C., Schmidt, J.C., Smith, S.Y., Couch, F.J., Earls, J.C., Price, N.D., Dudley, J.T., Mason, C.E., Zhang, B., Phipps, S.M., Schmidt, M.A., A Multiomics, Molecular Atlas of Breast Cancer Survivors, Metabolites, 14(7):396 (2024) PMID: 39057719

Paquette, A., Ahuna, K., Hwang, Y.M., Pearl, J., Liao, H., Shannon, P., Kadam, L., Lapehn, S., Bucher, M., Roper, R., Funk, C., MacDonald, J., Bammler, T., Baloni, P., Brockway, H., Mason, W.A., Bush, N., Lewinn, K.Z., Karr, C.J., Stamatoyannopoulos, J., Muglia, L.J., Jones, H., Sadovsky, Y., Myatt, L., Sathyanarayana, S., Price, N.D., A genome scale transcriptional regulatory model of the human placenta, Science Advances, 10(26):eadf3411 (2024) PMID: 38941464

Hwang, Y..M, Roper, R.T., Piekos, S.N., Enquobahrie, D.A., Hebert, M.F., Paquette, A.G., Baloni, P., Price, N.D., Hood, L., Hadlock, J.J., Timing of selective serotonin reuptake inhibitor use and risk for preterm birth and related adverse events: with a consideration of the COVID-19 pandemic period, Journal of Maternal Fetal Neonatal Medicine, 37(1):2313364 (2024) PMID: 38342572

Bunyavanich, S., Becker, P.M., Altman, M.C., Lasky-Su, J., Ober, C., Zengler, K., Berdyshev, E., Bonneau, R., Chatila, T., Chatterjee, N., Chung, K.F., Cutcliffe, C., Davidson, W., Dong, G., Fang, G., Fulkerson, P., Himes, B.E., Liang, L., Mathias, R.A., Ogino, S., Petrosino, J., Price, N.D., Schadt, E., Schofield, J., Seibold, M.A., Steen, H., Wheatley, L., Zhang, H., Togias, A., Hasegawa, K., Analytical Challenges in Omics Research on Asthma and Allergy: A National Institute of Allergy and Infectious Diseases Workshop. Journal of Allergy Clinical Immunology, 29:S0091-6749(24)00082-4 (2024) PMID: 38295882

Barak, O., Lovelace, T., Piekos, S., Chu, T., Cao, Z., Sadovsky,. E, Mouillet, J.F., Ouyang, Y., Parks, W.T., Hood, L., Price, N.D., Benos, P.V., Sadovsky, Y., Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes, BMC Medicine, 21(1):349 (2023) PMID: 37679695

Piekos, S.N., Hwang, Y.M., Roper, R.T., Sorensen, T., Price, N.D., Hood, L., Hadlock, J.J., Effect of COVID-19 vaccination and booster on maternal-fetal outcomes: a retrospective multicenter cohort study, The Lancet Digital Health, 1:S2589-7500(23)00093-6. (2023) PMID: 37537121

Watanabe, K., Wilmanski, T., Baloni, P., Robinson, M., Garcia, G.G., Hoopmann, M.R., Midha, M.K., Baxter, D.H., Maes, M., Morrone, S.R., Crebs, K.M., Kapil, C., Kusebauch, U., Wiedrick, J., Lapidus, J., Pflieger, L., Lausted, C., Roach, J.C., Glusman, G., Cummings, S.R., Schork, N.J., Price, N.D., Hood, L., Miller, R.A., Moritz, R.L., Rappaport, N.., Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers, Communications Biology, 22;6(1):768 (2023) PMID: 37481675

Watanabe, K., Wilmanski, T., Diener, C., Earls, J.C., Zimmer, A., Lincoln, B., Hadlock, J.J. Lovejoy, J.C., Gibbons, S.M., Magis, A.T., Hood, L., Price, N.D., and Rappaport, N., Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention, Nature Medicine, online ahead of print (2023) PMID: 36941332

Piekos, S.N., Price, N.D., Hood, L., Hadlock, J.J., The impact of maternal SARS-CoV-2 infection and COVID-19 vaccination on maternal-fetal outcomes, Reproductive Toxicology, 114:33-43 (2022) PMID: 36283657

Baloni, P., Arnold, M., Buitrago, L., Nho, K., Moreno, H., Huynh, K., Brauner, B., Louie, G., Kueider-Paisley, A., Suhre, K., Saykin, A.J., Ekroos, K., Meikle, P.J., Hood, L., Price, N.D., Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer’s disease, Communications Biology, 5(1):1074 (2022) PMID: 36209301

Hua, H., Meydan, C., Afshin, E.E., Lili, L.N., D’Adamo, C.R., Rickard, N., Dudley, J.T., Price, N.D., Zhang, B., Mason, C.E., A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling, Frontiers in Immunology, 13:889702 (2022) PMID: 35711426

Wilmanski T, Kornilov SA, Diener C, Conomos MP, Lovejoy JC, Sebastiani P, Orwoll ES, Hood L, Price N.D., Rappaport N, Magis AT, Gibbons SM., Heterogeneity in statin responses explained by variation in the human gut microbiome, Med, 3(6):388-405 (2022) PMID: 35690059

Molani, S., Hernandez, P.V., Roper, R.T., Duvvuri, V.R., Baumgartner, A.M., Goldman, J.D., Ertekin-Taner, N., Funk, C.C., Price, N.D., Rappaport, N., Hadlock, J.J., Risk factors for severe COVID-19 differ by age for hospitalized adults, Scientific Reports, 12(1):6568 (2022) PMID: 35484176

Heath, L., Earls, J.C., Magis, A.T., Kornilov, S.A., Lovejoy, J.C., Funk, C.C., Rappaport, N., Logsdon, B.A., Mangravite, L.M., Kunkle, B.W., Martin, E.R., Naj, A.C., Ertekin-Taner, N., Golde, T.E., Hood, L., Price, N.D., Manifestations of Alzheimer’s disease genetic risk in the blood are evident in a multiomic analysis in healthy adults aged 18 to 90, Scientific Reports, 12(1):6117 (2022) PMID: 35413975     

Su, Y., Yuan, D., Chen, D.G., Ng, R.H., Wang, K., Choi, J., Li, S., Hong, S., Zhang, R., Xie, J., Kornilov, S.A., Scherler, K., Pavlovitch-Bedzyk, A.J., Dong, S., Lausted, C., Lee, I., Fallen, S., Dai, C.L., Baloni, P., Smith, B., Duvvuri, V.R., Anderson, K.G., Li, J., Yang, F., Duncombe, C.J., McCulloch, D.J., Rostomily, C., Troisch, P., Zhou, J., Mackay, S., DeGottardi, Q., May, D.H., Taniguchi, R., Gittelman, R.M., Klinger, M., Snyder, T.M., Roper, R., Wojciechowska, G., Murray, K., Edmark, R., Evans, S., Jones, L., Zhou, Y., Rowen, L., Liu, R, Chour, W., Algren, H.A., Berrington, W.R., Wallick, J.A., Cochran, R.A., Micikas, M.E.; ISB-Swedish COVID-19 Biobanking Unit, Wrin, T., Petropoulos, C.J., Cole, H.R., Fischer, T.D., Wei, W., Hoon, D.S.B., Price, N.D., Subramanian, N., Hill, J.A., Hadlock, J., Magis, A.T., Ribas, A., Lanier, L.L., Boyd, S.D., Bluestone, J.A., Chu, H., Hood, L., Gottardo, R., Greenberg, P.D., Davis, M.M., Goldman, J.D., Heath, J.R., Multiple early factors anticipate post-acute COVID-19 sequelae, Cell, 185(5):881-895.e20 (2022) PMID: 35216672

Gunn, S., Wainberg, M., Song, Z., Andersen, S., Boudreu, R. Feitosa, M.F., Tan, Q., Montasser, M., O’Connell, J., Stitziel, N., Price, N.D., Perls, T., Schork, N.J., Sebastiani, P., Distribution of 54 polygenic risk scores for common diseases in long lived individuals and their offspring, Geroscience, (2):719-729 (2022) PMID: 35119614

Piekos, S.N., Roper, R.T., Hwang, Y.M., Sorensen, T., Price, N.D., Hood, L., Hadlock, J.J., The effect of maternal SARS-CoV-2 infection timing on birth outcomes: a retrospective multicentre cohort study, The Lancet Digital Health, 4(2):e95-e104 (2022) PMID: 35034863

