Publication

  1. Kachman M, Habra H, Duren W, Wigginton J, Sajjakulnukit P, Michailidis G,Burant C, Karnovsky A. Deep annotation of untargeted LC-MS metabolomics data with Binner. Bioinformatics. 2019 Oct 23. pii: btz798. doi: 10.1093/bioinformatics/btz798. [Epub ahead of print] PubMed PMID: 31642507.
  2. Wilinski D, Winzeler J, Duren W, Persons JL, Holme KJ, Mosquera J, Khabiri M, Kinchen JM, Freddolino PL, Karnovsky A, Dus M. Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster. Nat Commun. 2019 Sep 6;10(1):4052. doi: 10.1038/s41467-019-11933-z. PubMed PMID: 31492856; PubMed Central PMCID: PMC6731244.
  3. Evans CR, Karnovsky A, Puskarich MA, Michailidis G, Jones AE, Stringer KA. Untargeted Metabolomics Differentiates l-Carnitine Treated Septic Shock 1-Year Survivors and Nonsurvivors. J Proteome Res. 2019 May 3;18(5):2004-2011. doi: 10.1021/acs.jproteome.8b00774. Epub 2019 Apr 1. PubMed PMID: 30895797; PubMed Central PMCID: PMC6501183.
  4. Ma J, Karnovsky A, Afshinnia F, Wigginton J, Rader DJ, Natarajan L, Sharma K, Porter AC, Rahman M, He J, Hamm L, Shafi T, Gipson D, Gadegbeku C, Feldman H, Michailidis G, Pennathur S. Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease. Bioinformatics. 2019 Sep 15;35(18):3441-3452. doi: 10.1093/bioinformatics/btz114. PubMed PMID: 30887029; PubMed Central PMCID: PMC6748777.
  5. Ward KM, Yeoman L, McHugh C, Kraal AZ, Flowers SA, Rothberg AE, Karnovsky A, Das AK, Ellingrod VL, Stringer KA. Atypical Antipsychotic Exposure May Not Differentiate Metabolic Phenotypes of Patients with Schizophrenia. Pharmacotherapy. 2018 Jun;38(6):638-650. doi: 10.1002/phar.2119. PubMed PMID: 29722909; PubMed Central PMCID: PMC6014920.
  6. Afshinnia F, Rajendiran TM, Wernisch S, Soni T, Jadoon A, Karnovsky A, Michailidis G, Pennathur S. Lipidomics and Biomarker Discovery in Kidney Disease. Semin Nephrol. 2018 Mar;38(2):127-141. doi: 10.1016/j.semnephrol.2018.01.004. Review. PubMed PMID: 29602396; PubMed Central PMCID: PMC5881936.
  7. Puskarich MA, Evans CR, Karnovsky A, Das AK, Jones AE, Stringer KA. Septic Shock Nonsurvivors Have Persistently Elevated Acylcarnitines Following Carnitine Supplementation. Shock. 2018 pr;49(4):412-419. doi: 10.1097/SHK.0000000000000997. PubMed PMID: 29384504; PubMed Central PMCID: PMC5847421.
  8. Jin M, Fuller GG, Han T, Yao Y, Alessi AF, Freeberg MA, Roach NP, Moresco JJ, Karnovsky A, Baba M, Yates JR 3rd, Gitler AD, Inoki K, Klionsky DJ, Kim JK. Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress. Cell Rep. 2017 Jul 25;20(4):895-908. doi: 10.1016/j.celrep.2017.06.082. PubMed PMID: 28746874; PubMed Central PMCID: PMC5586494.
  9. Afshinnia F, Rajendiran TM, Karnovsky A, Soni T, Wang X, Xie D, Yang W, Shafi T, Weir MR, He J, Brecklin CS, Rhee EP, Schelling JR, Ojo A, Feldman H, Michailidis G, Pennathur S. Lipidomic Lipidomic Signature of Progression of Chronic Kidney Disease in the Chronic Renal Insufficiency Cohort. Kidney Int Rep. 2016 Nov;1(4):256-268. doi: 10.1016/j.ekir.2016.08.007. Epub 2016 Aug 18. Erratum in: Kidney Int Rep. 2017 Sep 18;2(6):1265. PubMed PMID: 28451650; PubMed Central PMCID: MC5402253.
  10. Basu S, Duren W, Evans CR, Burant CF, Michailidis G, Karnovsky A. Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data. Bioinformatics. 2017 May 15;33(10):1545-1553. doi: 10.1093/bioinformatics/btx012. PubMed PMID: 28137712; PubMed Central PMCID: PMC5860222.
