My Bibliography

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Taylor SL, Ruhaak LR, Kelly K, Weiss RH, Kim K. Effects of imputation on correlation: implications for analysis of mass spectrometry data from multiple biological matrices. Brief Bioinform. 2017 Mar 1;18(2):312-320. doi: 10.1093/bib/bbw010. PubMed PMID: 26896791; PubMed Central PMCID: PMC5862252.

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Cheng MY, Sukhov A, Sultani H, Kim K, Maverakis E. Trends in National Institutes of Health Funding of Principal Investigators in Dermatology Research by Academic Degree and Sex. JAMA Dermatol. 2016 Aug 1;152(8):883-8. doi: 10.1001/jamadermatol.2016.0271. PubMed PMID: 27191545.

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Tomilov A, Tomilova N, Shan Y, Hagopian K, Bettaieb A, Kim K, Pelicci PG, Haj F, Ramsey J, Cortopassi G. p46Shc Inhibits Thiolase and Lipid Oxidation in Mitochondria. J Biol Chem. 2016 Jun 10;291(24):12575-12585. doi: 10.1074/jbc.M115.695577. Epub 2016 Apr 8. PubMed PMID: 27059956; PubMed Central PMCID: PMC4933453.

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Ruhaak LR, Kim K, Stroble C, Taylor SL, Hong Q, Miyamoto S, Lebrilla CB, Leiserowitz G. Protein-Specific Differential Glycosylation of Immunoglobulins in Serum of Ovarian Cancer Patients. J Proteome Res. 2016 Mar 4;15(3):1002-10. doi: 10.1021/acs.jproteome.5b01071. Epub 2016 Feb 24. PubMed PMID: 26813784; PubMed Central PMCID: PMC5637400.

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Syed R, Shibata NM, Kharbanda KK, Su RJ, Olson K, Yokoyama A, Rutledge JC, Chmiel KJ, Kim K, Halsted CH, Medici V. Effects of Nonpurified and Choline Supplemented or Nonsupplemented Purified Diets on Hepatic Steatosis and Methionine Metabolism in C3H Mice. Metab Syndr Relat Disord. 2016 May;14(4):202-9. doi: 10.1089/met.2015.0147. Epub 2016 Feb 16. PubMed PMID: 26881897; PubMed Central PMCID: PMC4841906.

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López-Domínguez JA, Cánovas Á, Medrano JF, Islas-Trejo A, Kim K, Taylor SL, Villalba JM, López-Lluch G, Navas P, Ramsey JJ. Omega-3 fatty acids partially revert the metabolic gene expression profile induced by long-term calorie restriction. Exp Gerontol. 2016 May;77:29-37. doi: 10.1016/j.exger.2016.02.002. Epub 2016 Feb 11. PubMed PMID: 26875793.

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Polage CR, Gyorke CE, Kennedy MA, Leslie JL, Chin DL, Wang S, Nguyen HH, Huang B, Tang YW, Lee LW, Kim K, Taylor S, Romano PS, Panacek EA, Goodell PB, Solnick JV, Cohen SH. Overdiagnosis of Clostridium difficile Infection in the Molecular Test Era. JAMA Intern Med. 2015 Nov;175(11):1792-801. doi: 10.1001/jamainternmed.2015.4114. PubMed PMID: 26348734; PubMed Central PMCID: PMC4948649.

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Ruhaak LR, Taylor SL, Stroble C, Nguyen UT, Parker EA, Song T, Lebrilla CB, Rom WN, Pass H, Kim K, Kelly K, Miyamoto S. Differential N-Glycosylation Patterns in Lung Adenocarcinoma Tissue. J Proteome Res. 2015 Nov 6;14(11):4538-49. doi: 10.1021/acs.jproteome.5b00255. Epub 2015 Sep 30. PubMed PMID: 26322380; PubMed Central PMCID: PMC4644186.

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Wilken R, Li CS, Sharon VR, Kim K, Patel FB, Patel F, Maverakis E. Topical clobetasol for the treatment of toxic epidermal necrolysis: study protocol for a randomized controlled trial. Trials. 2015 Aug 22;16:374. doi: 10.1186/s13063-015-0879-7. PubMed PMID: 26297574; PubMed Central PMCID: PMC4546316.