Wang, X., Allen, M., İş, Ö., Reddy, J.S., Tutor-New, F.Q., Castanedes Casey, M., Carrasquillo, M.M., Oatman, S.R., Min, Y., Asmann, Y.W., Funk, C., Nguyen, T., Ho, C.C., Malphrus, K.G., Seyfried, N.T., Levey, A.I., Younkin, S.G., Murray, M.E., Dickson, D.W., Price, N.D., Golde, T.E., Ertekin-Taner, N., Alzheimer’s disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions, The Journal of Clinical Investigation, 132:e149904 (2022) PMID: 34813500

Ojanen, X., Cheng, R., Törmäkangas, T., Rappaport, N., Wilmanski, T., Wu, N., Fung, E., Nedelec, R., Sebert, S., Vlachopoulos, D., Yan, W., Price, N.D., Cheng, S., Wiklund, P., Towards early risk biomarkers: serum metabolic signature in childhood predicts cardio-metabolic risk in adulthood, EBioMedicine, 72:103611 (2021) PMID: 34628356

Diener C, Qin S, Zhou Y, Patwardhan S, Tang L, Lovejoy JC, Magis AT, Price ND, Hood L, Gibbons SM., Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans, mSytems, 6(5):e0096421 (2021) PMID: 34519531

Lee, J.W., Su, Y., Baloni, P., Chen, D., Palovitch-Bedzyk, A.J., Duvvuri, V.R., Ng, R.H., Choi, J., Xie, J., Zhang, R., Murray, K., Kornilov, S., Smith, B., Magis, A.T., Hoon, D.S.B., Hadlock, J.J., Goldman, J.D., Price, N.D., Gottardo, R., Davis, M.M., Hood, L., Greenberg, P.D, Heath, J.R., Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19, Nature Biotechnology, 40(1):110-120 (2022) PMID: 34489601

Paquette, A.G., MacDonald, J., Lapehn, S., Bammler, T., Kruger, L., Day, D.B., Price, N.D., Loftus, C., Kannan, K., Marsit, C., Mason, W.A., Bush, N.R., LeWinn, K.Z., Enquobahrie, D.A., Prasad, B., Karr, C.J., Sathyanarayana, S., A Comprehensive Assessment of Associations between Prenatal Phthalate Exposure and The Placental Transcriptomic Landscape, Environmental Health Perspectives, 29(9):97003 (2021) PMID 34478338

McEwen, S.C., Merrill, D.A., Bramen, J., Porter, V., Panos, S., Kaiser, S., Hodes, J., Ganapathi, A., Bell, L., Bookheimer, T., Glatt, R., Rapozo, M., Ross, M.K., Price, N.D., Kelly, D., Funk, C.C., Hood, L., Roach, J.C., A systems-biology clinical trial of a personalized multimodal lifestyle intervention for early Alzheimer’s disease, Alzheimer’s & Dementia, 7(1):e12191 (2021) PMID: 34295960

Zimmer, A., Korem, Y., Rappaport, N., Wilmanski, T., Baloni, P., Jade, K., Robinson, M., Magis, A.T., Lovejoy, J., Gibbons, S.M., Hood, L., Price, N.D., The geometry of clinical labs and wellness states from deeply phenotyped humans, Nature Communications, 12(1):3578 (2021) PMID: 34117230

Levites, Y., Funk, C., Wang, X., Chakrabarty, P., McFarland, K, Bramblett, B., O’Neal, V., Liu, X., Ladd, T., Robinson, M., Allen, M.A., Carrasquillo, M.M., Dickson, D.W., Cruz, P., Ryu, D. Li, H.D., Price, N.D., Taner, N., Golde, T.E., Modulating Innate Immune Activation States Impacts the Efficacy of Specific Aβ Immunotherapy, Molecular Neurodegeneration, 16(1):32 (2021) PMID: 3395736

Wilmanski, T., Diener, C., Rappaport, N., Patwardhan, S., Wiedrick, J., Lapidus, J., Earls, J.C., Zimmer, A., Glusman, G., Robinson, M., Yurkovich, J.T., Kado, D.M., Cauley, J.A., Zmuda, J., Lane, N.E., Magis, A.T., Lovejoy, J.C., Hood, L., Gibbons, S.M., Orwoll, E.S., Price, N.D., Gut microbiome pattern reflects healthy aging and predicts survival in humans, Nature Metabolism, 3(2):274-286 (2021) PMID: 33619379

Li, H.D., Funk, C.C., McFarland, K., Dammer, E.B., Allen, M., Carrasquillo, M.M., Levties, Y., Chakrabarty, P., Burgess, J.D., Wand, X., Dickson, D., Seyfried, N.T., Duong, D.M., Lah, J.J., Younkin, S.G., Levey, A.I., Omenn, G.S., Ertekin-Taner, N., Golde, T.E., Price, N.D., Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer’s disease, Alzheimer’s & Dementia, [Online ahead of print] (2020) PMID: 33480174

Baloni, P., Funk, C.C., Yan, J., Yurkovich, J.T., Kueider-Paisley, A., Nho, K., Heinken, A., Jia, W., Mahmoudiandehkordi, S., Louie, G., Saykin, A.J., Arnold, M., Kastenmüller, G., Griffiths, W.J., Thiele, I.; Alzheimer’s Disease Metabolomics Consortium, Kaddurah-Daouk, R., Price, N.D., Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer’s Disease, Cell Reports Medicine, 1(8):100138 (2020) PMID: 33294859

Baloni, P., Dinalankara, W., Earls, J.C., Knijnenburg, T.A., Geman, D., Marchionni, L., Price, N.D., Identifying Personalized Metabolic Signatures in Breast Cancer, Metabolites, 11(1):E20 (2020) PMID: 33396819

Su, Y., Chen, D., Yuan, D., Lausted, C., Choi, J., Dai, C.L., Voillet, V., Duvvuri, V.R., Scherler, K., Troisch, P., Baloni, P., Qin, G., Smith, B., Kornilov, S.A., Rostomily, C., Xu, A., Li, J., Dong, S., Rothchild, A., Zhou, J., Murray, K., Edmark, R., Hong, S., Heath, J.E., Earls, J., Zhang, R., Xie, J., Li, S., Roper, R., Jones, L., Zhou, Y., Rowen, L., Liu, R., Mackay, S., O’Mahony, D.S., Dale, C.R., Wallick, J.A., Algren, H.A., Zager, M.A.; ISB-Swedish COVID19 Biobanking Unit, Wei, W., Price, N.D., Huang, S., Subramanian, N., Wang, K., Magis, A.T., Hadlock, J.J., Hood, L., Aderem, A., Bluestone, J.A., Lanier, L.L., Greenberg, P.D., Gottardo, R., Davis, M.M., Goldman, J.D., Heath, J.R., Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19, Cell, 183(6):1479-1495 (2020) PMID: 33171100

Manor, O., Dai, C.L., Kornilov, S.A., Smith, B., Price, N.D., Lovejoy, J.C., Gibbons, S.M., Magis, A.T., Health and disease markers correlate with gut microbiome composition across thousands of people, Nature Communications, 11(1):5206 (2020) PMID: 33060586

Magis, A.T., Rappaport, N., Conomos, M.P., Omenn, G.S., Lovejoy, J.C., Hood, L., Price, N.D., Untargeted longitudinal analysis of a wellness cohort identifies markers of metastatic cancer years prior to diagnosis, Scientific Reports, 10(1):16275 (2020) PMID: 33004987

Wainberg, M., Magis, A.T., Earls, J.C., Lovejoy, J.C., Sinnott-Armstrong, N.A., Omenn, G.S., Hood, L., and Price, N.D., Multiomic blood correlates of genetic risk identify presymptomatic disease alterations, Proceedings of the National Academy of Sciences, 117(35):21813-21820 (2020) PMID: 32817414

Funk, C.C., Casella, A.M., Jung, S., Richards, M.A., Rodriguez, A., Shannon, P., Donovan-Maiye, R., Heavner, B., Chard, K., Xiao, Y., Glusman, G., Ertekin-Taner, N., Golde, T.E., Toga, A., Hood, L., Van Horn, J.D., Kesselman, C., Foster, I., Madduri, R., Price, N.D., Ament, S.A., Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types, Cell Reports, 32(7):108029 (2020) PMID 32814038

