Publications

Featured Network Publications


Rima Kaddurah-Daouk

  • Rozen S., Cudkowicz M.E., Bogdanov M., Matson W.R., Kristal B.S., Beecher C., Harrison S., Vouros P., Flarakos J., Vigneau-Callahan K., Matson T.D., Newhall K.M., Beal M.F., Brown Jr R.H., and Kaddurah-Daouk R. (2005). Metabolomic Analysis and Signatures in Motor Neuron Disease. Metabolomics 1(2), 101 – 108.
  • Kaddurah-Daouk R.(2006). Metabolic Profiling of Patients with Schizophrenia. PLoS Med. Aug 22;3(8).
  • Paige LA, Mitchell MW, Krishnan KR, Kaddurah-Daouk R, Steffens DC. (2006). A preliminary metabolomic analysis of older adults with and without depression. Int J Geriatr Psychiatry. Oct 17
  • Kaddurah-Daouk R, McEvoy J, Baillie RA, Lee D, Yao JK, Doraiswamy PM, Krishnan KR (2007). Metabolomic mapping of atypical antipsychotic effects in schizophrenia. Mol Psychiatry. 12(10):934-945.
  • Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O. (2007). The metabolomics standards initiative. Nat Biotechnol. Aug;25(8):846-8.
  • Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N, Sumner LW ,Goodacre R,Hardy NW, Taylor C, Fostel J, Kristal B, Kaddurah-Daouk R, Mendes P, van Ommen B, Lindon JC, and Sansone SA (2007). The metabolomics standards initiative (MSI). Metabolomics: 3(3), 175-178.
  • Kaddurah-Daouk R, Kristal BS, Weinshilboum RM.(2008) Metabolomics: A Global Biochemical Approach to Drug Response and Disease. Annu Rev Pharmacol Toxicol. Feb 10;48:653-683.
  • Kaddurah-Daouk R and Krishnan KR (2008). Metabolomics: A Global Biochemical Approach to the Study of Central Nervous System Diseases. Neuropsychopharmacology. Jan 34(1):173-86.
  • Yao JK, Dougherty GG Jr, Reddy RD, Keshavan MS, Montrose DM, Matson WR, Rozen S, Krishnan RR, McEvoy J, Kaddurah-Daouk R. (2009) Altered interactions of tryptophan metabolites in first-episode neuroleptic-naive patients with schizophrenia. Mol Psychiatry. April 28:1-16.
  • Patkar AA, Rozen S, Mannelli P, Matson W, Pae CU, Krishnan RR, Kaddurah-Daouk R (2009). Alterations in tryptophan and purine metabolism in cocaine addiction: A metabolomic study. Psychopharmacology (Berl). 2009 Aug 1.
  • Mannelli P, Patkar A, Rozen S, Matson W, Krishnan R, Kaddurah-Daouk R. Opioid use affects antioxidant activity and purine metabolism: Preliminary results. Hum Psychopharmacol. 2009 Dec; 24(8):666-75.
  • Steffens DC, Jiang W, Krishnan KR, Karoly ED, Mitchell MW, O'Connor CM, Kaddurah-Daouk. Metabolomic Differences in Heart Failure Patients With and Without Major Depression. J Geriatr Psychiatry Neurol. 2010 Jun;23(2):138-46.
  • Yao JK, Dougherty GG, Reddy RD, Keshavan MS, Montrose DM, Matson WR, McEvoy J, Kaddurah-Daouk R. Homeostatic imbalance of purine catabolism in first-episode neuroleptic-naïve patients with schizophrenia. PLoS One. 2010 Mar 3;5(3):e9508.PMID: 20209081 [PubMed - in process].
  • Kaddurah-Daouk R, Baillie RA, Zhu H, Zeng ZB, Wiest MM, Nguyen UT, Watkins SM, Krauss RM. Lipidomic analysis of variation in response to simvastatin in the Cholesterol and Pharmacogenetics Study. Metabolomics 2010, 6:191–201.
  • Fan TWM, Yuan P, Lane AN, Higashi RM, Wang Y, Hamidi AB, Zhou R, Guitart Z, Chen G, Manji HK, Kaddurah-Daouk R. Metabolomics 2010.

Richard Weinshilboum

  • Weinshilboum, R.M., Raymond, F.A., Elveback, L.R. and Weidman, W.H.: Correlation of erythrocyte catechol O methyltransferase activity between siblings. Nature 252:490 491, 1974.
  • Weinshilboum, R.M. and Raymond, F.A.: Inheritance of low erythrocyte catechol O methyltransferase activity in man. Amer. J. Human Genet. 29:125 135, 1977.
  • Weinshilboum, R.M. and Sladek, S.L.: Mercaptopurine pharmacogenetics: monogenic inheritance of erythrocyte thiopurine methyltransferase activity. Amer. J. Human Genet. 32:651 662, 1980.
  • Lennard, L., Van Loon, J.A. and Weinshilboum, R.M.: Pharmacogenetics of acute azathioprine toxicity: relationship to thiopurine methyltransferase genetic polymorphism. Clin. Pharmacol. Ther. 46:149-154, 1989.
  • Honchel, R., Aksoy, I.A., Szumlanski, C., Wood, T.C., Otterness, D.M., Wieben, E.D. and Weinshilboum, R.M.: Human thiopurine methyltransferase: molecular cloning and expression of T84 colon carcinoma cell cDNA. Mol. Pharmacol. 43:878-887, 1993.
  • Szumlanski, C., Otterness, D., Her, C., Lee, D., Brandriff, B., Kelsell, D., Spurr, N., Lennard, L., Wieben, E. and Weinshilboum, R.: Thiopurine methyltransferase pharmacogenetics: human gene cloning and characterization of a common polymorphism. DNA and Cell Biol. 15:17-30, 1996.
  • Lachman, H.M., Papolos, D.F., Saito, T., Yu, Y.-M., Szumlanski, C.L. and Weinshilboum, R.M.: Human catechol O methyltransferase pharmacogenetics: description of a functional polymorphism and its potential application to neuropsychiatric disorders. Pharmacogenetics 6:243-250, 1996.
  • Weinshilboum, R.: Inheritance and drug response. New Engl. J. Med. 348:529-537, 2003.
  • Wang, L., Sullivan, W., Toft, D. and Weinshilboum, R.: Thiopurine S-methyltransferase pharmacogenetics: chaperone protein association and allozyme degradation. Pharmacogenetics 13:555-564, 2003.
  • Wang, L., Nguyen, T.V., McLaughlin, R.W., Sikkink, L.A., Ramirez-Alvarado, M. and Weinshilboum, R.M.: Human thiopurine S-methyltransferase (TPMT) pharmacogenetics: variant misfolding and aggresome formation. Proc. Natl. Acad. Sci. 102:9394-9399, 2005.
  • Weinshilboum, R.M. and Wang, L.: Pharmacogenetics and pharmacogenomics: development, science and translation. Annu. Rev. Genomics & Hum. Genet. 7:223-245, 2006.
  • Kaddurah-Daouk, R., Kristal, B.S. and Weinshilboum, R.M.: Metabolomics: a global biochemical approach to drug response and disease. Annu. Rev. Pharmacol. Toxicol. 48:653-683, 2008.
  • Ji, Y., Olson, J.E., Zhang, J., Hildebrandt, M.A.T., Wang, L., Ingle, J.N., Fredericksen, Z.S., Sellers, T.A., Miller, W.R., Dixon, J.M., Brauch, H., Eichelbaum, M., Justenhoven, C., Hamann, U., Ko, Y., Buning, T., Chang-Claude, J., Wang-Gohrke, S., Schaid, D.J. and Weinshilboum, R.M.: Breast cancer risk reduction and membrane-bound catechol O-methyltransferase (COMT) genetic polymorphisms. Cancer Res. 68(14):5997-6005, 2008. PMC2518124
  • Wang, L. and Weinshilboum, R.M.: Pharmacogenomics: candidate gene identification, functional validation and mechanisms. Hum. Mol. Genet. 17:R174-R179, 2008. PMC2574004
  • Moyer, A., Sun, Z., Batzler, A., Li. L., Schaid, D., Yang, P. and Weinshilboum, R.: Glutathionine pathway genetic polymorphisms and lung cancer survival after platinum-based chemotherapy. Cancer Epidemiol. Biomarkers & Prevent. 19(3):811-21, 2010. PMC2837367

Shankar Subramaniam

  • Pradervand S, Maurya MR and Subramaniam S. Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages. Genome Biology 2006 Feb 20;7(2):R11.
  • Kim Y and Subramaniam S. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins. 2006 Mar 1;62(4):1115-24
  • Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A. Pairwise alignment of protein interaction networks. J Comput Biol. 2006 Mar;13(2):182-99.
  • Koyuturk M, Kim Y, Subramaniam S, Szpankowski W, Grama A. Detecting conserved interaction patterns in biological networks. J Comput Biol. 2006 Sep;13(7):1299-322.
  • Maurya MR, Subramaniam S. A kinetic model for calcium dynamics in RAW 264.7 cells:1.Mechanisms, parameters, and subpopulational variability. Biophys J. 2007 Aug 1;93(3):709-28. Epub 2007 May 4. PubMed PMID:17483174; PubMed Central PMCID: PMC1913151.
  • Pandey J, Koyuturk M, Kim Y, Szpankowski W, Subramaniam S, Grama A. Functional annotation of regulatory pathways. Bioinformatics. 2007 Jul 1;23(13):i377-86. PubMed PMID: 17646320.
  • Ramachandran S, Xie LH, John SA, Subramaniam S*, Lal R*. A novel role for connexin hemichannel in oxidative stress and smoking-induced cell injury. PLoS One. 2007 Aug 8;2(1):e712. PubMed PMID: 17684558; PubMed Central PMCID:PMC1933596. (*corresponding authors)
  • Maurya MR, Benner C, Pradervand S, Glass C, Subramaniam S. Systems biology of macrophages. Adv Exp Med Biol. 2007; 598:62-79. Review. PubMed PMID: 17892205.
  • Pandey J, Koyuturk M, Subramaniam S, Grama A. Functional coherence in domain interaction networks. Bioinformatics. 2008 Aug 15;24(16):i28-34. PubMed PMID:18689835.
  • Maurya MR, Bornheimer SJ, Venkatasubramaniam V, Subramaniam S. Mixed-integer nonlinear optimization approach to coarse-graining biochemical networks. IET Syst Biol. 2009 Jan;3(1):24-39. PubMed PMID: 19154082; PubMed Central PMCID: PMC2749294.
  • Gupta S, Maurya MR, Stephens DL, Dennis EA, Subramaniam S. An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. Biophys J. 2009 Jun 3;96(11):4542-51. PubMed PMID: 19486676; PubMed Central PMCID: PMC2711499.
  • Hsiao A, Subramaniam S. Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data. Syst Synth Bio. 2008 Dec;2(3-4):95-104. Epub 2009 Aug 13. PubMed PMID: 19680790; PubMed Central PMCID: PMC2735646.
  • Byrnes RW, Cotter D, Maer A, Li J, Nadeau D, Subramaniam S. An editor for pathway drawing and data visualization in the Biopathways Workbench. BMC Syst Biol. 2009 Oct 2;3(1):99. PubMed PMID:19799790 ; PubMed Central PMCID: PMC2763869
  • Sears DD, Hsiao G, Hsiao A, Yu JG, Courtney CH, Ofrecio JM, Chapman J, Subramaniam S. Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18745-50. PubMed PMID:19841271 ; PubMed Central PMCID: PMC2763882
  • Gupta S, Maurya MR, and Subramaniam S. Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells. PLoS Comput Biol. 2010 Jan 29;6(1).

David Wishart

  • Wishart, D.S., Knox, C., Guo, A., Shrivastava, S., Hassanali, M., Stothard, P. and Woolsey, J. (2006) DrugBank: A Comprehensive Resource for In Silico Drug Discovery and Exploration. Nucleic Acids. Res. 34(Database issue):D668-672.
  • Wishart, D.S., Tzur, D., Knox, C., Eisner, R., Guo, A.C., et al. HMDB: the Human Metabolome Database. Nucleic Acids Res. 35(Database issue):D521-526. (2007).
  • Wishart, D.S. (2007) Current Progress in Computational Metabolomics. Brief. Bioinform. 8:275-284.
  • Wishart, D.S. (2008) Quantitative Metabolomics using NMR. Trends Analyt. Chem. 27:228-237.
  • Wishart, D.S. (2008) DrugBank and its Relevance to Pharmacogenomics. Pharmacogenomics. 9:1155-1162.
  • Wishart, D.S. (2008) Applications of Metabolomics in Drug Discovery and Development. Drugs in R&D 9:307-322.
  • Wishart, D.S., Knox, C., Guo, A.C., Eisner, R., Young, N., Gautam, B., Hau, D.D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J.A., Lim, E., Sobsey, C.A., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., Li, L., Vogel, H.J. and Forsythe, I. (2009) HMDB: a Knowledgebase for the Human Metabolome. Nucleic Acids Res. 37(Database issue):D603-610.
  • Wishart, D.S. (2009) “Bioinformatics for Metabolomics” in Bioinformatics for Systems Biology (ed. S. Krawetz) Humana Press, Totowa NJ pp. 581-600.
  • Wishart, D.S. (2008) Applications of Metabolomics in Drug Discovery and Development. Drugs in R&D 9:307-322.
  • Xia, J., Bjorndahl, T.C., Tang, P., Wishart, D.S. (2008) MetaboMiner--Semi-automated Identification of Metabolites from 2D NMR Spectra of Complex Biofluids. BMC Bioinformatics. 9:507.
  • Wishart, D.S., Knox, C., Guo, A.C., Eisner, R., Young, N., et al. (2009) HMDB: a Knowledgebase for the Human Metabolome. Nucleic Acids Res. 37(Database issue):D603-610.
  • Goudie, A.D., Lynch, K.H., Seed, K.D., Stothard, P., Shrivastava, S., Wishart, D.S. and Dennis J. J. (2008) Genomic Sequence and Activity of KS10, a Transposable Phage of the Burkholderia cepacia Complex. BMC Genomics. 9:615.
  • Soh, J., Turinsky, A.L., Trinh Q.M., Chang, J., Sabhaney, A., Dong, X., Gordon, P.M., Janzen, R.P., Hau, D., Xia, J., Wishart, D.S and Sensen, C.W. (2009) Spatiotemporal Integration of Molecular and Anatomical Data in Virtual Reality Using Semantic Mapping. Int. J. Nanomedicine 4:79-89.
  • Perez-Pineiro, R., Burgos, A., Jones, D.C., Andrew, L.C., Rodriguez, H., Suarez, M., Fairlamb, A.H. and Wishart, D.S. (2009) Development of a Novel Virtual Screening Cascade Protocol to Identify Potential Trypanothione Reductase Inhibitors. J. Med. Chem. 52:1670-1680.
  • Forsythe, I.J. and Wishart, D.S. (2009) “Exploring Human Metabolites using the Human Metabolome Database” in Curr. Protoc. Bioinformatics. Chapter 14: Unit 14.8.
  • Xia, J., Psychogios, N., Young, N. and Wishart, D.S. (2009) MetaboAnalyst: A Web Server for Metabolomic Data Analysis and Interpretation. Nucleic Acids Res. 37(Web Server Issue):W652-660.