  11. Stringer KA, McKay RT, Karnovsky A, Quémerais B, Lacy P. Metabolomics and Its Application to Acute Lung Diseases. Front Immunol. 2016 Feb 29;7:44. doi: 10.3389/fimmu.2016.00044. eCollection 2016. Review. PubMed PMID: 26973643; PubMed Central PMCID: PMC4770032.
  12. Cavalcante RG, Patil S, Weymouth TE, Bendinskas KG, Karnovsky A, Sartor MA. ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. Bioinformatics. 2016 May 15;32(10):1536-43. doi: 10.1093/bioinformatics/btw016. Epub 2016 Jan 21. PubMed PMID: 26794319; PubMed Central PMCID: PMC5860403.
  13. Stringer KA, Younger JG, McHugh C, Yeomans L, Finkel MA, Puskarich MA, Jones AE, Trexel J, Karnovsky A. Whole Blood Reveals More Metabolic Detail of the Human Metabolome than Serum as Measured by 1H-NMR Spectroscopy: Implications for Sepsis Metabolomics. Shock. 2015 Sep;44(3):200-8. doi: 10.1097/SHK.0000000000000406. PubMed PMID: 26009817; PubMed Central PMCID: PMC4537695.
  14. Sas KM, Karnovsky A, Michailidis G, Pennathur S. Metabolomics and diabetes: analytical and computational approaches. Diabetes. 2015 Mar;64(3):718-32. doi: 10.2337/db14-0509. Review. PubMed PMID: 25713200; PubMed Central PMCID: PMC4338589.
  15. Lee JS, Wu Y, Schnepp P, Fang J, Zhang X, Karnovsky A, Woods J, Stemmer PM, Liu M, Zhang K, Chen X. Proteomics analysis of rough endoplasmic reticulum in pancreatic beta cells. Proteomics. 2015 May;15(9):1508-11. doi: 10.1002/pmic.201400345. PubMed PMID: 25546123; PubMed Central PMCID: PMC4489703.
  16. Puskarich MA, Finkel MA, Karnovsky A, Jones AE, Trexel J, Harris BN, Stringer KA. Pharmacometabolomics of l-carnitine treatment response phenotypes in patients with septic shock. Ann Am Thorac Soc. 2015 Jan;12(1):46-56. doi: 10.1513/AnnalsATS.201409-415OC. PubMed PMID: 25496487; PubMed Central PMCID: PMC4342803.
  17. Duren W, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A. MetDisease--connecting metabolites to diseases via literature. Bioinformatics. 2014 Aug 1;30(15):2239-41. doi: 10.1093/bioinformatics/btu179. Epub 2014 Apr 8. PubMed PMID: 24713438; PubMed Central PMCID: PMC4103594.
  18. Reka AK, Chen G, Jones RC, Amunugama R, Kim S, Karnovsky A, Standiford TJ, Beer DG, Omenn GS, Keshamouni VG. Epithelial-mesenchymal transition-associated secretory phenotype predicts survival in lung cancer patients. Carcinogenesis. 2014 Jun;35(6):1292-300. doi: 10.1093/carcin/bgu041. Epub 2014 Feb 7. PubMed PMID: 24510113; PubMed Central PMCID: PMC4043235.
  19. Lacy P, McKay RT, Finkel M, Karnovsky A, Woehler S, Lewis MJ, Chang D, Stringer KA. Signal intensities derived from different NMR probes and parameters contribute to variations in quantification of metabolites. PLoS One. 2014 Jan 21;9(1):e85732. doi: 10.1371/journal.pone.0085732. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e102929. PubMed PMID: 24465670; PubMed Central PMCID: PMC3897511.
  20. Evans CR, Karnovsky A, Kovach MA, Standiford TJ, Burant CF, Stringer KA. Untargeted LC-MS metabolomics of bronchoalveolar lavage fluid differentiates acute respiratory distress syndrome from health. J Proteome Res. 2014 Feb 7;13(2):640-9. doi: 10.1021/pr4007624. Epub 2013 Dec 9. PubMed PMID: 24289193; PubMed Central PMCID: PMC4068805.
  21. Kim JH, Karnovsky A, Mahavisno V, Weymouth T, Pande M, Dolinoy DC, Rozek LS, Sartor MA. LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types. BMC Genomics. 2012 Oct 4;13:526. doi: 10.1186/1471-2164-13-526. PubMed PMID: 23033966; PubMed Central PMCID: PMC3505188.