Wan, Y.W., Al-Ouran, R., Mangleburg, C.G., Perumal, T.M., Lee, T.V., Allison, K., Swarup, V., Funk, C.C., Gaiteri, C., Allen, M., Wang, M., Neuner, S.M., Kaczorowski, C.C., Philip, V.M., Howell, G.R., Martini-Stoica, H., Zheng, H., Mei, H., Zhong, X., Kim, J.W., Dawson, V.L., Dawson, T.M., Pao, P.C., Tsai, L.H., Haure-Mirande, J.V., Ehrlich, M.E., Chakrabarty, P., Levites, Y., Wang, X., Dammer, E.B., Srivastava, G., Mukherjee, S., Sieberts, S.K., Omberg, L., Dang, K.D., Eddy, J.A., Snyder, P., Chae, Y., Amberkar, S., Wei, W., Hide, W., Preuss, C., Ergun, A., Ebert, P.J., Airey, D.C., Mostafavi, S., Yu, L., Klein, H.U., Accelerating Medicines Partnership-Alzheimer’s Disease Consortium, Carter, G.W., Collier, D.A., Golde, T.E., Levey, A.I., Bennett, D.A., Estrada, K., Townsend, T.M., Zhang, B., Schadt, E., De Jager, P.L., Price, N.D., Ertekin-Taner, N., Liu, Z., Shulman, J.M., Mangravite, L.M., Logsdon, B.A., Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models, Cell Reports, 32(2):107908 (2020) PMID: 32668255

Sadovsky, Y., Mesiano, S., Burton, G.J., Lampl, M., Murray, J.C., Freathy, R.M., Mahadevan-Jansen, A., Moffett, A., Price, N.D., Wise, P.H., Wildman, D.E., Snyderman, R., Paneth, N., Capra, J.A., Nobrega, M.A., Barak, Y., Muglia, L.J.; Burroughs Wellcome Fund Pregnancy Think-Tank Working Group, Advancing Human Health in the Decade Ahead: Pregnancy as a Key Window for Discovery A Burroughs Wellcome Fund Pregnancy Think-Tank, American Journal of Obstetrics and Gynecology, S0002-9378(20)30637-2 (2020) PMID: 32565236

Madin, J.S., Nielsen, D.A., Brbic, M., Corkrey, R., Danko, D., Edwards, K., Engqvist, M.K.M., Fierer, N., Geoghegan, J.L., Gillings, M., Kyrpides, N.C., Litchman, E., Mason, C.E., Moore, L., Nielsen, S.L., Paulsen, I.T., Price, N.D., Reddy, T.B.K., Richards, M.A., Rocha, E.P.C., Schmidt, T.M., Shaaban, H., Shukla, M., Supek, F., Tetu, S.G., Vieira-Silva, S., Wattam, A.R., Westfall, D.A., Westoby, M., A synthesis of bacterial and archaeal phenotypic trait data. Scientific Data, 7(1):170 (2020) PMID: 32503990

Levy, R., Magis, A.T., Earls, J.C., Manor, O., Wilmanski, T., Lovejoy, J., Gibbons, S.M., Omenn, G.S., Hood, L., Price, N.D.., Longitudinal Analysis Reveals Transition Barriers Between Dominant Ecological States in the Gut Microbiome, Proceedings of the National Academy of Sciences, 117(24):13839-13845 (2020) PMID: 32471946

Gillespie, M.A., Palii, C.G., Sanchez-Taltavull, D., Shannon, P., Longabaugh, W.J.R., Downes, D.J., Sivaraman, K., Espinoza, H.M., Hughes, J.R., Price, N.D., Perkins, T.J., Ranish, J.A., Brand, M., Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis, Molecular Cell, S1097-2765(20)30199-4 (2020) PMID: 32330456

Lieven, C., Beber, M.E., Olivier, B.G., Bergmann, F.T., Ataman, M., Babaei, P., Bartell, J.A., Blank, L.M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B.E., Edirisinghe, J.N., Faria, J.P., Feist, A.M., Fengos, G., Fleming, R.M.T., García-Jiménez, B., Hatzimanikatis, V., van Helvoirt, W., Henry, C.S., Hermjakob, H., Herrgård, M.J., Kaafarani, A., Kim, H.U., King, Z., Klamt, S., Klipp, E., Koehorst, J.J., König, M., Lakshmanan, M., Lee, D.Y., Lee, S.Y., Lee, S., Lewis, N.E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G.L., Monk, J.M., Nielsen, J., Nielsen, L.K., Nogales, J., Nookaew, I., Palsson, B.O., Papin, J.A., Patil, K.R., Poolman, M., Price, N.D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sánchez, B.J., Schaap, P.J., Malik Sheriff, R.S., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J.O., Wodke, J.A.H., Xavier, J.C., Yuan, Q., Zakhartsev, M., Zhang, C., MEMOTE for standardized genome-scale metabolic model testing, Nature Biotechnology, 38(3):272-276 (2020) PMID 32123384

Li, H.D., Funk, C.C., Price, N.D., iREAD: a tool for intron retention detection from RNA-seq data, BMC Genomics, 21(1):128 (2020) PMID 32028886

Kim, T.K., Lee, I., Cho, J.H., Canine, B., Keller, A., Price, N.D., Hwang, D., Carlson, G., Hood, L., Core transcriptional regulatory circuits in prion diseases, Molecular Brain, 13:10 (2020) PMID: 31959236

Earls, J.C., Rappaport, N., Heath, L., Wilmanski, T., Magis, A.T., Schork, N.J., Omenn, G.S., Lovejoy, J., Hood, L., Price, N.D., Multi-Omic Biological Age Estimation and Its Correlation With Wellness and Disease Phenotypes: A Longitudinal Study of 3,558 Individuals, The Journals of Gerontology, Series A, 74(Supplement_1):S52-S60 (2019) PMID: 31724055

Zhou, Y., Qin, S., Sun, M., Tang, L., Yan, X., Kim, T.K., Caballero, J., Glusman, G., Brunkow, M.E., Soloski, M.J., Rebman, A.W., Scavarda, C., Cooper, D., Omenn, G.S., Moritz, R.L., Wormser, G.P., Price, N.D., Aucott, J.N., Hood, L., Measurement of Organ-Specific and Acute-Phase Blood Protein Levels in Early Lyme Disease, Journal of Proteome Research, 19(1):346-359 (2019) PMID: 31618575

Dean, K.R., Hammamieh, R., Mellon, S.H., Abu-Amara. D., Flory, J.D., Guffanti, G., Wang, K., Daigle, B.J. Jr., Gautam, A., Lee, I., Yang, R., Almli, L.M., Bersani, F.S., Chakraborty, N., Donohue, D., Kerley, K., Kim, T.K., Laska, E., Young Lee, M., Lindqvist, D., Lori, A., Lu, L., Misganaw, B., Muhie, S., Newman, J., Price, N.D., Qin, S., Reus, V.I., Siegel, C., Somvanshi, P.R., Thakur, G.S., Zhou, Y.; PTSD Systems Biology Consortium, Hood, L., Ressler, K.J., Wolkowitz, O.M., Yehuda, R., Jett, M., Doyle, F.J. 3rd, Marmar, C., Multi-omic biomarker identification and validation for diagnosing warzone-related post-traumatic stress disorder, Molecular Psychiatry, [Epub ahead of print] (2019) PMID: 31501510

Wilmanski, T., Rappaport, N., Earls, J.C., Magis, A.T., Manor, O., Lovejoy, J., Omenn, G.S., Hood, L., Gibbons, S., and Price, N.D., Blood metabolome signature predicts gut microbiome alpha-diversity in health and disease, Nature Biotechnology, 37(10):1217-1228 (2019) PMID: 31477923

Paquette, A.G., Shynlova, O., Wu, X., Kibschull, M., Wang, K., Price, N.D., Lye, S.J., MicroRNA-transcriptome networks in whole blood and monocytes of women undergoing preterm labour, Journal of Cellular and Molecular Medicine, 23(10):6835-6845 (2019) PMID: 31342622

Baloni, P., Sangar, V., Yurkovich, J.T., Robinson, M., Taylor, S. Karbowski, C.M., Hamadeh, H.K., He, Y.D., Price, N.D., Genome-scale metabolic model of the rat liver predicts effects of diet restriction, Scientific Reports, 9(1):9807 (2019) PMID: 31285465

Zubair, N., Conomos, M.P., Hood, L., Omenn, G.S., Price, N.D., Spring, B.J., Magis, A.T., Lovejoy, J.C., Genetic Predisposition Impacts Clinical Changes in a Lifestyle Coaching Program, Scientific Reports, 9(1):6805 (2019) PMID: 31048771

Palii, C.G., Cheng, Q., Gillespie, M.A., Shannon, P., Mazurczyk, M., Napolitani, G., Price, N.D., Ranish. J.A., Morrissey, E., Higgs, D.R., Brand, M., Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate, Cell Stem Cell, 24(5): 812-820 (2019) PMID: 30880026

Shen, F., Sun, R., Yao, J., Li, J., Liu, Q., Price, N.D., Liu, C., Wang, Z., OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling, PLoS Comput Biol, 15(3):e1006835 (2019) PMID: 30849073

Pearl, J.R., Colantuoni, C., Bergey, D.E., Funk, C.C., Shannon, P., Basu, B., Casella, A.M., Oshone, R.T., Hood, L., Price, N.D., and Ament, S.A., Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders, Cell Systems, 8(2):122-125 (2019) PMID: 30772379