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Fahrmann JF, Kim K, DeFelice BC, Taylor SL, Gandara DR, Yoneda KY, Cooke DT, Fiehn O, Kelly K, Miyamoto S. Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer. Cancer Epidemiol Biomarkers Prev. 2015 Nov;24(11):1716-23. doi: 10.1158/1055-9965.EPI-15-0427. Epub 2015 Aug 17. PubMed PMID: 26282632; PubMed Central PMCID: PMC4633344.

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Hagopian K, Tomilov AA, Kim K, Cortopassi GA, Ramsey JJ. Key glycolytic enzyme activities of skeletal muscle are decreased under fed and fasted states in mice with knocked down levels of Shc proteins. PLoS One. 2015;10(4):e0124204. doi: 10.1371/journal.pone.0124204. eCollection 2015. PubMed PMID: 25880638; PubMed Central PMCID: PMC4400099.

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Miyamoto S, Taylor SL, Barupal DK, Taguchi A, Wohlgemuth G, Wikoff WR, Yoneda KY, Gandara DR, Hanash SM, Kim K, Fiehn O. Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry. Metabolites. 2015 Apr 9;5(2):192-210. doi: 10.3390/metabo5020192. PubMed PMID: 25859693; PubMed Central PMCID: PMC4495369.

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Enkhmaa B, Anuurad E, Zhang W, Kim K, Berglund L. Diverging trajectory patterns of systemic versus vascular inflammation over age in healthy Caucasians and African-Americans. Atherosclerosis. 2015 Apr;239(2):509-515. doi: 10.1016/j.atherosclerosis.2015.02.023. Epub 2015 Feb 16. PubMed PMID: 25710295; PubMed Central PMCID: PMC4361330.

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Wikoff WR, Grapov D, Fahrmann JF, DeFelice B, Rom WN, Pass HI, Kim K, Nguyen U, Taylor SL, Gandara DR, Kelly K, Fiehn O, Miyamoto S. Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma. Cancer Prev Res (Phila). 2015 May;8(5):410-8. doi: 10.1158/1940-6207.CAPR-14-0329. Epub 2015 Feb 5. PubMed PMID: 25657018; PubMed Central PMCID: PMC4618700.

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Maverakis E, Kim K, Shimoda M, Gershwin ME, Patel F, Wilken R, Raychaudhuri S, Ruhaak LR, Lebrilla CB. Glycans in the immune system and The Altered Glycan Theory of Autoimmunity: a critical review. J Autoimmun. 2015 Feb;57:1-13. doi: 10.1016/j.jaut.2014.12.002. Epub 2015 Jan 9. Review. PubMed PMID: 25578468; PubMed Central PMCID: PMC4340844.

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López-Domínguez JA, Ramsey JJ, Tran D, Imai DM, Koehne A, Laing ST, Griffey SM, Kim K, Taylor SL, Hagopian K, Villalba JM, López-Lluch G, Navas P, McDonald RB. The Influence of Dietary Fat Source on Life Span in Calorie Restricted Mice. J Gerontol A Biol Sci Med Sci. 2015 Oct;70(10):1181-8. doi: 10.1093/gerona/glu177. Epub 2014 Oct 13. PubMed PMID: 25313149; PubMed Central PMCID: PMC4612357.

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Wei A, Fascetti AJ, Kim K, Ramsey JJ. Post-castration variations in weight gain in a cohort of young adult male cats. J Nutr Sci. 2014;3:e37. doi: 10.1017/jns.2014.37. eCollection 2014. PubMed PMID: 26101606; PubMed Central PMCID: PMC4473175.

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Tomilov A, Bettaieb A, Kim K, Sahdeo S, Tomilova N, Lam A, Hagopian K, Connell M, Fong J, Rowland D, Griffey S, Ramsey J, Haj F, Cortopassi G. Shc depletion stimulates brown fat activity in vivo and in vitro. Aging Cell. 2014 Dec;13(6):1049-58. doi: 10.1111/acel.12267. Epub 2014 Sep 26. PubMed PMID: 25257068; PubMed Central PMCID: PMC4244234.

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Le A, Shibata NM, French SW, Kim K, Kharbanda KK, Islam MS, LaSalle JM, Halsted CH, Keen CL, Medici V. Characterization of timed changes in hepatic copper concentrations, methionine metabolism, gene expression, and global DNA methylation in the Jackson toxic milk mouse model of Wilson disease. Int J Mol Sci. 2014 May 7;15(5):8004-23. doi: 10.3390/ijms15058004. PubMed PMID: 24810691; PubMed Central PMCID: PMC4057715.