Bernhard Palsson

  • Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. Ø., "BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions", BMC Bioinformatics, 11:213, (2010).
  • Hyduke DR and Palsson BØ Towards genome-scale signalling network reconstructions Nature Reviews Genetics 11:297-307 Funded by NIH/NIAID: Y1-AI-8401-01
  • Jamshidi, N. and Palsson, B.O., Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models, Biophysical Journal, 98: 175-185 (2010).
  • Thiele, I. and Palsson, B.O., A protocol for generating a high-quality genome-scale metabolic reconstruction, Nature Protocols, 5: 93-121 (2010).
  • Li, F., Thiele, I., Jamshidi, N., and Palsson, B.O., Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling, PLOS Comput Biol. 5:e1000292. doi:10.1371/journal.pcbi.1000292 (2009).
  • Sigurdsson, M.I., Jamshidi, N., Jonsson J.J., and Palsson, B.O., ''Genome-scale network analysis of imprinted human metabolic genes''. Epigenetics. (2009)
  • Mo, M.L. and Palsson, B.Ø. Understanding human metabolic physiology: A genome-to-systems approach, Trends in Biotechnology. 27(1):37-44 (2009).
  • Shlomi, T., Cabili, M.N., Herrgard, M.J., Palsson, B.O. and Ruppin, E., Network-based prediction of human tissue-specific metabolism, Nature Biotechnology, 26: 1003-1010 (2008).
  • Vo, T. D., Lim, S. K., Lee, W. N. P., Palsson, B. O., "Isotopomer Analysis of Cellular Metabolism in Tissue Culture: A Comparative study between the pathway and network-based methods", Metabolomics, 2: 243-256 (2006).
  • Mo, M.L., Jamshidi, N., Palsson, B.Ø., "A Genome-scale, Constraint-based Approach to Systems Biology of Human Metabolism," Molecular Biosystems 3: 598 (2007).
  • Thiele, I. and Palsson, B. Ø., ''Reconstruction annotation jamborees: a community approach to systems biology'', Mol. Syst. Biol. 6, 361 (2010).
  • Jamshidi, N. and Palsson, B.O., Using In Silico Models to Simulate Dual Perturbation Experiments: Procedure Development and Interpretation of Outcomes. BMC Systems Biology. 3:44 (2009).
  • Jamshidi, N., Palsson, B.Ø., Flux-concentration duality in dynamic nonequilibrium biological networks. Biophys J. 97(5):L11-3 (2009).
  • Mo, M.L., Palsson, B.O., Herrgard, M.J., Connecting extracellular metabolomic profiles to intracellular metabolic states in yeast. BMC Systems Biology. 3:37 (2009).
  • Mo, M.L. and Palsson, B.Ø. Understanding human metabolic physiology: A genome-to-systems approach, Trends in Biotechnology. 27(1):37-44 (2009).

Zhao-Bang Zeng

  • Li, L., Cook, R.D., and Nachtsheim, C.J. (2005). Model-free variable selection. Journal of the Royal Statistical Society, Series B. 67, 285-299.
  • Li, L., Cook, R.D., and Tsai, C.L. (2007). Partial inverse regression. Biometrika. 94, 615-625.
  • Li, L. (2007). Sparse sufficient dimension reduction. Biometrika. 94, 603-613.
  • Li, L., and Lu, W. (2008). Sufficient dimension reduction with missing predictors. Journal of the American Statistical Association. 103, 822-831.
  • Bondell, H.D., and Li, L. (2009). Shrinkage inverse regression estimation for model free variable selection. Journal of the Royal Statistical Society, Series B. 71, 287-299.
  • Li, L., and Li, H. (2004). Dimension reduction methods for microarrays with application to censored survival data. Bioinformatics. 20, 3406-3412.
  • Li, L. (2006). Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information. Bioinformatics. 22, 466-471.
  • Azari, R., Li, L., and Tsai, C.L. (2006). Longitudinal data model selection. Computational Statistics and Data Analysis. 50, 3053-3066.
  • Li, L., and Nachtsheim, C.J. (2006). Sparse sliced inverse regression. Technometrics. 48, 503-510.
  • Li, L., and Yin, X. (2008). Sliced inverse regression with regularizations. Biometrics. 64, 124-131.
  • Lu, W., and Li, L. (2008). Boosting methods for nonlinear transformation models with censored survival data. Biostatistics. 9, 658-677.
  • Setodji, C.M., and Li, L. (2009). Model free multivariate reduced-rank regression with categorical predictors. Statistica Sinica. 19, 1119-1136.
  • Li, L. (2009). Exploiting predictor domain information in sufficient dimension reduction. Computational Statistics and Data Analysis. 53, 2665-2672.
  • Li, L., and Yin, X. (2009). Longitudinal data analysis using sufficient dimension reduction method. Computational Statistics and Data Analysis. 53, 4106-4115.
  • Cook, R.D., and Li, L. (2009). Dimension reduction in regressions with exponential family predictors. Journal of Computational and Graphical Statistics. 18, 774-791.

Peter Karp

  • Karp, P.D., and Latendresse, M., An advanced web query interface for biological databases, Database 2010; doi: 10.1093/database/baq006. PMC Journal – In Process.
  • Karp, P.D., Paley, S.M., Krummenacker, M., Latendresse, M., Dale, J.M., Lee, T., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., Altman, T., Paulsen, I., Keseler, I.M., and Caspi, R., Pathway Tools version 13.0: Integrated software for Pathway/Genome informatics and systems biology, Briefings in Bioinformatics 2010 11:40-79. PMC Journal – In Process.
  • Caspi, R., Altman, T., Dale, J.M., Dreher, K., Fulcher, C.A., Gilham, F., Kaipa, P., Karthikeyan, A.S., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A., Paley, S., Popescu, L., Pujar, A., Shearer, A.G., Zhang, P., and Karp, P.D., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nuc. Acids Res. 36:D623-31, 2010. PMC2238876
  • Keseler, I.M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Aaron Johnson, D., Krummenacker, M., Nolan, L.M., Paley, S.M., Paulsen, I.T., Peralta-Gil, M., Santos-Zavaleta, A., Shearer, A.G., and Karp, P.D., EcoCyc: A comprehensive view of E. coli biology, Nuc. Acids Res. 37:D464-70, 2009. PMC2686493
  • Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M., Santos-Zavaleta, A., Peñaloza-Spínola, M.I., Bonavides-Martinez, C., and Ingraham, J., Multidimensional annotation of the Escherichia coli K-12 genome, Nuc. Acids Res. 35(22):7577-90, 2007. PMC2190727
  • Paley, S.M., and Karp, P.D., The Pathway Tools Cellular Overview Diagram and Omics Viewer, Nuc. Acids Res. 34:3771-8, 2006. PMC1557788
  • Lee, T.J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D.W.J., Tenenbaum, J.D., and Karp, P.D., BioWarehouse: A bioinformatics database warehouse toolkit, BMC Bioinformatics 7:170, 2006. HIGHLY ACCESSED. PMC1444936
  • Karp, P.D., Arnaud, M., Collado-Vides, J. Ingraham, J., Paulsen, I.T., and Saier, M.H. Jr., The E. coli EcoCyc database: No longer just a metabolic pathway database, ASM News 70(1):25-30, 2004.
  • Romero, P., Wagg, J., Green, M.L., Kaiser, D., Krummenacker, M., and Karp, P.D., Computational prediction of human metabolic pathways from the complete human genome, Genome Biology 6(1):R2.1-17, 2004. PMC549063
  • Karp, P.D., Paley, S., and Romero, P., The Pathway Tools software, Bioinformatics 18:S225-32, 2002.
  • Karp, P.D., Pathway databases: A case study in computational symbolic theories, Science 293:2040-4, 2001.
  • Romero, P.R., and Karp, P.D., Nutrient-related analysis of pathway/genome databases, in Proc. Pacific Symposium on Biocomputing, 2001.
  • Tomb, J.-F., … Karp, P.D., et al., The complete genome sequence of the gastric pathogen Helicobacter pylori, Nature 388:539-547, 1997.
  • Karp, P.D., Ouzounis, C., and Paley, S., HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae, in Proc. Fourth International Conference on Intelligent Systems in Molecular Biology, AAAI Press, pp116-124, 1996.
  • Karp, P.D., and Riley, M., Representaions of metabolic knowledge, in Proc. First International Conference on Intelligent Systems in Molecular Biology, Washington, D.C., AAAI Press, June 1993.

Oliver Fiehn

  • Taylor SL, Ganti S, Bukanov NO, Chapman AB, Fiehn O, Osier MV, Kim K, Weiss RH (2010) A metabolomics approach using juvenile cystic mice to identify urinary biomarkers and altered pathways in polycystic kidney disease. Am J Physiol Renal Physiol. [Epub ahead of print] PMID: 20130118
  • Kind T, Wohlgemuth G, Lee DY, Lu L, Palazoglu M, Shahbaz S, Fiehn O (2009) FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal. Chem. 81, 10038-48 PMID: 19928838
  • Hartman A, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen J (2009) Human gut microbiome adopts an alternative state following small bowel transplantation. Proc. Natl. Acad. Sci. USA 106, 17187-17192 PMID: 19805153
  • Denkert C, Budczies J, Weichert W, Wohlgemuth G, Scholz M, Kind T, Niesporek S, Noske A, Buckendahl A, Dietel M, Fiehn O (2008) Metabolic profiling of human colon carcinoma - Deregulation of TCA and amino acid turnover. Mol. Cancer 7: 72 PMID: 18799019
  • Taylor CF et al (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnol. 26, 889-896 PMID: 18688244
  • Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Moon S, Nikolau BJ (2008) Quality control for plant metabolomics: Reporting MSI-compliant studies. Plant J. 53, 691-704 PMID: 18269577
  • Fiehn O (2008) Extending the breadth of metabolite profiling by gas chromatography/mass spectrometry. TrAC - Trends Anal. Chem. 27, 261-269 PMID: 18497891
  • Kind T, Fiehn O (2007) Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8: 115 PMID: 17389044
  • Huster D, Purnat TD, Burkhead JL, Ralle M, Fiehn O, Stuckert F, Olson NE, Teupser D, Lutsenko S (2007) Higher copper selectively alters lipid metabolism and cell cycle machinery in the mouse model of Wilson disease. J. Biol. Chem. 282, 8343-8355 PMID: 17205981
  • Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N, Sumner LW, Goodacre R, Hardy NW, Taylor C, Fostel J, Kristal B, Kaddurah-Daouk R, Mendes P, van Ommen B, Lindon JC, Sansone S-A (2007) The Metabolomics Standards Initiative (MSI). Metabolomics 3, 175-178 PMID: 17687353
  • Scholz M, Fiehn O (2007) SetupX - A Public Study Design Database for Metabolomic Projects. Pacific Symp. Biocomp. 12, 169-180 PMID: 17990490
  • Kind T, Tolstikov VV, Fiehn O, Weiss RH (2007) A comprehensive urinary metabolomics approach for identifying kidney cancer. Anal. Biochem. 363, 185-195 PMID: 17316536
  • Denkert C, Budczies J, Kind T, Weichert W, Tablack P, Sehouli J, Niesporek S, Koensgen D, Dietel M, Fiehn O (2006) GC-TOF based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumors. Cancer Res. 66, 10795-10804 PMID: 17108116
  • Kind T, Fiehn O (2006) Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics 7:234 PMID: 16646969
  • Perroud B, Lee J, Valkova N, Dhirapong A, Lin P-Y, Fiehn O, Kueltz D, Weiss RH (2006) Pathway analysis of kidney cancer using proteomics and metabolic profiling. BMC Mol. Cancer 5:64 PMID: 17123452

Thomas Hankemeier

  • Castro-Perez JM, Kamphorst J, Degroot J, Lafeber F, Goshawk J, Yu K, Shockcor JP, Vreeken RJ, Hankemeier T. Comprehensive LC-MS(E) Lipidomic Analysis using a Shotgun Approach and Its Application to Biomarker Detection and Identification in Osteoarthritis Patients. J Proteome Res. 2010 Mar 31 (Epub ahead of print)
  • Koek MM, Bakel F, Engel W, van den Maagdenberg A, Ferrari MD, Coulier L, Hankemeier T. Metabolic Profiling of Ultrasmall Sample Volumes with GC/MS: From Microliter to Nanoliter Samples. Anal Chem. (2010) 82:156-62.
  • Wang J, Reijmers T, Chen L, Van Der Heijden R, Wang M, Peng, S, Hankemeier T, Xu G, Van Der Greef J., Systems toxicology study of doxorubicin on rats using ultra performance liquid chromatography coupled with mass spectrometry based metabolomics, Metabolomics, 5 (2009) 407-418.
  • Hu C, Van Dommelen J, Van der Heijden R, Spijksma G, Rejmers TH, Wang M, Xu G, Slee E, Lu X, Van der Greef J, Hankemeier T. RPLC-FTMS Method for Lipid Profiling of Plasma: Method Validation and Application to p53 mutant Mouse Model. J Proteom. Research (2008) 7: 4982 -4991
  • Van der Werf MJ, Overkamp KM, Muilwijk B, Koek MM, van der Werff-van der Vat BJ, Jellema RH, Coulier L, Hankemeier T, Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources, Mol Biosyst. 2008 Apr;4(4):315-27.
  • Koek M, Muilwijk B, Van Stee LLP, Hankemeier T. Higher mass loadability in GC×GC–MS: improved analytical performance for metabolomics analysis, J Chromatogr A. (2008) 1186:420-9.
  • Kamphorst JJ, Heijden RV, Degroot J, Lafeber FP, Reijmers TH, El BV, Tjaden UR, Greef JV, Hankemeier T, Profiling of Endogenous Peptides in Human Synovial Fluid by NanoLC-MS: Method Validation and Peptide Identification, J Proteome Res. (2007) 6:4388-4396
  • Van der Werf M, Muilwijk B, Overkamp KM, Coulier L, Hankemeier T. Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem. (2007) 370:17-25.
  • Benavente F, Van der Heijden R, Tjaden UR, Van der Greef J, Hankemeier T, Metabolite profiling of human urine by capillary electrophoresis electrospray mass spectrometry using separation electrolytes at low pH, Electrophoresis (2006) 27 (22): 4570-4584
  • Koek M, Muilwijk B, van der Werf M, Hankemeier T. Microbial metabolomics with gas chromatography mass spectrometry. Anal Chem. (2006) 78(4):1272-81.