  22. McEachin RC, Sannareddy KS, Cavalcoli JD, Karnovsky A, Vink JM, Sartor MA. Convergence of genetic influences in comorbidity. BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S8. doi: 0.1186/1471-2105-13-S2-S8. PubMed PMID: 22536871; PubMed Central PMCID: PMC3375629.
  23. Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B, Karnovsky A. Metab2MeSH: nnotating compounds with medical subject headings. Bioinformatics. 2012 May 15;28(10):1408-10. doi: 10.1093/bioinformatics/bts156. Epub 2012 Apr 6. PubMed PMID: 22492643; PubMed Central PMCID: PMC3348562.
  24. Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS. Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. Bioinformatics. 2012 Feb 1;28(3):373-80. doi: 10.1093/bioinformatics/btr661. Epub 2011 Nov 30. PubMed PMID: 22135418; PubMed Central PMCID: PMC3268237.
  25. Chen X, Karnovsky A, Sans MD, Andrews PC, Williams JA. Molecular characterization of the endoplasmic reticulum: insights from proteomic studies. Proteomics. 2010 Nov;10(22):4040-52. doi: 10.1002/pmic.201000234. Epub 2010 Nov 2. Review. PubMed PMID: 21080494; PubMed Central PMCID: PMC3517137.
  26. Stringer KA, Serkova NJ, Karnovsky A, Guire K, Paine R 3rd, Standiford TJ. Metabolic consequences of sepsis-induced acute lung injury revealed by plasma ¹H-nuclear magnetic resonance quantitative metabolomics and computational analysis. Am J Physiol Lung Cell Mol Physiol. 2011 Jan;300(1):L4-L11. doi: 10.1152/ajplung.00231.2010. Epub 2010 Oct 1. PubMed PMID: 20889676; PubMed Central PMCID: PMC3023293.
  27. Gao J, Tarcea VG, Karnovsky A, Mirel BR, Weymouth TE, Beecher CW, Cavalcoli JD, Athey BD, Omenn GS, Burant CF, Jagadish HV. Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Bioinformatics. 2010 Apr ;26(7):971-3. doi: 10.1093/bioinformatics/btq048. Epub 2010 Feb 7. PubMed PMID: 20139469; PubMed Central PMCID: PMC2844990.
  28. Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics. 2010 Feb 15;26(4):456-63. doi: 0.1093/bioinformatics/btp683. Epub 2009 Dec 9. PubMed PMID: 20007254; PubMed Central PMCID: PMC2852214.
  29. Chen X, Sans MD, Strahler JR, Karnovsky A, Ernst SA, Michailidis G, Andrews PC, Williams JA. Quantitative organellar proteomics analysis of rough endoplasmic reticulum from normal and acute pancreatitis rat pancreas. J Proteome Res. 2010 Feb 5;9(2):885-96. doi: 10.1021/pr900784c. PubMed PMID: 19954227; PubMed Central PMCID: PMC2818835.
  30. Miller JR, Dunham S, Mochalkin I, Banotai C, Bowman M, Buist S, Dunkle B, Hanna D, Harwood HJ, Huband MD, Karnovsky A, Kuhn M, Limberakis C, Liu JY, Mehrens S, Mueller WT, Narasimhan L, Ogden A, Ohren J, Prasad JV, Shelly JA, Skerlos L, Sulavik M, Thomas VH, VanderRoest S, Wang L, Wang Z, Whitton A, Zhu T, Stover CK. A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1737-42. doi: 10.1073/pnas.0811275106. Epub 2009 Jan 22. PubMed PMID: 19164768; PubMed Central PMCID: PMC2644107.
  31. Karnovsky AM, Gotow LF, McKinley DD, Piechan JL, Ruble CL, Mills CJ, Schellin KA, Slightom JL, Fitzgerald LR, Benjamin CW, Roberds SL. A cluster of novel serotonin receptor 3-like genes on human chromosome 3. Gene. 2003 Nov 13;319:137-48. PubMed PMID: 14597179.
  32. Karnovsky A, Klymkowsky MW. Anterior axis duplication in Xenopus induced by the over-expression of the cadherin-binding protein plakoglobin. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4522-6. PubMed PMID: 7753837; PubMed Central PMCID: PMC41976.
  33. Klymkowsky MW, Karnovsky A. Morphogenesis and the cytoskeleton: studies of the Xenopus embryo. Dev Biol. 1994 Oct;165(2):372-84. Review. PubMed PMID: 7525386.