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Wei A, Fascetti AJ, Kim K, Lee A, Graham JL, Havel PJ, Ramsey JJ. Early effects of neutering on energy expenditure in adult male cats. PLoS One. 2014;9(2):e89557. doi: 10.1371/journal.pone.0089557. eCollection 2014. PubMed PMID: 24586869; PubMed Central PMCID: PMC3935885.

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Kim K, Ruhaak LR, Nguyen UT, Taylor SL, Dimapasoc L, Williams C, Stroble C, Ozcan S, Miyamoto S, Lebrilla CB, Leiserowitz GS. Evaluation of glycomic profiling as a diagnostic biomarker for epithelial ovarian cancer. Cancer Epidemiol Biomarkers Prev. 2014 Apr;23(4):611-21. doi: 10.1158/1055-9965.EPI-13-1073. Epub 2014 Feb 20. PubMed PMID: 24557531; PubMed Central PMCID: PMC4230493.

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Stern JH, Kim K, Ramsey JJ. The influence of shc proteins on the whole body energetic response to calorie restriction initiated in 3-month-old mice. ISRN Nutr. 2014;2014:562075. doi: 10.1155/2014/562075. eCollection 2014. PubMed PMID: 24967271; PubMed Central PMCID: PMC4045305.

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Kim K, Mall C, Taylor SL, Hitchcock S, Zhang C, Wettersten HI, Jones AD, Chapman A, Weiss RH. Mealtime, temporal, and daily variability of the human urinary and plasma metabolomes in a tightly controlled environment. PLoS One. 2014;9(1):e86223. doi: 10.1371/journal.pone.0086223. eCollection 2014. PubMed PMID: 24475090; PubMed Central PMCID: PMC3901684.

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Ramsey JJ, Tran D, Giorgio M, Griffey SM, Koehne A, Laing ST, Taylor SL, Kim K, Cortopassi GA, Lloyd KC, Hagopian K, Tomilov AA, Migliaccio E, Pelicci PG, McDonald RB. The influence of Shc proteins on life span in mice. J Gerontol A Biol Sci Med Sci. 2014 Oct;69(10):1177-85. doi: 10.1093/gerona/glt198. Epub 2013 Dec 14. PubMed PMID: 24336818; PubMed Central PMCID: PMC4172037.

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Taylor SL, Leiserowitz GS, Kim K. Accounting for undetected compounds in statistical analyses of mass spectrometry 'omic studies. Stat Appl Genet Mol Biol. 2013 Dec;12(6):703-22. doi: 10.1515/sagmb-2013-0021. PubMed PMID: 24246290; PubMed Central PMCID: PMC3905689.

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Medici V, Shibata NM, Kharbanda KK, Islam MS, Keen CL, Kim K, Tillman B, French SW, Halsted CH, LaSalle JM. Maternal choline modifies fetal liver copper, gene expression, DNA methylation, and neonatal growth in the tx-j mouse model of Wilson disease. Epigenetics. 2014 Feb;9(2):286-96. doi: 10.4161/epi.27110. Epub 2013 Nov 12. PubMed PMID: 24220304; PubMed Central PMCID: PMC3962539.

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Chen Y, Hagopian K, Bibus D, Villalba JM, López-Lluch G, Navas P, Kim K, Ramsey JJ. The influence of dietary lipid composition on skeletal muscle mitochondria from mice following eight months of calorie restriction. Physiol Res. 2014;63(1):57-71. doi: 10.33549/physiolres.932529. Epub 2013 Nov 1. PubMed PMID: 24182343; PubMed Central PMCID: PMC4138957.

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Ruhaak LR, Nguyen UT, Stroble C, Taylor SL, Taguchi A, Hanash SM, Lebrilla CB, Kim K, Miyamoto S. Enrichment strategies in glycomics-based lung cancer biomarker development. Proteomics Clin Appl. 2013 Oct;7(9-10):664-76. doi: 10.1002/prca.201200131. Epub 2013 Aug 6. PubMed PMID: 23640812; PubMed Central PMCID: PMC3884000.

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Ruhaak LR, Taylor SL, Miyamoto S, Kelly K, Leiserowitz GS, Gandara D, Lebrilla CB, Kim K. Chip-based nLC-TOF-MS is a highly stable technology for large-scale high-throughput analyses. Anal Bioanal Chem. 2013 May;405(14):4953-8. doi: 10.1007/s00216-013-6908-z. Epub 2013 Mar 23. PubMed PMID: 23525540; PubMed Central PMCID: PMC3640767.