Wayne Matson

  • Matson, W. R.; Langlais, P.; Volicer, L.; Gamache, P. H.; Bird, E.; Mark, K. A. "n-Electrode three-dimensional liquid chromatography with electrochemical detection for determination of neurotransmitters"Clin Chem 1984, 30, 1477-1488.
  • Volicer, L.; Langlais, P. J.; Matson, W. R.; Mark, K. A.; Gamache, P. H. "Serotoninergic system in dementia of the Alzheimer type. Abnormal forms of 5-hydroxytryptophan and serotonin in cerebrospinal fluid"Arch Neurol 1985, 42, 1158-1161.
  • Matson, W. R.; Gamache, P. G.; Beal, M. F.; Bird, E. D. "EC array sensor concepts and data"Life Sci 1987, 41, 905-908.
  • Beal, M. F.; Matson, W. R.; Swartz, K. J.; Gamache, P. H.; Bird, E. D. "Kynurenine pathway measurements in Huntington's disease striatum: evidence for reduced formation of kynurenic acid"J Neurochem 1990, 55, 1327-1339.
  • Godefroy, F.; Matson, W. R.; Gamache, P. H.; Weil-Fugazza, J. "Simultaneous measurements of tryptophan and its metabolites, kynurenine and serotonin, in the superficial layers of the spinal dorsal horn. A study in normal and arthritic rats"Brain Res 1990, 526, 169-172.
  • Swartz, K. J.; Matson, W. R.; MacGarvey, U.; Ryan, E. A.; Beal, M. F. "Measurement of kynurenic acid in mammalian brain extracts and cerebrospinal fluid by high-performance liquid chromatography with fluorometric and coulometric electrode array detection"Anal Biochem 1990, 185, 363-376.
  • Uemura, Y.; Miller, J. M.; Matson, W. R.; Beal, M. F. "Neurochemical analysis of focal ischemia in rats"Stroke 1991, 22, 1548-1553.
  • Beal, M. F.; Matson, W. R.; Storey, E.; Milbury, P.; Ryan, E. A.; Ogawa, T.; Bird, E. D. "Kynurenic acid concentrations are reduced in Huntington's disease cerebral cortex"J Neurol Sci 1992, 108, 80-87.
  • LeWitt, P. A.; Galloway, M. P.; Matson, W.; Milbury, P.; McDermott, M.; Srivastava, D. K.; Oakes, D. "Markers of dopamine metabolism in Parkinson's disease. The Parkinson Study Group"Neurology 1992, 42, 2111-2117.
  • Ogawa, T.; Matson, W. R.; Beal, M. F.; Myers, R. H.; Bird, E. D.; Milbury, P.; Saso, S. "Kynurenine pathway abnormalities in Parkinson's disease"Neurology 1992, 42, 1702-1706.
  • Kristal, B. S.; Vigneau-Callahan, K. E.; Matson, W. R. "Simultaneous analysis of the majority of low-molecular-weight, redox-active compounds from mitochondria"Anal Biochem 1998, 263, 18-25.
  • Milbury, P. E.; Vaughan, M. R.; Farley, S.; Matula, G. J., Jr.; Convertino, V. A.; Matson, W. R. "A comparative bear model for immobility-induced osteopenia"Ursus 1998, 10, 507-520.
  • Bogdanov, M. B.; Beal, M. F.; McCabe, D. R.; Griffin, R. M.; Matson, W. R. "A carbon column-based liquid chromatography electrochemical approach to routine 8-hydroxy-2'-deoxyguanosine measurements in urine and other biologic matrices: a one-year evaluation of methods"Free Radic Biol Med 1999, 27, 647-666.
  • Kristal, B. S.; Vigneau-Callahan, K. E.; Moskowitz, A. J.; Matson, W. R. "Purine catabolism: links to mitochondrial respiration and antioxidant defenses?"Arch Biochem Biophys 1999, 370, 22-33.
  • Bogdanov, M.; Brown, R. H.; Matson, W.; Smart, R.; Hayden, D.; O'Donnell, H.; Flint Beal, M.; Cudkowicz, M. "Increased oxidative damage to DNA in ALS patients"Free Radic Biol Med 2000, 29, 652-658.

Xianlin Han

  • Han, X. and Gross, R. W. (2003) Global analyses of cellular lipidomes directly from crude extracts of biological samples by electrospray ionization mass spectrometry: A bridge to lipidomics. J. Lipid Res. 44, 1071-1079.
  • Han, X. and Gross, R.W. (2005) Shotgun lipidomics: Electrospray ionization mass spectrometric analysis and quantitation of the cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom. Rev. 24, 367-412.
  • Cheng, H., Jiang, X. and Han, X. (2007) Alterations in lipid homeostasis of mouse dorsal root gan-glia induced by apolipoprotein E deficiency: A shotgun lipidomics study. J. Neurochem. 101, 57-76.
  • Yang, K., Cheng, H., Gross, R.W., and Han, X. (2009) Automated lipid identification and quantification by multidimensional mass spectrometry-based shotgun lipidomics. Anal. Chem. 81, 4356-4368.
  • Han, X. (2010) Multi-dimensional mass spectrometry-based shotgun lipidomics and the altered lipids at the mild cognitive impairment stage of Alzheimer's disease. BBA-Mol. Cell Biol. Lipids doi:10.1016/j.bbalip.2010.01.010.
  • Han, X., Fagan, A.M., Morris, J. C., Xiong, C., and Holtzman, D.M. (2003) CSF sulfatide is de-creased in individuals with mild cognitive impairment/very mild dementia. Ann. Neurol. 54, 115-119.
  • Pike, L.J., Han, X., and Gross, R.W. (2005) EGF receptors are localized to lipid rafts that contain a balance of inner and outer leaflet lipids: A shotgun lipidomics study. J. Biol. Chem. 280, 26796-26804.
  • Han, X. and Gross, R.W. (2005) Shotgun lipidomics: multi-dimensional mass spectrometric analysis of cellular lipidomes. Expert Rev. Proteomics 2, 253-264.
  • Han, X., Yang, K., Yang, J., Cheng, H., and Gross, R.W. (2006) Shotgun lipidomics of cardiolipin molecular species in lipid extracts of biological samples. J. Lipid Res. 47, 864-879.
  • Jiang, X., Cheng, H., Yang, K., Gross, R.W. and Han, X. (2007) Alkaline methanolysis of lipid extracts extends shotgun lipidomics analyses to the low abundance regime of cellular sphingolipids. Anal. Biochem. 371, 135-145.
  • Han, X., Yang, J., Yang, K., Zhao, Z., Abendschein, D.R., and Gross, R.W. (2007) Alterations in myocardial cardiolipin content and composition occur at the very earliest stages of diabetes: A shotgun lipidomics study. Biochemistry 46, 6417-6428.
  • Han, X. (2007) Neurolipidomics: challenges and developments. Front. Biosci. 12, 2601-2615.
  • Cheng, H., Mancuso, D.J., Jiang, X., Guan, S., Yang, J., Yang, K., Sun, G., Gross, R.W. and Han, X. (2008) Shotgun lipidomics reveals the temporally dependent, highly diversified cardiolipin profile in the mammalian brain: Coordinated postnatal diversification of cardiolipin molecular species with neuronal remodeling Biochemistry 47, 5869-5880.
  • Yang, K., Zhao, Z, Gross, R.W., and Han, X. (2009) Systematic analysis of choline-containing phospholipids using multi-dimensional mass spectrometry-based shotgun lipidomics. J. Chromatogr. B, 877, 2924–2936.
  • Cheng, H., Sun, G., Yang, K., Gross, R.W., and Han, X. (2010) Selective desorption/ionization of sulfatides by MALDI-MS facilitated using 9-aminoacridine as matrix. J. Lipid Res. doi:10.1194/jlr.D004077.

Dan Raftery

  • H. Chen, Z. Pan, N. Talaty, D. Raftery, and R. G. Cooks, “Combining Desorption Electrospray Ionization Mass Spectrometry and Nuclear Magnetic Resonance for Differential Metabolomics without Sample Preparation,” Rapid Comm. Mass Spec. 20, 1577-1584 (2006).
  • Z. Pan, H. Gu, N. Talaty, H. Chen, B. E. Hainline, R. G. Cooks and D. Raftery, “Principal Component Analysis of Urine Metabolites Detected by NMR and DESI-MS in Patients with Inborn Errors of Metabolism,” Anal. Bioanal. Chem. 387, 539-549 (2007).
  • N. Shanaiah, A. Desilva, G. A. N. Gowda, M. A. Raftery, B. E. Hainline, and D. Raftery, “Class Selection of Amino Acid Metabolites in Body Fluids Using Chemical Derivatization and Their 13C NMR Detection,” Proc. Natl. Acad. Sci. 104, 11540-11544 (2007). PMCID: PMC1913896
  • S. Zhang, G. A. N. Gowda, V. Asiago, N. Shanaiah, C. Barbas, and D. Raftery, “Correlative and quantitative 1H NMR-based metabolomics reveals specific metabolic pathway disturbances in diabetic rats,” Anal. Biochem. 383, 76-84 (2008).
  • G. A. N. Gowda, S. Zhang, H. Gu, V. Asiago, N. Shanaiah and D. Raftery, "Metabolomics-Based Methods for Early Disease Diagnostics: A Review," Expert Rev. Mol. Diagnost. 8, 617-633 (2008).
  • T. Ye, H. Mo, N. Shanaiah, G. A. N. Gowda, S. Zhang, D. Raftery, “Chemoselective 15N Tag for Sensitive and High-Resolution Nuclear Magnetic Resonance Profiling of the Carboxyl-Containing Metabolome,” Anal. Chem. 81, 4882-4888 (2009). PMCID: PMC2861042
  • E. E. Appiah-Amponsah, N. Shanaiah, G. A. Nagana Gowda, K. Owusu-Sarfo, T. Ye and D. Raftery, "Identification of 4-deoxythreonic acid present in human urine using HPLC and NMR techniques," J. Pharm. Biomed. Anal. 50, 878-885 (2009). PMCID: PMC2861046
  • D. Djukovic, S. Liu, I. Henry, B. Tobias, and D. Raftery “Signal Enhancement in HPLC/Microcoil NMR Using Automated Column Trapping,” Anal. Chem. 78, 7154-7160 (2006). PMCID: PMC2577147
  • H. Gu, H. Chen, Z. Pan, A. U. Jackson, N. Talaty, B. Xi, C. Kissinger, C. Duda, D. Mann, D. Raftery, and R. G. Cooks, “Monitoring Diet Effects from Biofluids and Their Implications for Metabolomics Studies,” Anal. Chem., 79, 89-97 (2007).
  • H. Mo and D. Raftery, “Solvent Signal as an NMR Concentration Reference,” Anal. Chem. 80, 9835-9839 (2008).
  • G. A. Nagana Gowda, N. Shanaiah, A. Cooper, M. Maluccio, and D. Raftery, “Visualization of Bile Homeostasis using 1H NMR Spectroscopy as a Route for Assessing Liver Cancer,” Lipids 44, 27-35 (2009).
  • G. A. Nagana Gowda, N. Shanaiah, A. Cooper, M. Maluccio, D. Raftery, “Bile Acids Conjugation in Human Bile is not Random: New Insights from 1H NMR Spectroscopy at 800 MHz,” Lipids 44, 527-535 (2009).
  • H. Gu, Z. Pan, B. Xi, B. E. Hainline, N. Shanaiah, V. Asiago, G. A. Nagana Gowda, D. Raftery, “1H NMR Metabolomics Study of Age Profiling in Children,” NMR Biomed. 22, 826-833 (2009).
  • R. Kc, I. D. Henry, G. H. J. Park, D. Raftery, “Design and Construction of a Versatile Dual Volume Heteronuclear Double Resonance Microcoil NMR Probe,” J. Magn. Reson. 197, 186-192 (2009). PMCID: PMC2679250
  • S. Zhang, C. Zheng, I. R. Lanza, K. Streekumaran Nair, D. Raftery, O. Vitek, “Interdependence of Signal Processing and Analysis of Urine 1H NMR Spectra for Metabolic Profiling,” Anal. Chem. 81, 6080-6088 (2009).