Sorrentino, Z.A., Xia, Y., Funk, C., Riffe, C.J., Rutherford, N.J., Ceballos Diaz, C., Sacino, A.N., Price, N.D., Golde, T.E., Giasson, B.I., Chakrabarty, P., Motor neuron loss and neuroinflammation in a model of α-synuclein-induced neurodegeneration, Neurobiology of Disease, 120:98-106 (2018) PMID: 30195075

Paquette, A.G., Chu, T., Wu, X., Wang, K., Price, N.D., Sadovsky, Y., Distinct communication patterns of trophoblastic miRNA among the maternal-placental-fetal compartments, Placenta, 72-73:28-35 (2018) PMID:30501878

Allen, M., Wang X, Serie, D.J., Strickland, S.L., Burges,s J.D., Koga, S., Younkin, C.S., Nguyen, T.T., Malphrus, K.G., Lincoln, S.J., Alamprese, M., Zhu, K., Chan,g R., Carrasquillo, M.M., Kouri, N., Murray, M.E., Reddy, J.S., Funk, C., Price, N.D., Golde, T.E., Younkin, S.G., Asmann, Y.W., Crook, J.E., Dickson, D.W., Ertekin-Taner, N., Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy, Acta Neuropathologica, 136:709-727 (2018) PMID: 30136084

Chakrabarty, P., Li, A., Ladd, T., Cruz, P.E., Koller, E.J., Strickland, M.R., Burgess, J., Funk, C.C., Li, H., Younkin, M.A., Moore, B., Liu, X., Ceballos-Diaz, C., Rosario, A.M., Janus, C., Price, N.D., Younkin, S.G., Ertekin-Taner, N., Golde, T.E., TLR5 decoy receptor as a novel anti-amyloid therapeutic for Alzheimer’s disease, J Exp Med, 215:2247-2264 (2018) PMID: 30158114

Magis, A.T., Earls, J.C., Glusman, G., Omenn, G.S., Lovejoy, J.C., Price, N.D., Hood, L., Reply to “Precision medicine in the clouds”, Nature Biotechnology, 36(8):680-682 (2018) PMID: 30080845

Readhead, B., Haure-Mirande, J.V., Funk, C.C., Richards, M.A., Shannon, P., Haroutunian, V., Sano, M., Liang, W.S., Beckmann, N.D., Price, N.D., Reiman, E.M., Schadt, E.E., Ehrlich, M.E., Gandy, S., and Dudley, J.T., Multiscale analysis of three independent Alzheimer’s cohorts finds disruption of molecular, genetic, and clinical networks by Human herpesvirus, Neuron, 99(1):64-82. e7 (2018) PMID: 29937276 

Paquette, A., Price, N.D., Lye, S.J., Reply, American Journal of Obstetrics & Gynecology, 219(1):123-124 (2018) PMID: 29604285

Paquette, A., Baloni, P., Holloman, A., Nigam, S., Bammler, T., Mao, Q., Price, N.D., Temporal Transcriptomic Analysis of Metabolic Genes in Maternal Organs and Placenta During Murine Pregnancy, Biology of Reproduction,99(6):1255-1265 (2018) PMID: 29939228 

Price, N.D., Segal, E., Editorial overview: Systems biology: Data, discovery, delivery, Current Opinion in Biotechnology, 51:vii-viii (2018) PMID: 29891032

Mikheev, A.M., Mikheeva, S.A., Severs L.J., Funk, C., Schwensen, J., Huang, L., Price, N.D., McFaline, J.L., Trapnell, C., Wong, S., and Rostomily, R.C., Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma, Molecular Oncology, 12(7):1188-1202 (2018) PMID: 29754406 

King, B., Farrah, T., Richards, M.A., Mundy, M., Simeonidis, E., Price, N.D., ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions, Bioinformatics, 34(9):1594-1596 (2018) PMID: 29267848

Dinalankara, W., Ke, Q., Xu, Y., Ji, L., Pagane, N., Lien, A., Matam, T., Fertig, E.J., Price, N.D., Younes, L., Marchionni, L., Geman, D., Digitizing omics profiles by divergence from a baseline, Proceedings of the National Academy of Sciences, 115(18):4545-4552 (2018) PMID: 29666255 

Trachana, K., Bargaje, R., Glusman, G., Price, N.D., Huang, S., Hood, L.E., Taking Systems Medicine to Heart, Circulation Research, 122(9):1276-1289 (2018) PMID: 29700072

Ament, S.A., Pearl, J.R., Cantle, J.P., Bragg, R.M., Skene, P.J., Coffey, S.R., Bergey, D.E., Wheeler, V.C., MacDonald, M.E., Baliga, N.S., Rosinski, J., Hood, L.E., Carroll, J.B., Price, N.D., Transcriptional regulatory networks underlying gene expression changes in Huntington’s disease, Molecular Systems Biology, 14(3):e7435 (2018) PMID: 29581148

Allen, M.*, Burgess, J.*, Wang, X.*, Serie, D., Chai, H-S, Younkin, C.S., Nguyen, T., Malphrus, K.G., Lincoln, S., Golde, T.E., Price, N.D., Petersen, R.C., Graff-Radford, N.R., Younkin, S.G., Dickson, D.W., Crook, J.R., Asmann, Y.W., and Ertekin-Taner, N., Conserved brain myelination networks are altered in human neurodegenerative diseases, Alzheimer’s and Dementia, 14(3):352-366 (2018) PMID: 29107053

Paquette, A.G., Shynlova, O., Kibschull, M., Price, N.D., Lye, S.J., Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor, American Journal of Obstetrics & Gynecology, 218(3):345.e1-345.e30 (2018) PMID: 29305255

Chung, J., Zhang, X., Allen, M., Wang, X., Ma, Y., Beecham, G., Montine, T.J., Younkin, S.G., Dickson, D.W., Golde, T.E., Price, N.D., Ertekin-Taner, N., Lunetta, K.L., Mez, J., Alzheimer’s Disease Genetics Consortium, Mayeux, R., Haines, J.L., Pericak-Vance, M.A., Schellenberg, G., Jun, G.R., Farrer, L.A., Genome-wide Pleiotropy Analysis of Neuropathological Traits Related to Alzheimer’s Disease, Alzheimer’s Research & Therapy, 10(1):22 (2018) PMID: 29458411

Ridge, P.G., Karch, C.M., Hsu, S., Arano, I., Teerlink, C.C., Ebbert, M.T.W., Murcia, J.D.G., Farnham, J.M., Damato, A.R., Allen, M., Wang, X., Harari, O., Fernandez, V.M., Guerreiro, R., Bras, J., Hardy, J., Munger, R., Norton, M., Sassi, C., Singleton, A., Younkin, S.G., Dickson, D.W., Golde, T.E., Price, N.D., Ertekin-Taner, N., Cruchaga, C., Goate, A.M., Corcoran, C., Tschanz, J., Cannon-Albright, L.A., Kauwe, J.S.K., Correction to: Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience, Genome Medicine, 10(1):4 (2018) PMID: 29329552

Paquette, A.G., Brockway, H.M., Price, N.D., Muglia, L.J., Comparative transcriptomic analysis of human placentae at term and preterm delivery, Biology of Reproduction, 98(1):89-101 (2018) PMID: 29228154

Ridge, P.G., Karch, C.M., Hsu, S., Arano, I., Teerlink, C.C., Ebbert, M.T.W., Gonzalez, J., Farnham, J.M., Allen, M., Wang, X., Harari, O., Fernandez, V.M., Guerreiro, R., Hardy, J., Munger, R., Norton, M., Sassi, C., Singleton, A., Younkin, S.G., Dickson, D.W., Golde, T.E., Price, N.D., Ertekin-Taner, N., Cruchaga, C., Goate, A.M., Corcoran, C., Tschanz, J., Cannon-Albright, L.A., Kauwe, J., Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience, Genome Medicine, 10(1):4 (2018) PMID:29183403

Alfano, C.M, Zucker, D.S., Pergolotti, M., Ness, K.K., Jones, L.W., Price, N.D., Schmitz, K.H., and Ligibel, J.A., A Precision Medicine Approach to Improve Cancer Rehabilitation’s Impact and Integration with Cancer Care and Optimize Patient Wellness, Curr Phys Med Rehabil Rep,  5: 64 (2017) 

Pearl, J., Heath, L., Bergey, D.E., Kelly, J.P., Smith, C., Laurino, M., Weiss, A., Price, N.D., LaSpada, A., Bird, T.D., Jayadev, S., Enhanced retinal responses in Huntington’s disease patients, Journal of Huntington’s Disease, 6(3):237-247 (2017) PMID: 28968243

Samal, A., Craig, J.P., Coradetti, S.T., Benz, J.P., Eddy, J.A., Price, N.D., Glass, N.L., Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa, Biotechnology Biofuels, 10:225 (2017) PMID: 28947916

Seo, S.O., Jenssen, H., Magis, A., Wang, Y., Lu, T., Price, N.D., Jin, Y.S., and Blaschek, H.P.

