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Publications | Clinical Systems Biology Group

Please find below a list by topic or in chronological order of the Clinical Systems Biology Group publications.

2014

  • A role for homeostatic drive in the perpetuation of complex chronic illness: gulf war illness and chronic fatigue syndrome. Craddock TJ, Fritsch P, Rice MA Jr, Del Rosario RM, Miller DB, Fletcher MA, Klimas NG, Broderick G. PLoS One. 2014 Jan 8;9(1):e84839. doi:10.1371/journal.pone.0084839. PMID: 24416298

2013

  • A comparison of sex-specific immune signatures in Gulf War illness and chronic fatigue syndrome. Smylie AL, Broderick G, Fernandes H, Razdan S, Barnes Z, Collado F, Sol C, Fletcher MA, Klimas N. BMC Immunol. 2013 Jun 25;14:29. doi: 10.1186/1471-2172-14-29. PMID: 23800166
  • Altered immune pathway activity under exercise challenge in Gulf War Illness: an exploratory analysis. Broderick G, Ben-Hamo R, Vashishtha S, Efroni S, Nathanson L, Barnes Z, Fletcher MA, Klimas N. Brain Behav Immun. 2013 Feb;28:159-69. doi: 10.1016/j.bbi.2012.11.007. Epub 2012 Nov 29. PMID: 23201588
  • Systems biology of complex symptom profiles: capturing interactivity across behavior, brain and immune regulation. Broderick G, Craddock TJ. Brain Behav Immun. 2013 Mar;29:1-8. doi: 10.1016/j.bbi.2012.09.008. Epub 2012 Sep 28. Review. PMID: 23022717

2012

  • Cytokine expression profiles of immune imbalance in post-mononucleosis chronic fatigue. Broderick G, Katz BZ, Fernandes H, Fletcher MA, Klimas N, Smith FA, O'Gorman MR, Vernon SD, Taylor R. J Transl Med. 2012 Sep 13;10:191. doi: 10.1186/1479-5876-10-191. PMID: 22973830
  • Psychoneuroimmunology and natural killer cells: the chromium release whole blood assay. Fletcher MA, Barnes Z, Broderick G, Klimas NG. Methods Mol Biol. 2012;934:313-24. doi: 10.1007/978-1-62703-071-7_16. PMID: 22933153
  • Exploring the diagnostic potential of immune biomarker coexpression in Gulf War Illness. Broderick G, Fletcher MA, Gallagher M, Barnes Z, Vernon SD, Klimas NG. Methods Mol Biol. 2012;934:145-64. doi: 10.1007/978-1-62703-071-7_8. PMID: 22933145
  • Biomarkers for chronic fatigue. Klimas NG, Broderick G, Fletcher MA. Brain Behav Immun. 2012 Nov;26(8):1202-10. doi: 10.1016/j.bbi.2012.06.006. Epub 2012 Jun 23. Review. PMID: 22732129
  • Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin. Tuszynski JA, Craddock TJ, Mane JY, Barakat K, Tseng CY, Gajewski M, Winter P, Alisaraie L, Patterson J, Carpenter E, Wang W, Deyholos MK, Li L, Sun X, Zhang Y, Wong GK. Pharm Res. 2012 Nov;29(11):3007-21. doi: 10.1007/s11095-012-0829-y. PMID: 22833053
  • Computational predictions of volatile anesthetic interactions with the microtubule cytoskeleton: implications for side effects of general anesthesia. Craddock TJ, St George M, Freedman H, Barakat KH, Damaraju S, Hameroff S, Tuszynski JA. PLoS One. 2012;7(6):e37251. doi: 10.1371/journal.pone.0037251. PMID: 22761654
  • The zinc dyshomeostasis hypothesis of Alzheimer's disease. Craddock TJ, Tuszynski JA, Chopra D, Casey N, Goldstein LE, Hameroff SR, Tanzi RE. PLoS One. 2012;7(3):e33552. doi: 10.1371/journal.pone.0033552. PMID: 22457776
  • Cytoskeletal signaling: is memory encoded in microtubule lattices by CaMKII phosphorylation? Craddock TJ, Tuszynski JA, Hameroff S. PLoS Comput Biol. 2012;8(3):e1002421. doi: 10.1371/journal.pcbi.1002421. PMID: 22412364
  • An investigation of the plausibility of stochastic resonance in tubulin dimers. Saha AA, Craddock TJ, Tuszynski JA. Biosystems. 2012 Feb;107(2):81-7. doi: 10.1016/j.biosystems.2011.09.005. PMID: 22001523
  • Molecular Models of Information Processing at the Level of Individual Neurons and Their Significance. Craddock TJA, Tuszynski JA.  J Paritantra - J Syst Sci Eng 2012; 20(1): 15-31.