David Millington

  • D.S. Millington, N. Kodo, D.L. Norwood, C.R. Roe, Tandem Mass Spectrometry: A New Method for Acylcarnitine Profiling with Potential for Neonatal Screening for Inborn Errors of Metabolism. J. Inher. Metab. Dis. 13:321-324, 1990. PMID: 2122093
  • R.D. Stevens, S. Hillman, L.S. Worthy, D. Sanders and D.S. Millington. Assay for Free and Total Carnitine in Human Plasma using Tandem Mass Spectrometry. Clin. Chem. 46:727-729 (2000). PMID: 10794762
  • D.S. Millington. Tandem Mass Spectrometry in Clinical Diagnosis. In: Physician’s Guide to the Laboratory Diagnosis of Metabolic Diseases, 2nd Edition. N. Blau, M. Duran, M.E. Blaskovics and M. Gibson (eds) Springer (Berlin) Chapter E, pp 57-75 (2003).
  • S.P. Young, R.D. Stevens, Y. An, Y.T. Chen and D.S. Millington. Analysis of a glucose tetrasaccharide elevated in Pompe disease by stable isotope dilution-electrospray ionization tandem mass spectrometry. Analyt. Biochem. 316:175-180 (2003). PMID: 12711338
  • D.D. Koeberl, S.P. Young, N. Gregersen, J. Vockley, W.E. Smith, D.K. Benjamin, Jr., Y. An, S.D. Weavil, S.H. Chaing, D. Bali, M.T. McDonald, P.S. Kishnani, Y.T. Chen and D.S. Millington. Rare disorders of metabolism with elevated butyryl and isobutyryl carnitine detected by tandem mass spectrometry newborn screening. Ped. Res. 54:219-223 (2003). PMID: 12736383
  • D.S. Millington and D.D. Koeberl. Metabolic Screening in the Newborn. Growth, Genetics & Hormones, 3:33-38 (2003). PMID: 14568186
  • J.-Y. Wu, H.-J. Kao, S.-C. Li, R.D. Stevens, S.L. Hillman, D.S. Millington and Y.T. Chen. ENU mutagenesis identifies mice with mitochondrial branched-chain aminotransferase deficiency resembling human maple syrup urine disease. J. Clin. Invest. 113:434-440 (2004). PMID: 17116638
  • J. An, D.M. Muio, M. Shiota, Y. Fujimoto, G.W. Cline, G.I. Shulman, T.R. Koves, R.D. Stevens, D.S. Millington and C. Newgard. Hepatic Expression of Malonyl-coA Dehydrogenase Reverses Muscle, Liver and Whole-Animal Insulin Resistance. Nature Medicine, 10:268-274, 2004. PMID: 14770177
  • D.S. Millington. Newborn Screening for Lysosomal Storage Disorders (Editorial). Clin. Chem. 51: 808-9, 2005. PMID: 15855665
  • S.P. Young, Y. An, P.S. Kishnani, D.S. Millington, A. Amalfitano, D. Corzo, Y.T. Chen. Glucose Tetrasaccharide as a Biomarker for Monitoring the Therapeutic Response to Enzyme Replacement Therapy for Pompe Disease. Mol. Genet. Metab. 85:247-254, 2005. PMID: 15886040
  • D.S. Millington. Metabolite Profiling in Urine and Blood for the Diagnosis of Metabolic Disorders. In: Encyclopedia of Mass Spectrometry Volume 3, Chapter 48. M.L. Gross, R. Caprioli (eds) Elsevier, New York, NY (2005).
  • D. M. Frazier, D. S. Millington, S. E. McCandless, D. D. Koeberl, S. D. Weavil, S. H. Chaing and J. Muenzer. The tandem mass spectrometry newborn screening experience in North Carolina: 1997–2005. J. Inherit. Metab. Dis. 29:76-85, 2006. PMID: 16601872
  • C.B. Newgard, J.An, J.R. Bain, M.J. Muehlbauer, R.D. Stevens, L.F. Lien, A.M. Haqq, S.H. Shah, M. Arlotto, C.A. Slentz, J. Rochon, D. Gallup, O. Ilkayeva, B.R. Wenner, W.S. Yancey Jr, H.Eisenson, G.Musante, R.Surwit, D.S. Millington, M.D. Butler, L.P. Svetkey. A branched-chain amino acid-related metabolic signature that differentiates obese and lean humans and contributes to insulin resistance. Cell Metabolism 9:311-326, 2009. PMID 19356713
  • H. Zhang, D. Il'yasova, J. Sztaray, S.P. Young, F. Wang and D.S. Millington. Quantification of the Oxidative Damage Biomarker 2,3-Dinor-8-Isoprostaglandin-F2a in Human Urine Using Liquid Chromatography-Tandem Mass Spectrometry. Analyt Biochem 399:302-304, 2010. PMCID 2853187.
  • D.S. Millington, R. Sista, A. Eckhardt, J. Rouse, D. Bali, R. Goldberg, M.Cotten, R. Buckley and V. Pamula. Digital Microfluidics: a Future Technology in the Newborn Screening Laboratory? Semin Perinatol 34:163-169, 2010. PMCID 2866525.

Teresa Fan

  • Fan, T. W-M., Yuan, P., Lane, A. N., Higashi, R. M., Wang, Y., Hamidi, A., Zhou, R., Guitart, X., Chen, G., Manji, H. K., and Rima Kaddurah-Daouk (in press, 2009) Stable Isotope-Resolved Metabolomic Analysis of Lithium Effects on Glial-Neuronal Metabolism and Interactions. Metabolomics.
  • Fan, T.W-M., Lane, A.N., Higashi, R.M., Farag, M.A., Gao, H., Bousamra, M., and Miller, D.M. (2009) Altered regulation of metabolic pathways in human lung cancer discerned by 13C stable isotope-resolved metabolomics (SIRM). Mol Cancer 8, 41.
  • Metabolic profiling identifies lung tumor responsiveness to erlotinib. Exp Mol Pathol 87, 83-86.
  • Fan, T. W-M., Bandura, L.L., Lane, A.N. & Higashi, R.M. (2005) “Metabolomics-Edited Transcriptomics Analysis of Se Anticancer Action in human lung cancer cells”. Metabolomics J. 1, 325-339
  • Lane, A. N., Fan, T. W.-M., Higashi, R. M., Tan, J., Bousamra, M. and Miller, D. M. (2009) Prospects for clinical cancer metabolomics using stable isotope tracers. Exp. Mol. Pathol. 86, 165-173 (invited review).
  • Fan T.W-M., R.M. Higashi, A.N. Lane, and O. Jardetzky.(1986) "Combined Use of 1H NMR and GC/MS for Metabolite Monitoring and In Vivo 1H NMR Assignments", Biochim. Biophysica Acta 882:154-67.
  • T.W.-M. Fan, T.D. Colmer, A.N. Lane, and R.M. Higashi. (1993). "Determination of Metabolites by 1H NMR and GC: Analysis for Organic Osmolytes in Crude Tissue Extracts", Anal. Biochemistry, 214, 260-271
  • Fan, T. W-M., Lane, A.N. & Higashi, R.M. (2004) “The Promise of Metabolomics in Cancer Molecular Therapeutics”. Current Opin. Molec. Ther. 6:584-592 (invited review)
  • Teresa W.-M. Fan, Richard M. Higashi, and Andrew N. Lane (2006) “Integrating Metabolomics and Transcriptomics for Probing Se Anticancer Mechanisms”. Drug Metabolism Review 38(4), 707-732 (invited review).
  • Lane, A. N. and Fan, T. W.-M., (2007) “Quantification and identification of isotopomer distributions of metabolites in crude cell extracts using 1H TOCSY”, Metabolomics 3, 79-86
  • Sansone, S., Nikolau, B., van Ommen, B., Kristal, B., Taylor, C., Robertson, D., Lindon, J., Griffin, J., Sumner, L., van der Werf, M., Hardy, N., Morrison, N., Mendes, P., Kaddurah-Daouk, R., Goodacre, R., Fan, T., and Fiehn, O.,(2007) “The Metabolomics Standards Initiative (MSI)”, Nature Biotech., 25 (8): 844-848
  • Lane, A.N., T.W.-M. Fan, and R.M. Higashi (2008). “Isotopomer-based metabolomic analysis by NMR and mass spectrometry”. Methods in Cell Biology, Vol 84. Biophysical Tools for Biologists, Volume 1, edited by Drs. John J. Correia and H. William Detrich. Elsevier Science & Technology Books Ch. 18. pp 541-588.
  • Fan, T.W.M. and Lane, A.N. (2008) “Structure-based profiling of Metabolites and Isotopomers by NMR”, Progress in NMR Spectroscopy. 52, 69-117 (invited review).
  • Fan, T., Kucia, M., Jankowski, K., Higashi, R., Ratajczak, J., Ratajczak, M. and Lane, A. Rhabdomyosarcoma cells show an energy producing anabolic metabolic phenotype compared with primary myocytes. Mol. Cancer. 7, 79 (2008).
  • Lane, A. N., Fan, T. W. M., Xie, Z., Moseley, H. N. B. and Higashi, R. M. (2009) Isotopomer analysis of lipid biosynthesis by high resolution mass spectrometry and NMR. Analytica Chimica Acta. 651, 201-208.

Andrew Lane

  • Fan, T.W., Lane, A.N., Higashi, R.M., Farag, M.A., Gao, H., Bousamra, M., and Miller, D.M. (2009). Altered regulation of metabolic pathways in human lung cancer discerned by 13C stable isotope-resolved metabolomics (SIRM). Mol Cancer 8, 41.
  • Fan, T.W., Lane, A.N., Higashi, R.M., Bousamra, M., 2nd, Kloecker, G., and Miller, D.M. (2009). Metabolic Profiling identifies lung tumor responsiveness to erlotinib. Exp Mol Pathol 87, 83-86.
  • Fan, T. W-M., Bandura, L.L., Lane, A.N. & Higashi, R.M. (2005) “Metabolomics-Edited Transcriptomics Analysis of Se Anticancer Action in human lung cancer cells”. Metabolomics J. 1, 325-339
  • Fan, T., Kucia, M., Jankowski, K., Higashi, R., Ratajczak, J., Ratajczak, M. and Lane, A. Rhabdomyosarcoma cells show an energy producing anabolic metabolic phenotype compared with primary myocytes. Mol. Cancer. 7, 79 (2008).
  • Lane, A. N., Fan, T. W.-M., Higashi, R. M., Tan, J., Bousamra, M. and Miller, D. M. (2009) Prospects for clinical cancer metabolomics using stable isotope tracers. Exp. Mol. Pathol. 86, 165-173 (invited review).
  • Fan T.W-M., R.M. Higashi, A.N. Lane, and O. Jardetzky.(1986) "Combined Use of 1H NMR and GC/MS for Metabolite Monitoring and In Vivo 1H NMR Assignments", Biochim. Biophysica Acta 882:154-67.
  • T.W.-M. Fan, T.D. Colmer, A.N. Lane, and R.M. Higashi. (1993). "Determination of Metabolites by 1H NMR and GC: Analysis for Organic Osmolytes in Crude Tissue Extracts", Anal. Biochemistry, 214, 260-271
  • T. W.-M. Fan, R.M. Higashi, and A.N. Lane, "Effects of Temperature on In Vivo Unidirectional Rates of ATP Turnover in Tail Muscle of Intact Ridgeback Prawn (Sycionia ingentis) as Measured by 31P NMR Saturation Transfer", Biochimica et Biophysica Acta 1135, 44-49 (1992).
  • Larsen, E. H., Hansen, M., Fan, T., Vahl, M., J. (2001) “Speciation of selenoamino acids, selenonium ions and inorganic selenium by ion exchange HPLC with mass spectrometric detection and its application to yeast and algae”, Anal. At. Spectrom., 16(12), 1403-1408
  • T.W.-M. Fan, T.D. Colmer, A.N. Lane, and R.M. Higashi. (1993). "Determination of Metabolites by 1H NMR and GC: Analysis for Organic Osmolytes in Crude Tissue Extracts", Anal. Biochemistry, 214, 260-271
  • Fan, T. W-M., Lane, A.N. & Higashi, R.M. (2004) “The Promise of Metabolomics in Cancer Molecular Therapeutics”. Current Opin. Molec. Ther. 6:584-592 (invited review)
  • Teresa W.-M. Fan, Richard M. Higashi, and Andrew N. Lane (2006) “Integrating Metabolomics and Transcriptomics for Probing Se Anticancer Mechanisms”. Drug Metabolism Review 38(4), 707-732 (invited review).
  • Lane, A.N., T.W.-M. Fan, and R.M. Higashi (2008). “Isotopomer-based metabolomic analysis by NMR and mass spectrometry”. Methods in Cell Biology, Vol 84. Biophysical Tools for Biologists, Volume 1, edited by Drs. John J. Correia and H. William Detrich. Elsevier Science & Technology Books Ch. 18. pp 541-588.
  • Lane A., N., Fan, T. W.-M. and Higashi, R. M. (2009) Metabolic acidosis and the importance of balanced equations. Metabolomics. 5, 163-165.
  • Lane, A. N., Fan, T. W. M., Xie, Z., Moseley, H. N. B. and Higashi, R. M. (2009) Isotopomer analysis of lipid biosynthesis by high resolution mass spectrometry and NMR. Analytica Chimica Acta. 651, 201-208.

Richard Higashi

  • Fan, T.W., Lane, A.N., Higashi, R.M., Farag, M.A., Gao, H., Bousamra, M., and Miller, D.M. (2009). Altered regulation of metabolic pathways in human lung cancer discerned by 13C stable isotope-resolved metabolomics (SIRM). Mol Cancer 8, 41.
  • Fan, T.W., Lane, A.N., Higashi, R.M., Bousamra, M., 2nd, Kloecker, G., and Miller, D.M. (2009). Metabolic Profiling identifies lung tumor responsiveness to erlotinib. Exp Mol Pathol 87, 83-86.
  • Fan, T. W-M., Bandura, L.L., Lane, A.N. & Higashi, R.M. (2005) “Metabolomics-Edited Transcriptomics Analysis of Se Anticancer Action in human lung cancer cells”. Metabolomics J. 1, 325-339
  • Fan, T., Kucia, M., Jankowski, K., Higashi, R., Ratajczak, J., Ratajczak, M. and Lane, A. Rhabdomyosarcoma cells show an energy producing anabolic metabolic phenotype compared with primary myocytes. Mol. Cancer. 7, 79 (2008).
  • Lane, A. N., Fan, T. W.-M., Higashi, R. M., Tan, J., Bousamra, M. and Miller, D. M. (2009) Prospects for clinical cancer metabolomics using stable isotope tracers. Exp. Mol. Pathol. 86, 165-173 (invited review).
  • Fan T.W-M., R.M. Higashi, A.N. Lane, and O. Jardetzky.(1986) "Combined Use of 1H NMR and GC/MS for Metabolite Monitoring and In Vivo 1H NMR Assignments", Biochim. Biophysica Acta 882:154-67.
  • T.W.-M. Fan, T.D. Colmer, A.N. Lane, and R.M. Higashi. (1993). "Determination of Metabolites by 1H NMR and GC: Analysis for Organic Osmolytes in Crude Tissue Extracts", Anal. Biochemistry, 214, 260-271
  • T. W.-M. Fan, R.M. Higashi, and A.N. Lane, "Effects of Temperature on In Vivo Unidirectional Rates of ATP Turnover in Tail Muscle of Intact Ridgeback Prawn (Sycionia ingentis) as Measured by 31P NMR Saturation Transfer", Biochimica et Biophysica Acta 1135, 44-49 (1992).
  • Larsen, E. H., Hansen, M., Fan, T., Vahl, M., J. (2001) “Speciation of selenoamino acids, selenonium ions and inorganic selenium by ion exchange HPLC with mass spectrometric detection and its application to yeast and algae”, Anal. At. Spectrom., 16(12), 1403-1408
  • T.W.-M. Fan, T.D. Colmer, A.N. Lane, and R.M. Higashi. (1993). "Determination of Metabolites by 1H NMR and GC: Analysis for Organic Osmolytes in Crude Tissue Extracts", Anal. Biochemistry, 214, 260-271
  • Fan, T. W-M., Lane, A.N. & Higashi, R.M. (2004) “The Promise of Metabolomics in Cancer Molecular Therapeutics”. Current Opin. Molec. Ther. 6:584-592 (invited review)
  • Teresa W.-M. Fan, Richard M. Higashi, and Andrew N. Lane (2006) “Integrating Metabolomics and Transcriptomics for Probing Se Anticancer Mechanisms”. Drug Metabolism Review 38(4), 707-732 (invited review).
  • Lane, A.N., T.W.-M. Fan, and R.M. Higashi (2008). “Isotopomer-based metabolomic analysis by NMR and mass spectrometry”. Methods in Cell Biology, Vol 84. Biophysical Tools for Biologists, Volume 1, edited by Drs. John J. Correia and H. William Detrich. Elsevier Science & Technology Books Ch. 18. pp 541-588.
  • Lane A., N., Fan, T. W.-M. and Higashi, R. M. (2009) Metabolic acidosis and the importance of balanced equations. Metabolomics. 5, 163-165.
  • Lane, A. N., Fan, T. W. M., Xie, Z., Moseley, H. N. B. and Higashi, R. M. (2009) Isotopomer analysis of lipid biosynthesis by high resolution mass spectrometry and NMR. Analytica Chimica Acta. 651, 201-208.