Genomic, transcriptional and phenotypic analysis of the glucose derepressed Clostridium beijerinckii mutant exhibiting acid crash phenotype, Biotechnology Journal, 12(11) (2017) PMID: 28762642

Sims, R., … Price, N.D., …, et al., Rare coding variants in PLCG2, ABI3 and TREM2 implicate microglial-mediated innate immunity in Alzheimer’s disease, Nature Genetics, 49(9):1373-1384 (2017) PMID: 28714976

Price, N.D.*, Magis, A.T., Earls, J.C., Glusman, G., Levy, R., Lausted, C., McDonald, D.T., Kusebauch, U., Moss, C.L., Zhou, Y., Qin, S., Moritz, R.L., Brogaard, K., Omenn, G.S., Lovejoy, L.C., and Hood, L.*, A wellness study of 108 individuals using personal, dense, dynamic data clouds, Nature Biotechnology, 35(8):747-756 (2017). *Co-corresponding authors. PMID: 28714965

Marshall-Colon, A., Long, S.P., Allen, D.K, Allen, G., Beard, D.A., Benes, B., Christensen, A.J., Cox, D.J., Hart, J.C., Hirst, P.M., Kannan, K., Katz, D.S., Lynch, J.P., Millar, A.J., Panneerselvam, B., Price, N.D., Raila, D., Shekar, R.G., Shrivastava, S., Shukla, D., Srinivasan, V., Stitt, M., Voit, E.O., Wang, Y., Yin, X., Zhu, Xin-Guang, Crops in silico: generating virtual crops using an integrative and multi-scale modeling platform, Frontiers in Plant Science, 8:786 (2017) PMID: 28555150

Wang, Z., Danziger, S.A., Heavner, B.D., Ma, S., Smith, J.J., Li, S., Herricks, T., Simeonidis, E., Baliga, N.S., Aitchison, J.D., Price, N.D., Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast, PLOS Computational Biology, 13(5):e1005489 (2017) PMID: 28520713

Coffey, S.R., Bragg, R.M., Minnig, S., Ament, S.A., Cantle, J.P., Glickenhaus, A., Shelnut, D., Carrillo, J.M., Shuttleworth, D.D., Rodier, J.A., Noguchi, K., Bennett, C.F., Price, N.D., Kordasiewicz, H.B., Carroll, J.B., Peripheral huntingtin silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington’s disease, PLoS One, 12(4):e0145968 (2017) PMID: 28453524

Ghosh, D., Funk, C.C., Caballero, J., Shah, N., Rouleau, K., Earls, J.C., Soroceanu, L., Foltz, G., Cobbs, C.S., Price, N.D., Hood, L., A cell-surface membrane protein signature for glioblastoma, Cell Systems, 4(5):516-529 (2017) PMID: 28365151

Ament, S.A., Pearl, J.R., Grindeland, A., St Claire, J., Earls, J.C., Kovalenko, M., Gillis, T., Mysore, J., Gusella, J.F., Lee, J.M., Kwak, S., Howland, D., Lee, M.Y., Baxter, D., Scherler, K., Wang, K., Geman, D., Carroll, J.B., MacDonald, M.E., Carlson, G., Wheeler, V.C., Price, N.D., Hood, L.E., 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, 26(5):913-922 (2017) PMID: 28334820

Pollak, J., Rai, K.G., Funk, C.C., Arora, S., Lee, E., Zhu, J., Price, N.D., Paddison, P.J., Ramirez, J.M., Rostomily, R.C., Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy, PLoS One, 12(3): e0172884 (2017) PMID: 28264064

Bragg, R.M., Coffey, S.R., Weston, R.M., Ament, S.A., Cantle, J.P., Minnig, S., Funk, C.C., Shuttleworth, D., Woods, E., Sullivan, B., Jones, L., Glickenhaus, A., Anderson, J., Anderson, M., Dunnett, S.B., Wheeler, V.C., MacDonald, M.E., Brooks, S.P., Price, N.D., and Carroll, J.B., Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+ model of Huntington’s disease, Scientific Reports, 7:41570 (2017) PMID: 28176805 

Carrasquillo, M.M., Allen, M., Burgess, J., Wang, X., Strickland, S.L., Aryal, S., Siuda, J., Kachadoorian, M.L., Medway, C., Younkin, C.S., Nair, A., Wang, C., Chanana, P., Serie, D., Nguyen, T., Lincoln, S., Malphrus, K.G., Morgan, K., Golde, T.E., Price, N.D., White, C.C., De Jager, P.L,Bennett, D.A., Asmann, Y.W., Crook, J.E., Petersen, R.C., Graff-Radford, N.R., Dickson, D.W., Younkin, S.G., Ertekin-Taner, N., 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, 13(6):663-673 (2017) PMID: 27939925

Richards, M.A., Lie, T.J., Zhang, J., Ragsdale, S.W., Leigh, J.A., Price, N.D., Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis, Journal of Bacteriology, 198(24):3379-3390 (2016) PMID: 27736793

Allen, M*, Carrasquillo, M.M.*, Funk, C.C., Heavner, B.D., Zou F., Younkin, C.S., Burgess J.D., Chai, H.S., Crook, J., Eddy, J.A., Li, H., Logsdon, B., Wang, X., Serie, D., Wang, C., Nguyen, T., Lincoln S., Malphrus, K., Bisceglio, G., Li, M., Golde, T.E., Mangravite, L., Asmann, Y., Price, N.D., Petersen, R.C., Graff-Radford, N.R., Dickson, D.W., Younkin, S.G., Ertekin-Taner, N., Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases, Scientific Data, 3:160089 (2016) PMID: 27727239

Sagner, M., McNeil, A., Puska, P., Auffray, C., Price, N.D., Hood, L., Lavie, C.J., Han, Z., Chen, Z., Brahmachari, S.K., McEwen, B.S., Soares, M.B., Balling, R., Epel, E., and Arena, R. The P4 Health Spectrum – A Predictive, Preventive, Personalized and Participatory Continuum for Promoting Healthspan, Progress in Cardiovascular Diseases, 59(5):506-521 (2017) PMID: 27546358

Dinov, I.D., Heavner, B., Tang, M., Glusman, G., Chard, K., Darcy, M., Madduri, R., Pa, J., Spino, C., Kesselman, C., Foster, I., Deutsch, E.W., Price, N.D., Van Horn, J.D., Ames, J., Clark, K., Hood, L., Hampstead, B.M., Dauer, W., Toga, A.W., Predictive big data analytics: A study of Parkinson’s disease using large, complex, heterogeneous, incongruent, multi-source, and incomplete observations, PLOS ONE 11(8):e0157077 (2016) PMID: 27494614

Allen, M., Burgess, J.D., Ballard, T., Serie, D., Wang, X., Younkin, C.S., Sun, Z., Kouri, N., Baheti, S., Wang, C., Carrasquillo, M.M., Nguyen, T., Lincoln, S., Malphrus, K., Murray, M., Golde, T., Price, N.D., Younkin, S.G., Schellenberg, G.D., Asmann, Y., Ordog, T., Crook, J., Dickson, D., Ertekin-Taner, N., Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci, Acta Neuropathologica, 132(2):197-211(2016) PMID: 27115769

Zhou, J.X.*, Samal, A.*, Fouquier d’Hérouël, A., Price, N.D.,  Sui Huang, Relative stability of network states in Boolean network models of gene regulation in development, Biosystems 142-143:15-24 (2016) PMID: 26965665

McDonald, D.T., Glusman, G., and Price, N.D., Personalized nutrition through big data, Nature Biotechnology, 34(2):152-4 (2016). PMID: 26849520

Garcia de Lomana, A.L., Schäuble, S., Valenzuela, J., Imam, S., Carter, W., Bilgin, D.D., Yohn, C.B., Turkarslan, S., Reiss, D., Orellana, M.V., Price, N.D., and Baliga, N.S., Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii, BMC Biotechnology for Biofuels, 8:207 (2015) PMID: 26633994

Ma, S., Minch, K.J., Rustad, T.R., Hobbs, S., Zhou, S.L., Sherman, D.R., and Price, N.D., Integrated modeling of gene regulatory and metabolic networks in Mycobacterium tuberculosis, PLOS Computational Biology, 11(11):e1004543 (2015) PMID: 26618656