2011

  • Myalgic encephalomyelitis: International Consensus Criteria.  Carruthers BM, van de Sande MI, De Meirleir KL, Klimas NG, Broderick G, Mitchell T, Staines D, Powles AC, Speight N, Vallings R, Bateman L, Baumgarten-Austrheim B, Bell DS, Carlo-Stella N, Chia J, Darragh A, Jo D, Lewis D, Light AR, Marshall-Gradisbik S, Mena I, Mikovits JA, Miwa K, Murovska M, Pall ML, Stevens S.  J Intern Med. 2011 Oct;270(4):327-38. doi: 10.1111/j.1365-2796.2011.02428.x. Epub 2011 Aug 22. Review. PMID: 21777306
  • Using an agent-based model to analyze the dynamic communication network of the immune response. Folcik VA, Broderick G, Mohan S, Block B, Ekbote C, Doolittle J, Khoury M, Davis L, Marsh CB. Theor Biol Med Model. 2011 Jan 19;8:1. doi: 10.1186/1742-4682-8-1. PMID: 21247471
  • A pilot study of immune network remodeling under challenge in Gulf War Illness. Broderick G, Kreitz A, Fuite J, Fletcher MA, Vernon SD, Klimas N. Brain Behav Immun. 2011 Feb;25(2):302-13. doi: 10.1016/j.bbi.2010.10.011. Epub 2010 Oct 16. PMID: 20955779

2010

  • A formal analysis of cytokine networks in chronic fatigue syndrome. Broderick G, Fuite J, Kreitz A, Vernon SD, Klimas N, Fletcher MA. Brain Behav Immun. 2010 Oct;24(7):1209-17. doi: 10.1016/j.bbi.2010.04.012. Epub 2010 May 4. PMID: 20447453
  • Plasma neuropeptide Y: a biomarker for symptom severity in chronic fatigue syndrome. Fletcher MA, Rosenthal M, Antoni M, Ironson G, Zeng XR, Barnes Z, Harvey JM, Hurwitz B, Levis S, Broderick G, Klimas NG. Behav Brain Funct. 2010 Dec 29;6:76. doi: 10.1186/1744-9081-6-76. PMID: 21190576
  • Biomarkers in chronic fatigue syndrome: evaluation of natural killer cell function and dipeptidyl peptidase IV/CD26. Fletcher MA, Zeng XR, Maher K, Levis S, Hurwitz B, Antoni M, Broderick G, Klimas NG. PLoS One. 2010 May 25;5(5):e10817. doi: 10.1371/journal.pone.0010817. PMID: 20520837
  • A formal analysis of cytokine networks in chronic fatigue syndrome.  Broderick G, Fuite J, Kreitz A, Vernon SD, Klimas N, Fletcher MA. Brain Behav Immun. 2010 Oct;24(7):1209-17. doi: 10.1016/j.bbi.2010.04.012. Epub 2010 May 4. PMID: 20447453
  • "Memory bytes" - molecular match for CaMKII phosphorylation encoding of microtubule lattices. Hameroff SR, Craddock TJ, Tuszynski JA. J Integr Neurosci. 2010 Sep;9(3):253-67. PMID: 21064217
  • Microtubule ionic conduction and its implications for higher cognitive functions. Craddock TJ, Tuszynski JA, Priel A, Freedman H. J Integr Neurosci. 2010 Jun;9(2):103-22. Review. PMID: 20589950
  • A critical assessment of the information processing capabilities of neuronal microtubules using coherent excitations. Craddock TJ, Tuszynski JA. J Biol Phys. 2010 Jan;36(1):53-70. doi: 10.1007/s10867-009-9158-8. PMID: 19669419
  • Neuropsychiatric Illness: A Case for Impaired Neuroplasticity and Possible Quantum Processing Derailment in Microtubules. Woolf NJ, Craddock TJA, Friesen DE, Tuszynski JA.  NeuroQuant 2010; 8(1): 13-28.