Hunter Moseley

  • Moseley, H.N.B.; Riaz, N.; Aramini, J.M.; and Montelione, G.T. Journal of Magnetic Resonance 2004, 170: 263-277. A generalized approach to automated NMR peak list editing: Application to reduced dimensionality triple resonance spectra. Citations: 24. PMID: 15388090
  • Huang, Y.J.; Moseley, H.N.B.; Baran, M.C.; Arrowsmith, C.; Powers, R.; Tejero, R.; Szyperski, T.; and Montelione, G.T. Methods in Enzymology 2005, 394: 111-141. An integrated platform for automated analysis of protein NMR structures. Citations: 28. PMID: 15808219
  • Baran, M.; Moseley, H.N.B.; Aramini, J.A.; Bayro, M.J.; Monleon, D.; Lau, J.; and Montelione, G.T. Proteins: Structure Function Bioinformatics 2006, 62: 843-851. SPINS: A Laboratory Information Management System for Organizing and Archiving Intermediate and Final Results from NMR Protein Structure Determinations. Citations: 2. PMID: 16395675
  • Andrew N. Lane, Teresa W-M. Fan, Zhengzhi Xie, Hunter N.B. Moseley, and Richard M. Higashi. Anal. Chim. Acta. 2009, 651:201-208. Stable isotope analysis of lipid biosynthesis by high resolution mass spectrometry and NMR. PMID: 19782812
  • Moseley, H.N.B. BMC Bioinformatics 2010, 11:139-144. Correcting for the Effects of Natural Abundance in Stable Isotope Resolved Metabolomics Experiments Involving Ultra-High Resolution Mass Spectrometry. PMID: 20236542
  • Jackson, P.L.; Moseley, H.N.B.; and Krishna, N.R. Journal of Magnetic Resonance B 1995, 107: 289. Relative effects of protein-mediated and ligand-mediated spin diffusion pathways on transferred NOESY, and implications on the accuracy of the bound ligand conformation. Citations: 22 (ISI). PMID: 7788101
  • Moseley, H.N.B.; Curto, E.V.; and Krishna, N.R. Journal of Magnetic Resonance B 1995, 108: 243. Complete relaxation and conformational exchange matrix (CORCEMA) analysis of NOESY spectra of interacting systems: Two-dimensional transferred NOESY. Citations: 60. PMID: 7670757
  • Moseley, H.N.B.; Lee, W.; Arrowsmith, C. H.; and Krishna, N. R. Biochemistry 1997, 36: 5293. Quantitative determination of conformational, dynamic, and kinetic parameters of a ligand-protein/DNA complex from CORCEMA analysis of intermolecular transferred NOESY. Citations: 14 (Google Scholar). PMID: 9154911
  • Moseley, H.N.B. and Montelione, G.T. Current Opinion in Structural Biology 1999, 9: 635. Automated analysis of NMR assignments and structures for proteins. Citations: 136. PMID: 10508776
  • Moseley, H.N.B.; Monleon, D.; and Montelione, G.T. Methods in Enzymology 2001, 339: 91. Automatic determination of protein backbone resonance assignments from triple-resonance NMR data. Citations: 75. PMID: 11462827
  • Szyperski, T.; Yeh, D.C.; Sukumaran, D.K.; Moseley; H.N.B; and Montelione, G.T. Proceedings of the National Academy of Sciences USA 2002, 99: 8009-8014. Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Citations: 95. PMID: 12060747.
  • Zheng, D.; Huang, Y.J.; Moseley, H.N.B.; Xiao, R.; Aramini, J.; Swapna, G.V.T.; and Montelione, G.T. Protein Science 2003 12: 1232-1246. Rapid and automated protein fold determination using a minimal NOE and residual dipolar coupling constraint strategy. Citations: 32 (Google Scholar). PMID: 12761394
  • Moseley, H.N.B.; Sahota, G.; and Montelione, G.T. Journal of Biomolecular NMR 2004, 28:341-355. Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. Citations: 31. PMID: 14872126
  • Baran, M.C.; Huang, Y.J.; Moseley, H.N.; and Montelione, G.T. Chemical Reviews 2004, 104: 3541-3555. Automated analysis of protein NMR assignments and structures. Citations: 34 (Google Scholar). PMID: 15303826
  • Kornhaber, G.J.; Snyder, D.; Moseley, H.N.B.; and Montelione, G.T. Journal of Biomolecular NMR 2006, 34:259-269. Identification of Zinc-Ligated Cysteine Residues Based on 13Ca and 13Cb Chemical Shift Data. Citations: 15 (Google Scholar). PMID: 16645816

David Mrazek

  • Geda YE, Knopman DS, Mrazek DA, Edland SD, Jicha GA, Smith GE, Negash S, Boeve BF, Ivnik RJ, Petersen RC, Rocca WA. (2006), Depression, APOE Genotype and the Incidence of Mild Cognitive Impairment: A Prospective Cohort Study. Arch of Neurology, 63(3):435-44.
  • Mrazek DA (2006), Psychiatric Pharmacogenomics. Focus IV (3): 1-5.
  • Black JL, O’Kane DJ, Mrazek DA (2007), The impact of CYP allelic variation on antidepressant metabolism: a review. Expert Opin. Drug Metab.Toxicol.3(1): 21-31.
  • McAlpine DE, O’Kane DJ, Black JL, Mrazek DA (2007), Cytochrome P450 2D6 Genotype Variation and Venlafaxine Dosage. Mayo Clinic Proceedings 82(9):1065-1068.
  • Mrazek MD, Koenig BA, Skime M, Snyder, K, Hook CC Black, JL, Mrazek DA (2007) Assessing attitudes about genetic testing as a component of continuing medical education. Academic Psychiatry, 31(6):447-451.
  • Mrazek DA, O’Kane DJ, Black, JL, Drews MS, Courson VL, Biernacka JM, Snyder KA, Rush AJ, Weinshilboum RM. (2008) An association of cytochrome P450 2C19 genotype and remission in patients treated with citalopram. Biol. Psych. 63:251.
  • Karpyak VM, Kim JH, Biernacka JM, Wieben ED, Mrazek DA, Black JL, Choi DS. (2008) Sequence variations in the human MPDZ gene in Caucasian alcoholic population. Biol. Psych. 63:525.
  • Mohney BG, Mckenzie JA, Capo JA, Nusz KJ, Mrazek D, Diehl NN. (2008) Mental illness in young adults who had strabismus as children. Pediatrics 2008;122:1033-1038.
  • Mrazek DA, Rush J, Biernacka J, O’Kane D, Cunningham J, Wieben E, Schaid D, Drewes M, Courson V, Snyder K, Black JL, III, Weinshilboum RM. (2008) SLC6A4 variation and citalopram response. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 150:341-351.).
  • Brighina L, Schneider NK, Lesnick TG, de Andrade M, Cunningham JM, Mrazek D, Rocca WA, Maraganore DM. (2009) Alpha-synuclein, alcohol use disorders, and Parkinson disease: a case-control study. Parkinsonism Relat Disord 15(6):430-4.
  • Kramer WE, Walker DL, O’Kane DJ, Mrazek DA, Fisher PK, Dukek BA, Bruflat JK, Black III JL. (2009) CYP2D6: Novel genomic structures and alleles. Pharmacogenet. Genomics 19:813-822.
  • Mrazek DA. (2009) Pharmacogenomics of Methylphenidate Response: Making Progress. J. Amer. Acad. Child and Adolesc. Psych..48(12):1140-1142.
  • Karpyak VM, Biernacka JM, Black JL, Choi DS, Jeonghyun K, Wieben ED, Mrazek DA. (2009) Sequence variations of the human MPDZ gene and association with alcoholism in subjects with European ancestry. Alcohol Clin Exp Res [Epub Ahead of print] PMID:19175764. DOI:10.1111/j.1530-0277.2008.00888.x.
  • Mrazek DA (2010) Psychiatric pharmacogenomic testing in clinical practice. Dialogues in Clin Neurosci 12(1):69-76.
  • Sideras K, Ingle JN, Ames MM, Loprinzi CL, Mrazek DA, Black JL, Weinshilboum RM, Hawse JR, Spelsberg TC, Goetz MP. (2010) Practice recommendations regarding the co-administration of medications that inhibit CYP2D6 in women receiving tamoxifen. Clin.Oncol., in press.

Ron Krauss

  • Williams, P.T., Blanche, P.J., Rawlings, R.S., & Krauss, R.M. (2005). Concordant lipoprotein and weight responses to dietary fat change in identical twins with divergent exercise levels. Am. J. Clin. Nutr., 82, 181-187. PMCID: 16002817
  • Williams, P.T., Blanche, P.J., & Krauss, R.M. (2005). Behavioral versus genetic correlates of lipoproteins and adiposity in identical twins discordant for exercise. Circulation,, 112, 350-356. PMCID: 16009789
  • Krauss, R.M. (2005). Dietary and genetic probes of atherogenic dyslipidemia. Arterioscler. Thromb. Vasc. Biol., 25, 2265-2272. PMCID: 161666563
  • Krauss, R.M., Blanche, P.J., Rawlings, R.S., Fernstrom H.S., & Williams, P.T. (2006). Separate effects of reduced carbohydrate and weight loss on atherogenic dyslipidemia. Am. J. Clin. Nutr., 83, 1025-1031. PMCID: 16685042
  • Shin, M.J., Blanche, P.J., Rawlings, R.S., Fernstrom, H.S., & Krauss, R.M. (2007). Increased plasma concentrations of lipoprotein (a) during a low fat, high-carbohydrate diet are associated with increased plasma concentration of apolipoprotein C-III bound to apolipoprotein B-containing lipoproteins. Amer. J. Clin. Nutr., 85, 1527-32. PMCID: 17556688
  • Mangravite, L.M., Dawson, K., Davis, R.R., Gregg, J.P., & Krauss, R.M. (2007). Fatty acid desaturase regulation in adipose tissue by dietary composition is independent of weight loss and correlated with plasma triacylglycerol response. Amer. J. Clin. Nutr., 26, 759-67. PMCID: 17823443
  • Shin, M.J., Kanaya, A.M., & Krauss, R.M. (2008). Polymorphisms in the peroxisome proliferator activated receptor ? gene are associated with levels of apolipoprotein CIII and triglyceride in African-Americans but not Caucasians. Atherosclerosis, 198, 313-319. PMCID: 18061194
  • Krauss, R.M., Mangravite, L.M., Smith, J.D., Medina, M.W., Wang, et al. (2008). Variation in the hydroxymethyl glutaryl coenzyme a reductase gene is associated with racial cifferences in low-density lipoprotein cholesterol response to simvastatin treatment. Circulation, 117, 1537-44. PMCID: 18332269
  • Reiner, A.P., Barber, M.J., Guan, Y., Ridker, P.M., Lange, L.A., Chasman, D.I., Walston, J.D., Cooper, G.M., Jenny, N.S., Rieder, M.J., Durda, P., Smith, J.D., Novembre, J., Tracy, R.P., Rotter, J.I., Stephens, M., Nickerson D.A., & Krauss, R.M. (2008). Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1? are associated with C-reactive protein. Amer. J. Hum. Genetics, 82, 1-9. PMCID: 18439552
  • Caulfield, M.P., Li, S., Lee, K., Blanche, P.J., Salameh, W.A., Benner, W.H., Reitz, R.E., & Krauss, R.M. (2008). Direct determination of lipoprotein particle size and concentration by ion mobility analysis. Clin. Chem., 54, 1307-1316. PMCID: 18515257
  • Medina, M.W., Gao, F., Ruan, W., Rotter, J.I., & Krauss, R.M (2008). Alternative splicing of HMGCR is associated with plasma LDL cholesterol response to simvastatin. Circulation, 118, 355-362. PMCID: 18559695
  • Ruby, M.A., Nomura, D.K., Hudak, C.S., Mangravite, L.M., Chiu, S., Casida, J.E., & Krauss, R.M. (2008). Overactive endocannabinoid signaling impairs apolipoprotein E-mediated clearance of triglyceride-rich lipoproteins. Proc. Natl. Acad. Sci. USA, 105, 14561-14566. PMCID: 18794527
  • Siri-Tarino, P., Williams, P.T., Fernstrom, H.S., Rawlings, R.S., & Krauss, R.M. (2009). Reversal of small, dense LDL subclass phenotype by normalization of adiposity. Obesity, 17, 1768-75. PMCID: 19498345
  • Musunuru K., Orho-Melander, M., Caulfield, M.P., Li, S., Salameh, W.A., Reitz, R.E., Berglund, G., Hedblad, B., Engstrom, G., Williams, P.T., Kathiresan, S., Melander, O. & Krauss, R.M. (2009). Ion mobility analysis of liproprotein subfractions identified three independent axes of cardiovascular risk. Arterioscler Thromb Vasc Biol., 29, 1975-80. PMCID: 19729614
  • Siri-Tarino P, Sun Q, Hu, F. & Krauss, R.M. (2010). A meta-analysis of prospective cohort studies evaluating the association of saturated fat with cardiovascular disease. Amer. J. Clin. Nutr. [Epub ahead of print]. PMCID: 20071648