Pestal, K., Funk, C.C., Snyder, J.M., Price, N.D., Treuting, P.M., Stetson, D., Isoforms of RNA-Editing Enzyme ADAR1 independently control nucleic acid sensor MDA5-driven autoimmunity and multi-organ development, Immunity, 43(5):933-44 (2015) PMID: 26588779

Heavner, B.D., and Price, N.D., Comparative analysis of yeast metabolic network models highlights progress, opportunities for metabolic reconstruction, PLOS Computational Biology, 11(11):e1004530 (2015) PMID: 26566239

Imam, S., Schäuble, S., Valenzuela, J., García de Lomana, A.L., Carter, W., Price, N.D., and Baliga, N.S., A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses, The Plant Journal, 84(6): 1239-56 (2015) PMID: 26485611

Almaas, E., Bauer, E., Bordbar, A., Burgard, A.P., Chang, R.L., Dräger, A., Ebrahim, A., Famili, I., Feist, A.M., Fleming, R.M.T., Fong, S.S., Hatzimanikatis, V., Herrgård, M.J., Holder, A., Hyduke, D., Jamshidi, N., Lee, S.Y., Lerman, J.A., Lewis, N.E., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L.K., Nogales, J., Noronha, A., Pal, C., Palsson, B. Ø, Papin, J.A., Patil, K.R., Price, N.D., Reed, J.L., Saunders, M., Senger, R.S., Sonnenschein, N., Sun, Y., and Thiele, I. (author order alphabetical), Do Genome-scale Models Need Exact Solvers or Clearer Standards?, Molecular Systems Biology, 11(10):831 (2015) PMID: 26467284

Tian, Q., Sangar, V., and Price, N.D., Emerging proteomic technologies provide enormous and underutilized potential for brain cancer research, Molecular & Cellular Proteomics, 15(2): 362-7 (2016) PMID: 26407994

Magis, A.T., Funk, C.C., and Price, N.D., SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis, IEEE Life Science Letters, 1(2):22-35 (2015) PMID: 29270443

Toga, A.W., Foster, I., Kesselman, C., Madduri, R., Chard, K., Deutsch, E.W., Price, N.D., Glusman, G., Heavner, B.D., Dinov, I.D., Ames, J., Van Horn, J., Kramer, R., and Hood, L., Big biomedical data as the key resource for discovery science, Journal of the American Medical Informatics Association (JAMIA), 22(6):1126-31 (2015) PMID: 26198305

Hood, L., Brogaard, K., and Price, N.D., A Vision for 21st Century Healthcare, Cancer Medicine  (Eds. Kufe, D.W., Pollock, R.E., Weichselbaum, R.R., Bast, R.C., Gansler, T.S., Holland, J.F., and Frei, E), Ninth Edition, (2015)

Eddy, J.A., Funk, C.C., and Price, N.D., Fostering synergy between cell biology and systems biology, Trends in Cell Biology, 25(8):440-5 (2015) PMID: 26013981

Imam, S., Schauble, S., Brooks, A.N., Baliga, N.S., and Price, N.D., Data-driven integration of genome-scale regulatory and metabolic network models, Frontiers in Microbiology, 6:409 (2015) PMID: 25999934

Turkarslan, S., Peterson, E., Rustad, T., Minch, K., Reiss, D.J., Morrison, B., Ma., S., Price, N.D., Sherman, D.R., and Baliga, N.S., A comprehensive map of genome-wide regulation in Mycobacterium tuberculosis, Scientific Data 2:150010 (2015) PMID: 25977815

Ament, S.A., Szelinger, S., Glusman, G., Detera-Wadleigh, S., Ashworth, J., Hou, L., Akula, N., Shekhtman, T., Badner, J.A., Brunkow, M.E., Mauldin, D.E., Stittrich, A.B., Rouleau, K., Nurnberger, J.I., Edenberg, H.J., Gershon, E.S., Schork, N.J., The Bipolar Genome Study, Price, N.D., Gelinas, R., Hood, L., Craig, D.W., McMahon, F.J., Kelsoe, J.R., Roach, J.C., Rare variants in neuronal excitability genes influence risk for bipolar disorder, Proc. Natl. Acad. Sci. USA, 112(11):3576-81 (2015) PMID: 25730879

Chandrasekaran, S., Rittschof, C., Djukovic, D., Gu, H., Raftery, D., Price, N.D.*, and Robinson, G.* Aggression is Associated with Aerobic Glycolysis in the Honey Bee Brain, Genes, Brain, and Behavior 14(2):158-66 (2015). PMID: 25640316 *Corresponding authors

Chakrabarty, P., Li, A., Ceballos-Diaz, C., Funk, C.C., Eddy, J.A., Moore, B., Rosario, A.M., Verbeeck, C., Sacino, A., Nix, S., Janus, C., Price, N.D., Das, P., Golde, T.E., IL-10 Alters Immunoproteostasis in APP mice, Increasing Plaque Burden and Worsening Cognitive Behavior, Neuron, 85(3):519-33 (2015) PMID: 25619653

Minch, K.J., Rustad, T.R., Peterson, E. Winkler, J., Reiss, D.J., Ma, S., Hickey, M., Brabant, B., Morrison, B., Turkarslan, S., Mawhinney, C., Galagan, J., Price, N.D., Baliga, N.S., and Sherman, D.R., The DNA binding network of Mycobacterium tuberculosis, Nature Communications 6:5829 (2015) PMID: 25581030 

Simeonidis, E., and Price, N.D., Genome-scale modeling for metabolic engineering, Journal of Industrial Microbiology and Biotechnology, 42(3):327-338 (2015) PMID: 25578304

Hood, L., Lovejoy, J., and Price, N.D., Integrating big data and actionable health coaching to optimize wellness, BMC Medicine, 13:4  (2015). Highly Accessed (special distinction given to the most downloaded papers in the journal) PMID: 25575752

Heavner, B., and Price, N.D., Transparency in metabolic network reconstruction enables scalable biological discovery, Current Opinion in Biotechnology, 34:105-109 (2015) PMID: 25562137

Geman, D., Ochs, M., Price, N.D., Tomasetti, C., and Younes, L., An Argument for Mechanism-Based Statistical Inference in Cancer, Human Genetics, 134(5):479-95 (2015) PMID: 25381197

Rustad, T.R., Minch, K.J., Winkler, J., Hobbs, S., Hickey, M, Brabant, W., Turkarslan, S., Price, N.D., Baliga, N.S., and Sherman, D.R., Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network, Genome Biology, 15(11):502 (2014). Highly Accessed (special distinction given to the most downloaded papers in the journal) PMID: 25380655

Ma, S., Sung, J., Magis, A.T., Wang, Y., Geman, D., and Price, N.D., Measuring the effect of inter-study variability on estimating prediction error, PLOS ONE, 9(10):e110840, (2014) PMID: 25330348

Benedict, M.N., Mundy, M.B., Henry, C.S., Chia, N., and Price, N.D., Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models, PLOS Computational Biology, 10(10):e1003882 (2014) PMID: 25329157

Richards, M.A., Cassen, V., Heavner, B.D., Ajami, N., Herrmann, A., and Price, N.D., MediaDB: a database of microbial growth conditions in defined media, PLOS ONE, 9(8):e103548 (2014) PMID:25098325

Sangar, V., Funk, C.C., Kusebauch, U., Campbell, D.S., Moritz, R.L., and Price, N.D., Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells, Molecular and Cellular Proteomics, 13(10):2618-31 (2014) PMID: 24997998

Craig, T.A., Zhang, Y., Magis, A.T., Funk, C.C., Price, N.D., Ekker, S.C., and Kumar, R., Detection of 1α,25-Dihydroxyvitamin D-Regulated miRNAs in Zebrafish by Whole Transcriptome Sequencing, Zebrafish. 11(3):207-18 (2014) PMID: 24650217

Hood, L., and Price, N.D., Promoting Wellness and Demystifying Disease: The 100K Project, Clinical Omics, 1(3):20-23 (2014). Featured in Genetic Engineering & Biotechnology News.  