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Medici V, Shibata NM, Kharbanda KK, LaSalle JM, Woods R, Liu S, Engelberg JA, Devaraj S, Török NJ, Jiang JX, Havel PJ, Lönnerdal B, Kim K, Halsted CH. Wilson's disease: changes in methionine metabolism and inflammation affect global DNA methylation in early liver disease. Hepatology. 2013 Feb;57(2):555-65. doi: 10.1002/hep.26047. Epub 2013 Jan 10. PubMed PMID: 22945834; PubMed Central PMCID: PMC3566330.

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Chen Y, Hagopian K, Bibus D, Villalba JM, López-Lluch G, Navas P, Kim K, McDonald RB, Ramsey JJ. The influence of dietary lipid composition on liver mitochondria from mice following 1 month of calorie restriction. Biosci Rep. 2012 Dec 13;33(1):83-95. doi: 10.1042/BSR20120060. PubMed PMID: 23098316; PubMed Central PMCID: PMC3522480.

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Stern JH, Kim K, Ramsey JJ. The influence of shc proteins and aging on whole body energy expenditure and substrate utilization in mice. PLoS One. 2012;7(11):e48790. doi: 10.1371/journal.pone.0048790. Epub 2012 Nov 7. PubMed PMID: 23144971; PubMed Central PMCID: PMC3492242.

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Hunsaker MR, Kim K, Willemsen R, Berman RF. CGG trinucleotide repeat length modulates neural plasticity and spatiotemporal processing in a mouse model of the fragile X premutation. Hippocampus. 2012 Dec;22(12):2260-75. doi: 10.1002/hipo.22043. Epub 2012 Jun 18. PubMed PMID: 22707411; PubMed Central PMCID: PMC3449027.

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Hagopian K, Tomilov AA, Tomilova N, Kim K, Taylor SL, Lam AK, Cortopassi GA, McDonald RB, Ramsey JJ. Shc proteins influence the activities of enzymes involved in fatty acid oxidation and ketogenesis. Metabolism. 2012 Dec;61(12):1703-13. doi: 10.1016/j.metabol.2012.05.007. Epub 2012 Jun 7. PubMed PMID: 22683097; PubMed Central PMCID: PMC3442136.

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Ganti S, Taylor SL, Abu Aboud O, Yang J, Evans C, Osier MV, Alexander DC, Kim K, Weiss RH. Kidney tumor biomarkers revealed by simultaneous multiple matrix metabolomics analysis. Cancer Res. 2012 Jul 15;72(14):3471-9. doi: 10.1158/0008-5472.CAN-11-3105. Epub 2012 May 24. PubMed PMID: 22628425; PubMed Central PMCID: PMC3399039.

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Nagata N, Matsuo K, Bettaieb A, Bakke J, Matsuo I, Graham J, Xi Y, Liu S, Tomilov A, Tomilova N, Gray S, Jung DY, Ramsey JJ, Kim JK, Cortopassi G, Havel PJ, Haj FG. Hepatic Src homology phosphatase 2 regulates energy balance in mice. Endocrinology. 2012 Jul;153(7):3158-69. doi: 10.1210/en.2012-1406. Epub 2012 May 22. PubMed PMID: 22619361; PubMed Central PMCID: PMC3380313.

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Stern JH, Kim K, Ramsey JJ. The influence of acute, late-life calorie restriction on whole body energy metabolism in p66Shc(-/-) mice. Mech Ageing Dev. 2012 Jun;133(6):414-20. doi: 10.1016/j.mad.2012.05.001. Epub 2012 May 12. PubMed PMID: 22588161; PubMed Central PMCID: PMC3389126.

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Gungor Z, Anuurad E, Enkhmaa B, Zhang W, Kim K, Berglund L. Apo E4 and lipoprotein-associated phospholipase A2 synergistically increase cardiovascular risk. Atherosclerosis. 2012 Jul;223(1):230-4. doi: 10.1016/j.atherosclerosis.2012.04.021. Epub 2012 May 8. PubMed PMID: 22632920; PubMed Central PMCID: PMC3389284.

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Comerford KB, Almario RU, Kim K, Karakas SE. Lean mass and insulin resistance in women with polycystic ovary syndrome. Metabolism. 2012 Sep;61(9):1256-60. doi: 10.1016/j.metabol.2012.02.004. Epub 2012 Mar 17. PubMed PMID: 22424820.