Julie Johnson

  • Gong Y, Beitelshees AL, Wessel J, Langaee TY, Schork NJ, Johnson JA. SNP discovery and haplotype analysis of BK channel beta1 subunit. Pharmacogenet Genom 2007;17:267-276.
  • Langaee TY, Gong Y, Yarandi H, Katz D, Cooper-DeHoff RM, Pepine CJ, Johnson JA. Association of CYP3A5 polymorphisms with hypertension and antihypertensive response to verapamil. Clin Pharmacol Ther 2007;81:386-91.
  • Beitelshees AL, Gong Y, Wang D, Schork NJ, Cooper-DeHoff RM, Langaee TY, Shriver MJ, Sadee W, Knot HJ, Pepine CJ, Johnson JA, for the INVEST Investigators. KCNMB1 genotype influences response to verapamil and adverse outcomes in the INternational VErapamil SR/Trandolapril STudy (INVEST). KCNMB1 genotype influences response to verapamil and adverse outcomes in the INternational VErapamil SR/Trandolapril STudy (INVEST). Pharmacogenetic Genom 2007;17:719-729.
  • Pacanowski MA, Zineh I, Li H, Johnson BD, Cooper-DeHoff RM, Bittner V, McNamara DM, Sharaf BL, Bairey Merz CN,Pepine CJ, Johnson JA. Adrenergic gene polymorphisms and cardiovascular risk in the NHLBI-sponsored Women’s Ischemia Syndrome Evaluation. J Translational Med 2008;6:11. Epub 2008 Mar 10; PMID: 18331634
  • Gerhard T, Gong Y, Beitelshees AL, Lobmeyer M, Cooper-DeHoff RM, Langaee TY, Shriver MD, Schork NJ, Pepine CJ, Johnson JA, for the INVEST Investigators. Association between Cardiovascular Outcomes, Diuretic Therapy and the a-adducin Polymorphism: Results from the INternational VErapamil SR-trandolapril STudy GENEtic Substudy (INVEST-GENES). Am Heart J 2008;156:397-404. PMID: 18657677
  • Johnson JA. Interethnic differences in drug response: The contribution of pharmacogenetics. (Invited review). Circulation 2008;118:1383-93. PMID: 18809808
  • Cooper GM, Johnson JA, Langaee TY, Feng H, Stanaway IB, Schwarz U, Ritchie MD, Stein CM, Roden DM, Smith JD, Veenstra DL, Rettie AE, Reider MJ. A whole-genome scan for common genetic variants with a large influence on warfarin maintenance dose. Blood 2008;112:1022-1027. Epub ahead of print June 5, PMID: 18535201
  • Pacanowski MA, Gong Y, Cooper-DeHoff RM, Schork NJ, Shriver MD, Langaee TY, Pepine CJ, Johnson JA for the INVEST Investigators. ?-adrenergic receptor gene polymorphisms and ?-blocker treatment outcomes in hypertension. Clin Pharmacol Ther 2008;84:715-721. Epub 2008 July 9. PMID: 18615004.
  • Johnson AD, Gong Y, Wang D, Langaee TY, Shin J, Cooper-DeHoff RM, Schork NJ, Binkley P, Pepine CJ, Johnson JA, Sadee W. Novel promoter polymorphisms in ACE (angiotensin-I converting enzyme) associated with clinical outcomes in hypertension. Clin Pharmacol Ther 2009;85:36-44. Epub 2008 Oct 22. PMID: 18946466
  • Klein TE, Altman RB, Eriksson N, Gage BF, Kimmel SE, Lee MTM, Limdi NA, Page D, Roden DM, Wagner MJ, Caldwell MD, Johnson JA for the International Warfarin Pharmacogenetics Consortium. Warfarin dosing using clinical and pharmacogenetic data. N Engl J Med 2009;360:753-64. PMID: 19228618; NIHMSID: 106202.
  • Johnson JA, Gong Y, Bailey K, Cooper-DeHoff RM, Chapman AB, Turner ST, Schwartz GL, Campbell K, Schmidt S, Beitelshees AL, Boerwinkle E, Gums JG. Hydrochlorothiazide and atenolol combination therapy: Effects of drug initiation order. Clin Pharmacol Ther 2009, epub 1 July; PMID 19571804; PMCID 2765546.
  • Pacanowski MA, Zineh I, Cooper-DeHoff RM, Pepine CJ, Johnson JA. Genetic and pharmacogenetic associations between NOS3 polymorphisms and cardiovascular outcomes in hypertensive patients with coronary artery disease. Am J Hypertens 2009, E pub Apr 30. PMID 19407804.
  • Beitelshees AL, Navare H, Wang D, Gong Y, Wessel J, Moss J, Langaee TY, Cooper-DeHoff RM, Sadee W, Pepine CJ, Schork NJ, Johnson JA. CACNA1C gene polymorphisms, cardiovascular disease outcomes and treatment response. Circ Cardiovasc Genet 2009;2:362-70. NIHMSID: 131313; PMID IDHCG 200035
  • Cavallari LH, Langaee TY, Momary KM, Shapiro NL, Nutescu EA, Coty WA, Viana MAG, Patel SR, Johnson JA. Genetic and clinical predictors of warfarin dose requirements in African Americans. Clin Pharmacol Ther 2010, Epub Jan 13, 2010.
  • Limdi NA, Wadelius M, Cavallari LH, Eriksson N, Crawford DC, Lee MTM, Chen CH, Motsinger-Reif A, Sagreiya H, Liu N, Wu AHB, Gage BF, Jorgensen A, Pirmohamed M, Shin JG, Suarez-Kurtz G, Kimmel SE, Johnson JA, Klein TE and Wagner MJ on behalf of the IWPC. Warfarin Pharmacogenetics: A single VKORC1 polymorphism is predictive of dose across three racial groups. Blood 2010 Epub Mar 4. PMID 20203262.

Reginald Frye

  • Dravid PV, Frye RF. Determination of N-desethylamodiaquine by hydrophilic interaction liquid chromatography with tandem mass spectrometry: application to in vitro drug metabolism studies. J Chromatogr B 2008; 863: 129-34. PMID: 18255358.
  • Mohamed MF, Harvey SS, Frye RF. Determination of mycophenolic acid phenolic glucuronide in microsomal incubates using high performance liquid chromatography-tandem mass spectrometry. J Chromatogr B 2008; 870:251-4. PMID: 18602350.
  • Shin J, Pauly DF, Johnson JA, Frye RF. Simplified method for determination of clarithromycin in human plasma using protein precipitation in a 96 well format and liquid chromatography tandem mass spectrometry. J Chromatogr B 2008; 871:130-4. PMID: 18639501.
  • Mohamed MF, Frye RF, Langaee TY. Inter-population variation frequency of human inosine 5′ monophosphate dehydrogenase type II (IMPDH2) genetic polymorphisms. Genetic Testing 2008;12: 513-6. PMID: 18976158.
  • Alkharfy KM, Poloyac SM, Congiu M, Desmond PV, Frye RF. Effect of the acute phase response induced by endotoxin administration on the expression and activity of UGT isoforms in rats. Drug Metab Lett. 2008;2(4):248-55. PMID: 19356101.
  • Butterweck V, Zdrojewski I, Galloway C, Frye R, Derendorf H. Toxicological and pharmacokinetic evaluation of concomitant intake of grapefruit juice and simvastatin in rats after repeated treatment over 28 days. Planta Med. 2009;75(11):1196-202. PMID: 19350484.
  • Kim KM, Henderson GN, Frye RF, Galloway CD, Browne NJ, Segal MS, Imaram W, Angerhoferd A, Johnson RJ. Simultaneous determination of uric acid metabolites allantoin, 6-aminouracil, and triuret in human urine using liquid chromatography-mass spectrometry. J Chromatogr B 2009; 877: 65-70. PMID: 19081307.
  • Woelkart K, Frye RF, Derendorf H, Bauer R, Butterweck V. Pharmacokinetics and Tissue Distribution of Dodeca-2E,4E,8E,10E/Z-tetraenoic Acid Isobutylamides after Oral Administration in Rats. Planta Med. 2009; 75(12):1306-13. PMID: 19399718.
  • Kim KM, Henderson GN, Ouyang X, Frye RF, Sautin YY, Feig DI, Johnson RJ. A sensitive and specific liquid chromatography-tandem mass spectrometry method for the determination of intracellular and extracellular uric acid. J Chromatogr B 2009; 877: 2032-8. PMID: 19520625.
  • Elewa HF, Kozak A, Frye RF, Johnson MH, Ergul A, Fagan SC. Early atorvastatin reduces hemorrhage after acute cerebral ischemia in diabetic rats. J Pharmacol Exper Ther 2009; 330:532-40. PMID: 19478137.
  • Nolin TD, Frye RF, Le P, Sadr H, Naud J, Leblond FA, Pichette V, Himmelfarb J. Kidney disease alters nonrenal drug clearance by inhibiting transporter function. J Am Soc Nephrol 2009; 20: 2269-76. PMID: 19696225.
  • Mohamed MF, Frye RF. Inhibition of intestinal and hepatic glucuronidation of mycophenolic acid by Ginkgo biloba extract and flavonoids. Drug Metab Dispos. 2010;38(2):270-5. PMID: 19889883.
  • Joy MS, Frye RF, Stubbert K, Falk RJ, Brouwer KR, Kharasch E. Enantiomeric bupropion and 4 hydroxybupropion pharmacokinetics for assessment of CYP450 2B6 activity in glomerular kidney diseases. J Clin Pharmacol. 2010 Jan 26. [Epub ahead of print] PMID: 20103693.
  • Stanton ML, Joy MS, Frye RF. Validation and application of a liquid chromatography-tandem mass spectrometric method for quantification of the drug transport probe fexofenadine in human plasma using 96-well filter plates. J Chromatogr B 2009 Dec 24. [Epub ahead of print] PMID: 20045385.
  • Navare HA, Frye RF, Cooper-DeHoff RM, Shuster JJ, Hall K, Schmidt SOF, Turner ST, Johnson JA. Atenolol exposure and risk for development of adverse metabolic effects.(in press).

Rhonda Cooper-Dehoff

  • Cooper-DeHoff RM, Pepine CJ. Metabolic Syndrome and Cardiovascular Disease: Challenges and Opportunities. Clinical Cardiol 2007; 30:593-7.
  • Cooper-DeHoff RM. Thiazide Induced Dysglycemia – It’s Time To Take Notice. Exp Rev of Card Ther 2008;6:1291-1294.
  • Cooper-DeHoff RM, Pacanowski MA, Pepine, CJ. Cardiovascular Therapies and Associated Glucose Homeostasis: Implications across the Dysglycemia Continuum. J Am Coll Cardiol 2009;53:S28-34.
  • Karnes JH, Cooper-DeHoff RM. Antihypertensive Medications: Benefits of BP Lowering and Hazards of Metabolic Effects. Exp Rev of Card Ther 2009, 7:689-702.
  • Cooper-DeHoff RM, Wen S, Beitelshees AL, Zineh I, Gums JG, Turner ST, Gong Y, Hall K, Parekh V, Chapman AB, Boerwinkle E, Johnson JA. Impact of Abdominal Obesity on Incidence of Adverse Metabolic Effects Associated with Antihypertensive Medications. Hypertension, 2010;55:61-68.
  • Cooper-DeHoff R, Handberg E, Heissenberg, C, Johnson, K. Electronic prescribing via the internet for a coronary artery disease and hypertension megatrial. Clin Cardiol 2001;24(11):V14-V16.
  • Conti CR, Cooper-DeHoff RM. How will INVEST and other hypertension trials change clinical practice? Clin Cardiol 2001;24(11):V24-V29.
  • Pepine CJ, Handberg EM, Cooper-DeHoff RM, Marks RG, Kowey P, Messerli FH, Mancia G, Cangiano JL, Garcia-Barreto D, Keltai M, Erdine S, Bristol HA, Kolb HR, Bakris GL, Cohen JD, Parmley WW. A calcium antagonist vs a non-calcium antagonist hypertension treatment strategy for patients with coronary artery disease. The INternational VErapamil-Trandolapril STudy (INVEST). JAMA 2003;290(21):2805-2816.
  • Pepine CJ, Cooper-DeHoff RM. Cardiovascular therapies and risk for development of diabetes. J Am Coll Cardiol 2004;44(3):509-512.
  • Cooper-DeHoff RM, Handberg EM, Cohen J, Kowey P, Messerli F. Characteristics of contemporary patients with hypertension and coronary artery disease. Clin Cardiol. 2004;27(10):571-576.
  • Bakris GL, Gaxiola E, Messerli FH, Mancia G, Erdine S, Cooper-DeHoff RM, Pepine CJ; INVEST Investigators. Clinical outcomes in the diabetes cohort of the INternational VErapamil SR-trandolapril STudy. Hypertension 2004;44(5):637-42.
  • Cooper-DeHoff RM, Pepine CJ. Editorial: Ranolazine is associated with cardiovascular and metabolic improvement: A win-win for patients with diabetes. Eur Heart J 2006;27(1):5-6.
  • Cooper-DeHoff RM, Aranda JM, Gaxiola E, Cangiano JL, Garcia-Barreto D, Conti CR, Hewkin A, Pepine CJ. Blood pressure control and cardiovascular outcomes in high risk Hispanic patients – Findings from the International Verapamil SR – Trandolapril Study. Am Heart J 2006; 151(5):1072-79.
  • Cooper-Dehoff RM, Cohen JD, Bakris GL, Messerli FH, Erdine S, Hewkin AC, Kupfer S, Pepine CJ. Predictors of Development of Diabetes Mellitus in Patients with Coronary Artery Disease Taking Antihypertensive Medications (Findings from the INternational VErapamil SR-Trandolapril STudy [INVEST]). Am J Cardiol 2006, 98:89-894.
  • Uretsky S, Messerli FH, Bangalore S, Champion A, Cooper-DeHoff RM, Zhou Q, Pepine, CJ. Obesity Paradox in Patients with Hypertension and Coronary Artery Disease. The American Journal of Medicine. 2007. 120;10: 863-870.