Ma, S., Earls, J., Eddy, J.A., and Price, N.D., Integrative Omics Approaches in Network Medicine, Network Medicine, Eds. E. Silverman and J. Loscalzo (2014)

Benedict, M.N., Henriksen, J.R., Metcalf, W.W., Whitaker, R.J., and Price, N.D., ITEP: An integrated toolkit for exploration of pan-genomes, BMC Genomics, 15:8 (2014) PMID: 24387194

Chandrasekaran, S., and Price, N.D., Metabolic constraint-based refinement of transcriptional regulatory networks, PLOS Computational Biology, 9(12):e1003370 (2013). Highlighted in Nature Reviews Genetics. PMID: 24348226

Dong, Y., Kumar, C.G., Kim, P.J., Chia, N.L.P., Flynn, T., Miller, P., Cann, I.K.O., Mackie, R.M., Price, N.D., Sanford, R., … Friend, G., Yannarell, A.C., Shilts, W.W., Finley, R.J., and Fouke, B.W., Halomonas sulfidaeris-dominated microbial community inhabits 1.8 km-deep subsurface Cambrian Sandstone reservoir, Environmental Microbiology, 16(6):1695-708 (2014) PMID: 24238218

Lausted, C., Lee, I., Zhou, Y., Qin, S., Sung, J., Price, N.D., Hood, L. and Wang, K., Systems approach to neurodegenerative disease biomarker discovery, Annual Review of Pharmacology and Toxicology, 54:457-81 (2014) PMID: 24160693

Wang, C., Funk, C.C., Eddy, J.A., Price, N.D., Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytoma, PLOS ONE, 8(10):e76694 (2013) PMID: 24146911

Bai, J., Abernethy, D.R., Price, N.D., Sangar, V., Systems pharmacology modeling: an approach to improving drug safety, Biopharmaceutics & Drug Disposition, 35(1):1-14 (2013) PMID: 24136298

Li, X.J., Hayward, C., Fong, P.Y., Dominguez, M., Hunsucker, S.W., Lee, L.W., McLean, M., Law, S., Butler, H., Schirm, M., Gingras, O., Lamontagne, J., Allard, R., Chelsky, D., Price, N.D., Lam, S., Massion, P.P., Pass, H., Rom, W.N., Vachani, A., Fang, K.C., Hood, L., and Kearney, P., A blood-based proteomic classifier for the molecular characterization of pulmonary nodules, Science Translational Medicine, 5(207):207ra142 (2013) PMID: 24132637

Georgatos, F., Ballereau, S., Pellet, J., Ghanem, M., Price, N.D., Hood, L., Guo, Y.K., Boutigny, D., Auffray, C., Balling R., and Schneider, R., Computational infrastructures for data and knowledge management in systems biology, Systems Biology: Integrative Biology and Simulation Tools, Editors: Prokop, A. and Csukas, B., Springer (2013)

Price, N.D., Genome-scale models for microbial factories, Industrial Biotechnology, 9: 177-178 (2013)   

Sung, J., Kim, P.J., Ma, S., Funk, C.C., Magis, A.T., Wang, Y., Hood, L., Geman, D., and Price, N.D., Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures, PLOS Computational Biology, 9(7):e1003148 (2013) PMID 23935471

Heavner, B.D., Smallbone, K., Price, N.D., and Walker, L.P., Version 6 of the Consensus Yeast Metabolic Network Refines Biochemical Coverage and Improves Model Performance, Database, (2013) PMID: 23935056

Labhsetwar, P., Cole, J., Roberts, E., Price, N.D., and Luthey-Schulten, Z., Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population, Proceedings of the National Academy of Sciences USA, 110(34):14006-11 (2013)PMID: 23908403

Wang, Y., Li, X. Milne, C.B., Jansson, H., Lin, W., Phan, G., Jin, Y.S., Price, N.D., and Blaschek, H.P., 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(19):5853-63 (2013) PMID: 23872562

Earls, J.C., Eddy, J.A., Funk, C., Ko, Y., Magis, A., and Price, N.D., AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, BMC Bioinformatics, 14:78(2013). Highly Accessed (special distinction given to the most downloaded papers in the journal) PMID: 23496976

Thiele, I., Swainston, N., Fleming, R.M.T., Hoppe, A., Sahoo, S., …Price, N.D., … , Goryanin, I., Nielsen, J., Westerhoff, H.V., Kell, D.B., Mendes, P., and Palsson, B.O., A community-driven global reconstruction of human metabolism, Nature Biotechnology, 31(5):419-25 (2013) PMID: 23455439

Gonnerman, M.C., Benedict, M.N., Feist, A.M., Metcalf, W.W., Price, N.D., Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746, Biotechnology Journal, 8(9):1070-79 (2013) PMID: 23420771

Simeonidis, E., Chandrasekaran, S., and Price, N.D., A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism), Methods in Molecular Biology, 985:103-12 (2013) PMID: 23417801

Ko, Y.*, Ament, S.A.*, Eddy, J.A., Caballero, J., Earls, J.C., Hood, L., and Price, N.D., Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain, Proceedings of the National Academy of Sciences USA, 110(8):3095-3100 (2013). PMID: 23386717

Flores, M., Glusman, G., Brogaard, K., Price, N.D., and Hood, L., P4 Medicine: How Systems Medicine Will Transform the Healthcare Sector and Society, Personalized Medicine, 10(6):565-576 (2013) PMID: 25342952

Wang, Y., Eddy, J.A., and Price, N.D., Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE, BMC Systems Biology, 6:153 (2012). Highly Accessed (special distinction given to the most downloaded papers in the journal) PMID: 23234303

Yang, J.L., Cogdell, D., Eddy, J.A., Trent, J., Price, N.D., and Zhang, W., Expression of PRUNE2 mRNA and its positive correlation with non-coding RNA PCA3 in leiomyosarcoma, Chinese journal of oncology, 34: 497 (2012)

Simcha, D., Price, N.D., and Geman, D., The limits of de novo DNA motif discovery, PLOS ONE, 7(11):e47836 (2012) PMID: 23144830

Sangar, V., Eddy, J.A., Simeonidis, E., and Price, N.D., Mechanistic modeling of aberrant energy metabolism in disease, Frontiers in Computational Physiology and Medicine, 3:404 (2012) PMID: 23112774

Magis, A.T., and Price, N.D., The top-scoring ‘N’ algorithm: a generalized relative expression classification method from small numbers of biomolecules, BMC Bioinformatics, 13:227 (2012) PMID: 22966958

Craig, T.A., Zhang, Y. McNulty, M.S., Middha, S., Magis, A.T., Funk, C.C., Price, N.D., Ekker, S.C., and, R., Research Resource: Whole Transcriptome RNA Sequencing Detects Multiple 1α,25-Dihydroxyvitamin D3-Sensitive Metabolic Pathways in Developing Zebrafish, Molecular Endocrinology, 26(9):1630-42 (2012) PMID: 22734042

Committee for the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials (including Price, N.D.); Christine M. Micheel, Sharyl J. Nass, Gilbert S. Omenn, Editors; Evolution of Translational Omics: Lessons Learned and the Path Forward. Institute of Medicine (2012) National Academy of Sciences Press. 300 pages.

Hood, L., Flores, M.A., Brogaard, K.R., and Price, N.D., Systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized, and participatory, Handbook of Systems Biology (A. J. Marian Walhout, Marc Vidal, and Job Dekker, editors), Elsevier, San Diego, CA. (2012)

Sung, J., Wang, Y., Chandrasekaran, S., Witten, D.M., and Price, N.D., Molecular signatures from omics data: from chaos to consensus, Biotechnology Journal, 7(8):946-57 (2012) PMID: 22528809

Bebek, G., Koyuturk, M., Price, N.D., and Chance, M.R., Network biology methods integrating biological data for translational science, Briefings in Bioinformatics, 13(4):446-59 (2012) PMID: 22390873

Kim, P.-J., and Price, N.D., Genetic co-occurrence network across all sequenced microbes, PLoS Computational Biology, 7(12):e1002340 (2011) PMID: 22219725

Tian, Q., Price, N.D., and Hood, L., Systems cancer medicine: towards realization of predictive, preventive, personalized, and participatory (P4) medicine, Journal of Internal Medicine, 271(2):111-21 (2012) PMID: 22142401

Benedict, M.N., Gonnerman, M.C., Metcalf, W.W., and Price, N.D., Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A, Journal of Bacteriology, 194(4):855-65 (2012) PMID: 22139506

Ghosh, A., Zhao, H., and Price, N.D., Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae, PLoS ONE 6(11): e27316 (2011) PMID: 22076150

Chandrasekaran, S., Ament, S.A., Eddy, J.A., Rodriguez-Zas, S., Schatz, B.R., Price, N.D.* and Robinson, G.E.*, Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states, Proceedings of the National Academy of Sciences USA, 108(44):18020-5 (2011). PMID: 21960440 *Co-corresponding authors 

Milne, C.B., Eddy, J.A., Raju, R., Ardekani, S., Kim, P.-J., Senger, R.S., Jin, Y.-S., Blaschek, H.P., and Price, N.D., Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052, BMC Systems Biology, 5:130 (2011). Highly Accessed (special distinction given to the most downloaded papers in the journal) PMID: 21846360

Li, Q., Singh, C.R., Ma, S., Price, N.D., and Jagannath, C., Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages, Journal of Proteome Research, 10(5):2425-39 (2011) PMID: 21413810