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Diep AA, Hunsaker MR, Kwock R, Kim K, Willemsen R, Berman RF. Female CGG knock-in mice modeling the fragile X premutation are impaired on a skilled forelimb reaching task. Neurobiol Learn Mem. 2012 Feb;97(2):229-34. doi: 10.1016/j.nlm.2011.12.006. Epub 2011 Dec 21. PubMed PMID: 22202169; PubMed Central PMCID: PMC3278548.

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Weiss RH, Kim K. Metabolomics in the study of kidney diseases. Nat Rev Nephrol. 2011 Oct 25;8(1):22-33. doi: 10.1038/nrneph.2011.152. Review. PubMed PMID: 22025087.

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Ganti S, Taylor SL, Kim K, Hoppel CL, Guo L, Yang J, Evans C, Weiss RH. Urinary acylcarnitines are altered in human kidney cancer. Int J Cancer. 2012 Jun 15;130(12):2791-800. doi: 10.1002/ijc.26274. Epub 2011 Sep 14. PubMed PMID: 21732340; PubMed Central PMCID: PMC3258465.

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Anuurad E, Enkhmaa B, Gungor Z, Zhang W, Tracy RP, Pearson TA, Kim K, Berglund L. Age as a modulator of inflammatory cardiovascular risk factors. Arterioscler Thromb Vasc Biol. 2011 Sep;31(9):2151-6. doi: 10.1161/ATVBAHA.111.232348. Epub 2011 Jun 23. PubMed PMID: 21700927; PubMed Central PMCID: PMC3158295.

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Vargas ML, Almario RU, Buchan W, Kim K, Karakas SE. Metabolic and endocrine effects of long-chain versus essential omega-3 polyunsaturated fatty acids in polycystic ovary syndrome. Metabolism. 2011 Dec;60(12):1711-8. doi: 10.1016/j.metabol.2011.04.007. Epub 2011 Jun 2. PubMed PMID: 21640360; PubMed Central PMCID: PMC3210884.

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Taylor SL, Kim K. A jackknife and voting classifier approach to feature selection and classification. Cancer Inform. 2011 Apr 27;10:133-47. doi: 10.4137/CIN.S7111. PubMed PMID: 21584263; PubMed Central PMCID: PMC3091410.

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Hunsaker MR, von Leden RE, Ta BT, Goodrich-Hunsaker NJ, Arque G, Kim K, Willemsen R, Berman RF. Motor deficits on a ladder rung task in male and female adolescent and adult CGG knock-in mice. Behav Brain Res. 2011 Sep 12;222(1):117-21. doi: 10.1016/j.bbr.2011.03.039. Epub 2011 Mar 31. PubMed PMID: 21440572; PubMed Central PMCID: PMC3095688.

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Kim K, Taylor SL, Ganti S, Guo L, Osier MV, Weiss RH. Urine metabolomic analysis identifies potential biomarkers and pathogenic pathways in kidney cancer. OMICS. 2011 May;15(5):293-303. doi: 10.1089/omi.2010.0094. Epub 2011 Feb 24. PubMed PMID: 21348635; PubMed Central PMCID: PMC3125558.

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Kalgaonkar S, Almario RU, Gurusinghe D, Garamendi EM, Buchan W, Kim K, Karakas SE. Differential effects of walnuts vs almonds on improving metabolic and endocrine parameters in PCOS. Eur J Clin Nutr. 2011 Mar;65(3):386-93. doi: 10.1038/ejcn.2010.266. Epub 2010 Dec 15. PubMed PMID: 21157477.

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Tomilov AA, Ramsey JJ, Hagopian K, Giorgio M, Kim KM, Lam A, Migliaccio E, Lloyd KC, Berniakovich I, Prolla TA, Pelicci P, Cortopassi GA. The Shc locus regulates insulin signaling and adiposity in mammals. Aging Cell. 2011 Feb;10(1):55-65. doi: 10.1111/j.1474-9726.2010.00641.x. Epub 2010 Nov 15. PubMed PMID: 21040401; PubMed Central PMCID: PMC4157392.

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Kim K, Zakharkin SO, Allison DB. Expectations, validity, and reality in gene expression profiling. J Clin Epidemiol. 2010 Sep;63(9):950-9. doi: 10.1016/j.jclinepi.2010.02.018. Epub 2010 Jun 25. Review. PubMed PMID: 20579843; PubMed Central PMCID: PMC2910173.