Amber Beitelshees

  • Zineh I, Beitelshees AL, Gaedigk A, Walker JR, Pauly DF, Eberst K, Leeder JS, Phillips MS, Gelfand CA, Johnson JA. Pharmacokinetics and CYP2D6 genotypes do not predict metoprolol adverse events or efficacy in hypertension. Clin Pharmacol Ther 2004;76(6):536-44. PMID: 15592325
  • Beitelshees AL, Zineh I, Yarandi HN, Pauly DF, Johnson JA. Influence of phenotype and pharmacokinetics on ?-blocker drug target pharmacogenetics. Pharmacogenomics J 2006;6(3):174-8. PMID: 16402084
  • Beitelshees AL, Zineh I, Yarandi HN, Pauly DF, Johnson JA. Discordant ?-blocker effects on clinic, ambulatory, resting, and exercise hemodynamics in patients with hypertension. Pharmacotherapy 2006;26(9):1247-54. PMID: 16945046
  • Lobmeyer MT, Gong Y, Terra SG, Beitelshees AL, Langaee TY, Pauly DF, Scofield RS, Hamilton KK, Patterson JH, Adams KF, Hill JA, Aranda JM, Johnson JA. Synergistic polymorphisms of the ?1- and ?2c-adrenergic receptors and the influence on left ventricular ejection fraction response to ?-blocker therapy in heart failure. Pharmacoget Genom 2007;17(4):277-82. PMID: 17496726
  • Gong Y, Beitelshees AL, Wessel J, Langaee TY, Schork NJ, Johnson JA. SNP discovery and haplotype analysis of BK channel ?-1 subunit. Pharmacoget Genom 2007; 17(4):267-75. PMCID: PMC2713575
  • Beitelshees AL, Gong Y, Wang D, Schork NJ, Cooper-DeHoff RM, Langaee TY, Shriver MD, Sadee W, Knott HJ, Pepine CJ, Johnson JA. KCNMB1 genotype influences response to verapamil SR and adverse outcomes in the International VErapamil SR/Trandolapril STudy (INVEST). Pharmacogent Genom 2007;17(9):719-29. PMC2713584
  • Gerhard T, Gong Y, Beitelshees AL, Mao X, Lobmeyer MT, Cooper-DeHoff RM, Langaee TY, Schork NJ, Shriver MD, Pepine CJ, Johnson JA. Alpha-adducin polymorphism associated with increased risk of adverse cardiovascular outcomes: Results from INVEST-GENES. Am Heart J 2008; 156:397-404. PMC2547143
  • Zineh I, Beitelshees AL, Welder GJ, Hou W, Nasser C, Wu J, Cresci S, Province MA, Spertus JA. Epithelial neutrophil-activating peptide (ENA-78), acute coronary syndrome prognosis, and modulatory effect of statins. PLoS ONE 2008;3(9)e3117. PMC2518836
  • Johnson JA, Boerwinkle E, Zineh I, Chapman AB, Bailey KR, Cooper-DeHoff RM, Gums JG, Curry RW, Gong Y, Beitelshees AL, Schwartz GL, Turner ST. Pharmacogenomics of Antihypertensive drugs: Rationale and Design of the Pharmacogenomic evaluation of antihypertensive responses (PEAR) study. Am Heart J 2009;157(3):442-9. PMC2671287
  • Zineh I, Beitelshees AL, Silverstein JH, Haller MJ. Serum MCP-1 concentrations associate with diabetes status but not arterial stiffness in children with type 1 diabetes. Diabetes Care 2009;32(3):465-7. PMC2646030
  • Johnson JA, Gong Y, Bailey K, Cooper-DeHoff RM, Chapman AB, Turner ST, Schwartz GL, Campbell K, Schmidt S, Beitelshees AL, Boerwinkle E, Gums JG. Combination antihypertensive therapy with hydrochlorothiazide and atenolol: effect of initiation order. Clin Pharmacol Ther 2009;86:533-9. PMC2765524
  • Beitelshees AL, Gong Y, Bailey KR, Turner ST, Chapman AB, Schwartz GL, Gums JG, Boerwinkle E, Johnson JA. Comparison of office, ambulatory, and home blood pressure antihypertensive response to atenolol and hydrochlorthiazide. J Clin Hypertens (Greenwich) 2010;12(1):14-21. PMC2841560.
  • Beitelshees AL, Navare H, Wang D, Gong Y, Wessel J, Moss JI, Langaee TY, Cooper-DeHoff RM, Sadee W, Pepine CJ, Schork NJ, Johnson JA. CACNA1C gene polymorphisms, cardiovascular disease outcomes and treatment response. Circ Cardiovasc Genet 2009;2:362-370. PMC2761685
  • Cooper-DeHoff RM, Wen S, Beitelshees AL, Zineh I, Gums JG, Turner ST, Gong Y, Hall K, Parekh V, Chapman AB, Boerwinkle E, Johnson JA. Impact of abdominal obesity on incidence of adverse metabolic effects associated with antihypertensive medications. Hypertension 2010;55:61-68. PMC2811061.
  • Beitelshees AL, Finck BN, Leone TC, Cresci S, Wu J, Province, MA, Fabbrini E, Kirk E, Zineh I, Klein S, Spertus JA, Kelly DP. Interaction between the UCP2 -866 G>A polymorphism, diabetes, and beta-blocker use among patients with acute coronary syndromes. Pharmacogenet Genomics 2010;20(4):231-8. PMC2842450.

Alan Shuldiner

  • Pollin T.I., Damcott C.M., Shen H., Ott S.H., Shelton J., Horenstein R.B., Post W., McLenithan J.C., Bielak L.F., Peyser P.A., Mitchell B.D., Miller M., O’Connell J.R., Shuldiner A.R. A null mutation in human APOC3 confers a favorable plasma lipid profile and apparent cardioprotection (2008) Science 322, 1702-1705.
  • Wang Y., McArdle P.F., Wade J.B., O’Connell J., Dorff S.E., Shar S.J., Shi X., Pan L., Rampersaud E., Shen H., Kim J.D., Subramanya A.R., Steinle N.I., Parsa A., Ober C.C., Welling P.A., Chakravarti A., Weder A.B., Cooper R.S., Mitchell B.D., Shuldiner A.R., Chang Y.-P.C. Whole-genome association study identifies STK39 as a novel hypertension susceptibility gene (2009) Proc. Natl. Acad. Sci. USA 106, 226-31. PMID: 19114657.
  • Shen H., Herzog W., Drolet M. Pakyz R., Newcomer S., Sack P., Karon H., Ryan K.A., Zhao Y., Shi X., Mitchell B.D., Shuldiner A.R. Aspirin resistance in healthy drug-naïve men versus women (From the Heredity and Phenotype Intervention [HAPI] Heart Study) (2009) Am. J. Cardiol., 104, 606-612. PMID: 19660620.
  • Shuldiner A.R., O’Connell J.O., Bliden K.P., Gandhi A., Ryan K., Horenstein R.B., Damcott C.M., Pakyz R., Gibson Q., Pollin T.I., Post W., Parsa A., Mitchell B.D., Faraday N., Herzog W., Gurbel P.A. Cytochrome p450 2C19 genotype is a major determinant of the anti-platelet effect and clinical efficacy of clopidogrel therapy (2009) JAMA 302, 849-858. PMID: 19706858
  • Gurbel PA, Bliden KP, Antonino MJ, Stephens G, Gretler DD, Jurek MM, Pakyz RE, Shuldiner AR, Conley PB, Tantry US. The effect of elinogrel on high platelet reactivity during dual antiplatelet therapy and the relation to cyp 2c19*2 genotype: first experience in patients (2009) J Thromb. Haemost. [Epub ahead of print] PMID: 19817997
  • Walston J., Silver K., Bogardus C., Knowler W.S., Celi F.S., Austin S., Raben N., Manning B.StJ., Strosberg A.D., Sorkin J.D., Roth J., and Shuldiner A.R. Time of onset of non-insulin-dependent diabetes mellitus and genetic variation in the ?3-adrenergic–receptor gene (1995) N. Engl. J. Med. 333, 343-347. PMID: 7609750
  • Barzilai N., Atzmon G., Schechter C., Schaefer E.J., Cupples A.L., Lipton R., Cheng S., Shuldiner A.R. Unique lipoprotein phenotype and genotype associated with exceptional longevity (2003) JAMA 290, 2030-2040. PMID: 14559957
  • Florez J.C., Jablonski K.A., Bayley N., Pollin T.I., de Bakker P.I., Shuldiner A.R., Knowler W.C., Nathan D.M., Altshuler D. for the Diabetes Prevention Program Research Group. TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program (2006) N. Engl. J. Med. 355, 241-250. PMID: 16855264
  • Rampersaud E., Damcott C.M., Fu M., Shen H., McArdle P., Shi X., Shelton J., Yin J., Chang C.Y., Ott S.H., Zhang L., Zhao Y., Mitchell B.D., O’Connell J.O., Shuldiner A.R. Identification of novel candidate genes for type 2 diabetes from a genome-wide association scan in the Old Order Amish: Evidence for replication from diabetes-related quantitative traits and from independent populations (2007) Diabetes 56, 3053-3062. PMID: 17846126
  • McArdle P.F., Parsa A., Chang Y.-P.C., Weir M.R., O’Connell J.R., Mitchell B.D., Shuldiner A.R. A common non-synonymous variant in GLUT9 is a determinant of serum uric acid levels in Old Order Amish (2008) Arthritis and Rheumatism 58, 2874-2881. PMID: 18759275
  • Roy-Gagnon M.-H., Weir M.R., Sorkin J.D., Ryan K.A., Sack P., Hines S., Bielak L.F., Peyser P.A., Post W., Mitchell B.D., Shuldiner A.R., Douglas J.A. Genetic influences on the blood pressure response to stress: results from the HAPI Heart Study (2008) J. Hyperten. 26, 729-736. PMID: 18327083.
  • McArdle PF, Rutherford S, Mitchell BD, Damcott CM, Wang Y, Ott S, Chang YPC, Levy D, Shuldiner AR, Steinle N. Nicotinic acetylcholine receptor subunit variants on chromosome 2q are associated with blood pressure related traits in the Old Order Amish and the Framingham Heart Study (2008) BMC Medical Genetics Jul 14;9(1):67. PMCID: PMC2478679.
  • Willer C.J., Sanna S., Jackson A.U., Scuteri A., Bonnycastle L.L., Clarke R., Heath S.C., Timpson N.J., Najjar S.S., Stringham H.M., Strait J., Duren W.L., Maschio A., Busonero F., Mulas A., Albai G., Swift A.J., Morken M.A., Narisu N., Bennett D., Parish S., Shen H., Galan P., Meneton P., Hercberg S., Zelenika D., Chen W.-M., Li Y., Scott L.J., Scheet P.A., Sundvall J., Watanabe R.M., Nagaraja R., Ebrahim S., Lawlor D.A., Ben-Shlomo Y., Davey-Smith G., Shuldiner A.R., Collins R., Bergman R.N., Uda M., Tuomilehto J., Cao A., Collins F.S., Lakatta E., Lathrop G.M., Boehnke M., Schlessinger D., Mohlke K.L., Abecasis G.R. Newly identified loci that influence lipid concentrations and risk of coronary artery disease (2008) Nat. Genet. 40, 198-203. PMID: 18193043
  • Shen H., Pollin T.I., Damcott C.M., McLenithan J.C., Mitchell B.D, Shuldiner A.R. Glucokinase regulatory protein gene polymorphism affects postprandial lipemic response in a dietary intervention study (2009) Hum. Genet. 126, 567-74. PMID: 19526250
  • Dupuis J, Lan.nberg C., Prokopenko I., Saxena R., Soranzo N….Shuldiner A.R.…. Boehnke M, McCarthy MI†, Florez JC and Barroso I for the MAGIC investigators. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat. Genet., in press. PMID: 20081858

Kristen Newby

  • Newby LK, Storrow AW, Gibler WB, Garvey JL, Tucker JF, Kaplan AL, Schreiber DH, Tuttle RH, McNulty SE, Ohman EM. Bedside multimarker testing for risk stratification in chest-pain units: the CHECKMATE Study. Circulation 2001;103:1832-1837. PMID: 11294799
  • Newby LK, Ohman EM, Christenson RH, Moliterno DJ, Harrington RA, White HD, Armstrong PW, Van de Werf F, Pfisterer M, Hasselblad V, Califf RM, Topol EJ. Benefit of glycoprotein IIb/IIIa inhibition in patients with acute coronary syndromes and troponin T-positive status: the PARAGON B Troponin T Substudy. Circulation 2001;103:2891-2896. PMID: 11413076
  • Shah SH, Hauser ER, Crosslin D, Wang L, Haynes C, Connelly J, Nelson S, Johnson J, Gadson S, Nelson CL, Seo D, Gregory S, Kraus WE, Granger CB, Goldschmidt-Clermont P, Newby LK. ALOX5AP variants are associated with in-stent restenosis after percutaneous coronary intervention. Atherosclerosis 2008: Epub 2008 Feb 12. PMID: 18374923
  • Wingrove JA, Daniels SE, Sehnert AJ, Tingley W, Elashoff MR, Rosenberg S, Buellesfeld L, Grube E, Newby LK, Ginsburg GS, Kraus WE. Correlation of peripheral blood gene expression with the extent of coronary artery stenosis. Circ Cardiovasc Genetics 2008;1:31-38.
  • Giugliano RP, White JA, Bode C, Armstrong PW, Montalescot G, Lewis BS, van T Hof A, Berdan LG, Lee KL, Strony JT, Hildemann S, Veltri E, Van de Werf F, Braunwald E, Harrington RA, Califf RM, Newby LK, for the EARLY ACS Investigators. Early versus delayed, provisional eptifibatide in acute coronary syndromes. N Engl J Med 2009; 360:2176-2190. Epub 2009 Mar 31. PMID: 19332455
  • Shah SH, Bain JR, Crosslin DR, Muehlbauer MJ, Stevens RD, Haynes C, Dungan J, Newby LK, Hauser ER, Ginsburg GS, Newgard CB, Kraus WE. Association of a peripheral blood metabolic profile with CAD and risk of subsequent cardiovascular events. Circ Cardiovasc Genetics 2010: in press. Epub 2010 Feb 19.
  • Shah SH, Granger CB, Hauser ER, Kraus WE, Sun J-L, Pieper K, Nelson CL, Delong ER, Califf RM, Newby LK. Reclassification of cardiovascular risk using integrated clinical and molecular biosignatures: design and rationale of the MURDOCK Horizon 1 Cardiovascular Disease Study. Am Heart J 2010: in press.
  • Newby LK, Christenson RH, Ohman EM, Armstrong PW, Peck SL, Lee KL, Hamm CW, Katus HA, Cianciolo C, Granger CB, Topol EJ, Califf RM. The value of serial troponin T measurements for early and late risk stratification in patients with acute coronary syndromes. Circulation 1998;98:1853-1859. PMID: 9799204
  • The SYMPHONY Investigators. Comparison of sibrafiban with aspirin for prevention of cardiovascular events after acute coronary syndromes: a randomised trial. Lancet 2000;355:337-345.
  • Newby LK, Eisenstein EL, Califf RM, Thompson TD, Nelson CL, Peterson ED, Armstrong PW, Van de Werf F, White HD, Topol EJ, Mark DB. Cost effectiveness of early discharge after uncomplicated acute myocardial infarction. N Engl J Med 2000;342:749-755. PMID: 10717009
  • Newby LK, Kristinsson A, Bhapkar MV, Aylward PE, Dimas AP, Klein WW, McGuire DK, Moliterno DJ, Verheugt FWA, Weaver WD, Califf RM. Early statin initiation and outcomes in patients with acute coronary syndromes. JAMA 2002;287:3087-3095. PMID: 12069671
  • Grady D, Herrington D, Bittner V, Blumenthal R, Davidson M, Hlatky M, Hsia J, Hulley SB, Herd A, Khan S, Newby LK, Waters D, Vittinghoff E, Wenger N. Heart and Estrogen/progestin Replacement Study Follow-up (HERS II): 1. Cardiovascular outcomes during 6.8 years of hormone therapy. JAMA 2002;288:49-57. PMID: 12090862
  • Aviles RJ, Askari AT, Lindahl B, Wallentin L, Jia G, Ohman EM, Mahaffey KW, Newby LK, Califf RM, Topol EJ, Simoons ML, Lauer MS. Troponin T levels in patients with acute coronary syndromes, with or without renal dysfunction. N Engl J Med 2002;346:2047-2052. PMID: 12087140
  • Newby LK, Hasselblad V, Armstrong PW, Van de Werf F, Mark DB, White HD, Topol EJ, Califf RM. Time-based risk assessment after myocardial infarction: implications for timing of discharge and application to medical decision-making. Eur Heart J 2003;24:182-189. PMID: 12573275