Magis, A.T., Earls, J.C., Ko, Y.,-H, Eddy, J.A., and Price, N.D., Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, Bioinformatics, 27(6):872-3 (2011) PMID: 21257608

Yan, X., Ma, L., Yi, D., Yoon, J.G., Diercks, A., Foltz, G., Price, N.D., Hood, L., and Tian, Q., A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations, Proceedings of the National Academy of Sciences USA, 108(4):1591-1596 (2011) PMID 21220328

Ma, S., Funk, C., and Price, N.D., Systems approaches to molecular cancer diagnostics, Discovery Medicine, 10(55):531-42 (2010) PMID: 21189224

Chandrasekaran, S., and Price, N.D., Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis, Proceedings of the National Academy of Sciences USA, 107(41):17845-50 (2010) PMID: 20876091

Edelman, L.B., Eddy, J.A., and Price, N.D., In silico models of cancer, Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2(4): 438–459 (2010) PMID: 20836040

Shi, L., et al. (MAQC-II Consortium), The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models, Nature Biotechnology, 28(8): 827-838 (2010) PMID: 20676074

Price, N.D., and Lee, S.Y., Editorial: Systems biology for biotech applications, Biotechnology Journal, 5(7):636-637 (2010) PMID: 20665637 

Yang, J., Eddy, J.A., Pan, Y.,  Hategan, A., Tabus, I., Wang, Y., Cogdell, D., Price, N.D., Pollock, R.E., Lazar, A.J.F, Hunt, K.K.,  Trent, J.C., and Zhang, W., Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug, Molecular and Cellular Proteomics, 9(11):2405-13 (2010) PMID: 20651304

Eddy, J.A., Hood, L., Price, N.D.*, and Geman, D., Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC), PLoS Computational Biology, 6(5):e1000792 (2010) PMID: 20523739 *Corresponding author

Kim, P.J., and Price, N.D., Macroscopic kinetic effects of cell-to-cell variation in biochemical reactions, Physical Review Letters, 104(14):148103 (2010). Highlighted by Science News (“Enzymes Exposed”, 2010). PMID: 20481966

Eddy, J.A., Sung, J., Geman, D., and Price, N.D., Relative expression analysis for molecular cancer diagnosis and prognosis, Technology in Cancer Research and Treatment, 9(2):149-159 (2010) PMID: 20218737

Galas, D.J., Nykter, M., Carter, G.W., Price, N.D., and Shmulevich, I., Biological information as set-based complexity, IEEE Transactions on Information Theory, 56(2): 667 – 677 (2010) PMID: 27857450

Ezeji, T., Milne, C.B., Price, N.D., and Blaschek, H.P., Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol producing microorganisms, Applied Microbiology and Biotechnology, 85(6):1697-1712 (2010)  PMID: 20033401

Edelman, L.B., Chandrasekaran, S., Price, N.D., Systems biology of embryogenesis, Reproduction, Fertility, and Development, 22(1):98-105 (2009). PMID: 20003850

Eddy, J.A., Geman, D., Price, N.D., Relative expression analysis for identifying perturbed pathways, Conference Proceedings IEEE Engineering in Medicine and Biology Society., 2009:5456-9 (2009) PMID: 19964680

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, BMC Genomics, 10:e583 (2009). Highly Accessed (special distinction given to the most downloaded papers in the journal) PMID: 19961616

Milne, C.B., Kim, P.J., Eddy, J.A., and Price, N.D., Accomplishments of genome-scale in silico modeling for industrial and medical biotechnology, Biotechnology Journal, 4(12):1653-1670 (2009)  PMID: 19946878

Blaschek, H.P., Ezeji, T., and Price, N.D., Present and future possibilities for the deconstruction and utilization of lignocellulosic biomass, Handbook of Bioenergy (2009)

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., DeArmond, S.J., Carlson, G.A., Hood, L., A Systems Approach to Prion Disease, Molecular Systems Biology, 5:252 (2009) PMID: 19308092

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)

Price, N.D., Edelman, L.B., Lee, I., Yoo, H., Hwang, D., Carlson, G., Galas, D.J., Heath, J.R., and Hood, L., Systems biology and systems medicine, Genomic and Personalized Medicine: From Principles to Practice (Ginsburg, G. and Willard, H., editors). Vol.1, pp. 131-141, Elsevier, (2009)

Nykter, M., Price, N.D., Larjo, A., Aho, T., Kauffman, S.A., Yli-Harja, O., and Shmulevich, I., Critical networks exhibit maximal information diversity in structure-dynamics relationships, Physical Review Letters, 100(5):058702 (2008) PMID: 18352443

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) PMID: 18250330

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) PMID: 18031300

Price, N.D., and Shmulevich, I., Biochemical and statistical network models for systems biology, Current Opinion in Biotechnology, 18(4):365-370 (2007) PMID: 17681779

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(9):3414-3419 (2007) PMID: 17360660

Gianchandani, E.J., Papin, J.A., Price, N.D., Joyce, A., and Palsson, B.Ø., Matrix formalism to describe functional functional states of transcriptional regulatory systems, PLoS Computational Biology, 2(8): e101 (2006) PMID: 16895435

Price, N.D., Thiele, I., and Palsson, B.Ø., Candidate states of Helicobacter pylori‘s genome-scale metabolic network upon application of loop law thermodynamic constraints, Biophysical Journal, 90(11):3919-3928 (2006) PMID: 16533855

Barrett, C., Price, N.D., and Palsson, B.Ø., Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition, BMC Bioinformatics, 7:132 (2006) PMID: 16533395

Becker, S.A., Price, N.D., and Palsson, B.Ø., Metabolite coupling in genome-scale metabolic networks, BMC Bioinformatics, 7:111 (2006) PMID: 16519800

Allen, T.E., Price, N.D., Joyce, A., and Palsson, B.Ø., Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization, PLoS Computational Biology, 2(1): e2 (2006) PMID: 16410829

Thiele, I., Vo, T., Price, N.D., and Palsson, B.Ø., 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(16):5818-5830 (2005) PMID: 16077130

Thiele, I., Price, N.D., Vo, T. and Palsson, B.Ø., Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet, Journal of Biological Chemistry, 280(12):11683-11695 (2005) PMID: 15572364

Price, N.D., Reed, J.L., and Palsson, B.Ø., Genome-scale models of microbial cells: evaluating the consequences of constraints, Nature Reviews Microbiology, 2(11): 886-897 (2004) PMID: 15494745

Price, N.D., Schellenberger, J., and Palsson, B.Ø., Uniform sampling of steady state flux spaces: means to design experiments and interpret enzymopathies, Biophysical Journal, 87(4):2172-2186 (2004) PMID: 15454420

Papin, J.A., Stelling, J., Price, N.D., Klamt, S., Schuster, S., Palsson, B.Ø., Comparison of network-based pathway analysis methods, Trends in Biotechnology, 22(8):400-405 (2004) PMID: 15283984

Raghunathan, A., Price, N.D., Kolker, E., et al., 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) PMID: 15107235

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

Price, N.D., Reed, J.L., Papin, J.A., Wiback, S.J., and Palsson, B.Ø., Network-based analysis of metabolic regulation in the human red blood cell, Journal of Theoretical Biology, 225(2):185-194 (2003) PMID: 14575652

Papin, J.A., Price, N.D., Wiback, S.J., Fell, D.A., and Palsson, B.Ø., Metabolic pathways in the post-genome era, Trends in Biochemical Sciences, 28(5):250-258 (2003) PMID: 12765837

Palsson, B.Ø., 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) PMID: 12727379

Price, N.D., Papin, J.A., Schilling, C.H., and Palsson, B.Ø., Genome-scale microbial in silico models: the constraints-based approach, Trends in Biotechnology, 21(4):162-169 (2003) PMID: 12679064

Price, N.D., Reed, J.L., Papin, J.A., Famili, I. and Palsson, B.Ø., Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices, Biophysical Journal, 84(2 Pt1):794-804 (2003) PMID: 12547764

Papin, J.A., Price, N.D., and Palsson, B.Ø., Extreme pathway lengths and reaction participation in genome-scale metabolic networks, Genome Research, 12(12):1889-1900 (2002) PMID: 12466293

Price, N.D., Famili, I., Beard, D.A. and Palsson, B.Ø., Extreme pathways and Kirchhoff’s second law, Biophysical Journal, 83(5):2879-2882 (2002) PMID: 12425318

Papin, J.A., Price, N.D., Edwards, J.S., and Palsson, B.Ø., The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy, Journal of Theoretical Biology, 215(1):67-82 (2002) PMID: 12051985

Price, N.D., Papin, J.A., Palsson, B.Ø., Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis, Genome Research, 12(5):760-769 (2002) PMID: 11997342