Ranga Krishnan

  • Steffens DC, Jiang W, Krishnan KR, Karoly ED, Mitchell MW, O’Connor CM, Kaddurah-Daouk R,: Metabolomic differences in heart failure patients with and without major depression. J. Geriatric Psychiat. Neurol 23(2): 138-146, 2010.
  • Taylor, WD, McQuoid DR, Ashley-Koch A, MacFall JR, Bridges J, Krishnan KR, Steffens DC. The BDNF Val66Met genotype and six-month remission rates in late-life depression. E-published, The Pharmacogenomics Journal, March 2, 2010.
  • Mannelli P, Patkar A, Rozen S, Matson W, Krishnan R, Kaddurah-Daouk R: Opioid use affects antioxidant activity and purine metabolism: Preliminary Results. Hum Psychopharmacology, 24(8): 666-675, 2009,
  • Patkar AA, Rozen S, Mannelli P, Matson W, Pae CU, Krishnan KR, Kaddurah-Daouk R: Psychopharmacology 206 (3): 479-489, 2009.
  • Kaddurah-Daouk R, Krishnan KR. Metabolomics: a global biochemical approach to the study of central nervous system diseases. Neuropsychopharmacology, 34(1):173-186, 2009.
  • Venkatraman TN, Krishnan RR, Steffens DC, Song AW, Taylor WD. Biochemical abnormalities of medial temporal lobe and medial prefrontal cortex in late-life depression. Psychiatry Research: Neuroimaging (2009), doi 10.1016/j.pscyresns.2008.07.001.
  • Krishnan RR, Keefe R, Kraus M. Schizophrenia is a disorder of higher order hierarchical processing. Med Hypotheses (2009), doi:1031016/j.mehy.2008.12.039.
  • Eddington KM, Dolcos F, McLean AN, Krishnan KR, Cabeza R, Strauman TJ. Neural correlates of idiographic goal priming in depression: goal-specific dysfunctions in the orbitofrontal cortex. Social Cognitive and Affective Neuroscience 4(3):238-246, 2009.
  • Taylor WD, Steffens DC, Ashley-Koch A, Payne ME, MacFall JR, Potocky C, Krishnan KR. Angiotensin receptor gene polymorphisms and two-year change in cerebral hyperintense lesion volume in men. E-published, Molecular Psychiatry, March 10, 2009.
  • Züchner S, Wendland JR, Ashley-Koch AE, Collins AL, Tran-Viet KN, Quinn K, Timpano KC, Cuccaro ML, Pericak-Vance MA, Steffens DC, Krishnan KR, Feng G, Murphy DL. Multiple rare SAPAP3 missense variants in trichtillomania and OCD. Mol Psychaitry, 14(1):6-9, 2009.
  • Qiu A, Taylor WD, Zhao Z, MacFall JR, Miller MI, Key CR, Payne ME, Steffens DC, Krishnan KR. APOE related hippocampal shape alteration in geriatric depression. Neuroimage, 44(3);620-626, 2009.
  • Beyer JL, Burchitt B, Gersing K, Krishnan KR. Patterns of pharmacotherapy and treatment response in elderly adults with bipolar disorder. Psychopharmacol Bull, 41(1):102-114, 2008.
  • Sneed JR, Rindskopf D, Steffens DC, Krishnan KR, Roose SP. The vascular depression subtype: evidence of internal validity. Biol Psychiatry, 64(6):491-497, 2008.
  • Kaddurah-Daouk RK, McEvoy J, Baillie RA, Lee D, Yao JK, Doraiswamy PM, Krishnan KRR. Metabolomic mapping of atypical antipsychotic effects in schizophrenia. Molecular Psychiatry 12:934-945, 2007.
  • Paige LA, Mitchell MW, Krishnan KRR, Kaddurah-Daouk R, Steffens DC. A preliminary metabolomic analysis of older adults with and without depression. International Journal of Geriatric Psychiatry 22:418-423, 2006.

John Rush

  • Leuchter, A.F., Husain, M.M., Cook, I.A., Trivedi, M.H., Wisniewski, S.R., Gilmer, W., Luther, J.F., Fava, M., Rush, A.J. Painful physical symptoms and treatment outcome in major depressive disorder. A STAR*D report. Psychological Medicine, 2009 June 3, doi:10.1017/S0033291709006035.
  • Nierenberg, A.A., Husain, M.M., Trivedi, M.H., Fava, M., Warden, D., Wisniewski, S.R., Miyahara, S., Rush, A.J. Residual symptoms after remission of major depressive disorder with citalopram and risk of relapse: A STAR*D report. Psychological Medicine, 2009 May 22; doi:10.1017/S0033291709006011.
  • Fava, M., Hwang, I., Rush, A.J., Sampson, N., Walters, E.F., Kessler, R.C. The importance of irritability as a symptom of major depressive disorder: Results from the National Comorbidity Survey Replication. Molecular Psychiatry, 10 March 2009; doi:10.1038/mp.2009.20.
  • Kashner, T.M., Trivedi, M.H., Wicker, A., Fava, M., Shores-Wilson, K., Wisniewski, S.R., Rush, A.J. Release bias in accessing medical records in clinical trials: a STAR*D report. International Journal of Methods in Psychiatric Research,18:147-158, 2009.
  • Warden, D., Trivedi, M.H., Wisniewski, S.R., Lesser, I.M., Mitchell, J., Balasubramani, G.K., Fava, M., Shores-Wilson, K., Stegman, D., Rush, A.J. Identifying risk for attrition during treatment for depression. Psychotherapy and Psychosomatics, 78:372-379, 2009.
  • Stewart, J.W., McGrath, P.J., Fava, M., Wisniewski, S.R., Zisook, S., Cook, I., Nierenberg, A.A., Trivedi, M.H., Balasubramani, G.K., Warden, D., Lesser, I., Rush, A.J. Do atypical features affect outcome in depressed outpatients treated with citalopram? The International Journal of Neuropsychopharmacology, 2009, doi:10.1017/S1461145709000182.
  • Ising, M., Lucae, S., Binder, E.B., Bettecken, T., Uhr, M., Ripke, S., Kohli, M.A., Hennings, J.M., Horstmann, S., Kloiber, S., Menke, A., Bondy, B., Rupprecht, R., Domschke, K., Baune, B.T., Arolt, V., Rush, A.J., Holsboer, F., Muller-Myhsok, B. A genome-wide association study points to multiple loci predicting treatment outcome in depression. Archives of General Psychiatry, 66:966-975, 2009.
  • Nierenberg, A.A., Trivedi, M.H., Gaynes, B.N., Mitchell, J., Davis, L.L., Husain, M.M., Wisniewski, S.R., Fava, M., Warden, D., Luther, J.F., Morris, D.W., Shelton, R.C., Rush, A.J. An effectiveness study of venlafaxine-XR combined with aripiprazole for chronic or recurrent major depressive disorder. Australian and New Zealand Journal of Psychiatry, in press.
  • Kashner, T.M., Trivedi, M.H., Wicker, A., Fava, M., Wisniewski, S.R., Rush, A.J. The impact of non-clinical factors on care use for patients with depression: A STAR*D report. CNS Neuroscience & Therapeutics, 15:320-332, 2009.
  • Laje, G., Allen, A.S., Akula, N., Manji, H., Rush, A.J., McMahon, F.J. Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients. Pharmacogenetics and Genomics, in press.
  • Brown, E.S., Carmody, T.J., Schmitz, J.M., Caetano, R., Adinoff, B., Swann, A.C., Rush, A.J. A randomized, double-blind, placebo-controlled pilot study of naltrexone in outpatients with bipolar disorder and alcohol dependence. Alcoholism: Clinical and Experimental Research, in press.
  • Bryan, C., Songer, T., Brooks, M.M., Rush, A.J., Thase, M.E., Gaynes, B., Balasubramani, G.K., Trivedi, M.H., Fava, M., Wisniewski, S.R. The impact of diabetes on depression treatment outcomes. General Hospital Psychiatry, in press.
  • Binder, E.B., Owens, M.J., Wei, L., Deveau, T.J., Rush, A.J., Trivedi, M.H., Fava, M., Bradley, R.G., Ressler, K.J., Nemeroff, C.B. Association of polymorphisms in genes regulating the CRF system with antidepressant treatment response in the STAR*D sample. Archives of General Psychiatry, in press.
  • Howland, R.H., Rush, A.J., Wisniewski, S.R., Trivedi, M.H., Warden, D., Fava, M., Davis, L.L., Balasubramani, G.K., McGrath, P.J., Berman, S.R. Concurrent anxiety and substance use disorders among outpatients with major depression: Clinical features and effect on treatment outcome. Drug and Alcohol Dependence, 99:248-260, 2009.
  • Kashner, T.M., Stensland, M.D., Lind, L., Wicker, A., Rush, A.J., Golden, R.M., Henley, S.S. Measuring use and cost of care for patients with mood disorders: the utilization and cost inventory. Medical Care, 47:184-190, 2009.
  • Young, E.A., Kornstein, S.G., Marcus, S.M., Harvey, A.T., Warden, D., Wisniewski, S.R., Balasubramani, G.K., Fava, M., Trivedi, M.H., Rush, A.J. Sex differences in response to citalopram: A STAR*D report. Journal of Psychiatric Research, 43:503-511, 2009.
  • Husain, M.M., Rush, A.J., Wisniewski, S.R., McClintock, S.M, Fava, M., Nierenberg, A.A., Davis, L., Balasubramani, G.K., Young, E., Albala, A.A., Trivedi, M.H. Family history of mood disorder and therapeutic outcome: Findings from STAR*D. Journal of Clinical Psychiatry, 70:185-195, 2009.
  • Perlis, R.H., Fava, M., Trivedi, M.H., Alpert, J., Luther, A.J., Wisniewski, S.R., Rush, A.J. Irritability is associated with anxiety and greater severity, but not bipolar spectrum features, in major depressive disorder. Acta Psychiatrica Scandinavica, 119:282-289, 2009. 


 


 

 


Hongjie Zhu

  • Zhu, H., and Li, L. (2011). Biological pathway selection through nonlinear dimension reduction. Biostatistics, 12, 429-444.
  • Ji, Y.*, Hebbring, S.*, Zhu, H.*, Jenkins, G.D., Biernacka, J., Snyder, K., Drews, M., Fiehn, O., Zeng, Z., Schaid, D., Mrazek, D.A., Kaddurah-Daouk, R., and Weinshilboum, R.M. (2011). Glycine and a glycine dehydrogenase (GLDC) SNP as citalopram/escitalopram response biomarkers in depression: pharmacometabolomics-informed pharmacogenomics. Clinical Pharmacology and Therapeutics, 89, 97-104. [*Equal Contribution].
  • Trupp, M.*, Zhu, H.*, Wikoff, W., Zeng, Z., Karp, P.D., Fiehn, O., Krauss, R.M., Kaddurah-Daouk, R. (2012). Metabolomics reveals pleiotropic features of the simvastatin response. PLoS1, 7, e38386. [*Equal Contribution].
  • Kaddurah-Daouk, R., Boyle, S. H., Matson, W., Sharma, S., Matson, S., Zhu, H., Bogdanov, M.B., Churchill, E., Krishnan, R.R., Rush, A.J., Pickering, E., and Delnomdedieu, M. (2011). Pretreatment metabotype as a predictor of response to sertraline or placebo in depressed outpatients: a proof of concept. Translational Psychiatry, 1, e26.
  • Kaddurah-Daouk, R., Baillie, R.A., Zhu, H., Zeng, Z., Wiest, M.M., Nguyen, U.T., Wojnoonski, K., Watkins, S., Trupp, M., Krauss, R.M. (2011). Enteric microbiome metabolites correlate with response to simvastatin treatment. PLoS1, 6, e25482.
  • Kaddurah-Daouk, R., Baillie, R.A., Zhu, H., Zeng, Z., Wiest, M.M., Nguyen, U.T., Watkins, S.M., and Krauss, R.M. (2010). Lipidomic analysis of variation in response to simvastatin in the Cholesterol and Pharmacogenetics Study. Metabolomics, 6, 191-201.
  • Abo, R., Hebbring, S., Ji, Y., Zhu, H., Zeng, Z., Batzler, A., Jenkins, G.D., Biernack, J., Snyder, K., Drews, M., Fiehn, O., Fridley, B., Schaid, D., Kamatani, N., Nakamura, Y., Kubo, M., Mushiroda, T., Kaddurah-Daouk, R., Mrazekd, D.A. and Weinshilboum R.M. (2011). Merging Pharmacometabolomics with Pharmacogenomics using “1000 Genomes” SNP Imputation: Selective Serotonin
  • Reuptake Inhibitor Response Pharmacogenomics. Pharmacogenetics and Genomics, 22, 247-53.
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