2009

  • Model-based therapeutic correction of hypothalamic-pituitary-adrenal axis dysfunction.
    Ben-Zvi A, Vernon SD, Broderick G. PLoS Comput Biol. 2009 Jan;5(1):e1000273. doi: 10.1371/journal.pcbi.1000273. Epub 2009 Jan 23. PMID:19165314
  • Information processing mechanisms in microtubules at physiological temperature: Model predictions for experimental tests. Craddock TJ, Beauchemin C, Tuszynski JA.Biosystems. 2009 Jul;97(1):28-34. doi: 10.1016/j.biosystems.2009.04.001. PMID: 19477062

2008

  • Evidence of inflammatory immune signaling in chronic fatigue syndrome: A pilot study of gene expression in peripheral blood. Aspler AL, Bolshin C, Vernon SD, Broderick G. Behav Brain Funct. 2008 Sep 26;4:44. doi: 10.1186/1744-9081-4-44. PMID: 18822143
  • Neuroendocrine and immune network re-modeling in chronic fatigue syndrome: an exploratory analysis. Fuite J, Vernon SD, Broderick G. Genomics. 2008 Dec;92(6):393-9. doi: 10.1016/j.ygeno.2008.08.008. Epub 2008 Oct 1. PMID: 18775774
  • Extraction of elementary rate constants from global network analysis of E. coli central metabolism. Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M. BMC Syst Biol. 2008 May 7;2:41. doi: 10.1186/1752-0509-2-41. PMID: 18462493
  • Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Ridgway D, Broderick G, Lopez-Campistrous A, Ru'aini M, Winter P, Hamilton M, Boulanger P, Kovalenko A, Ellison MJ. Biophys J. 2008 May 15;94(10):3748-59. doi: 10.1529/biophysj.107.116053. Epub 2008 Jan 30. Erratum in: Biophys J. 2009 Mar 18;96(6):2548. PMID: 18234819
  • Bioferroelectricity at the Nanoscale. Tuszynski JA, Craddock TJA, Carpenter RJ.  J Theor Comput Nanosci 2008; 5: 2022-2032.

2007

  • Microarray analysis of rejection in human kidney transplants using pathogenesis-based transcript sets. Mueller TF, Einecke G, Reeve J, Sis B, Mengel M, Jhangri GS, Bunnag S, Cruz J, Wishart D, Meng C, Broderick G, Kaplan B, Halloran PF. Am J Transplant. 2007 Dec;7(12):2712-22.  PMID: 17941957
  • Transcriptome analysis reveals heterogeneity in the injury response of kidney transplants. Famulski KS, Broderick G, Einecke G, Hay K, Cruz J, Sis B, Mengel M, Halloran PF. Am J Transplant. 2007 Nov;7(11):2483-95. PMID: 17908279
  • Early loss of renal transcripts in kidney allografts: relationship to the development of histologic lesions and alloimmune effector mechanisms. Einecke G, Broderick G, Sis B, Halloran PF. Am J Transplant. 2007 May;7(5):1121-30. PMID: 17456200
  • On the Role of the Microtubules in Cognitive Brain Functions. Craddock TJA, Tuszynski JA. NeuroQuant 2007; 5(1): 32-57.

2006

  • Accommodating space, time and randomness in network simulation. Ridgway D, Broderick G, Ellison MJ. Curr Opin Biotechnol. 2006 Oct;17(5):493-8. Epub 2006 Sep 8. Review. PMID: 16962764
  • Exploration of statistical dependence between illness parameters using the entropy correlation coefficient. Craddock RC, Taylor R, Broderick G, Whistler T, Klimas N, Unger ER. Pharmacogenomics. 2006 Apr;7(3):421-8. PMID: 16610952
  • Identifying illness parameters in fatiguing syndromes using classical projection methods. Broderick G, Craddock RC, Whistler T, Taylor R, Klimas N, Unger ER. Pharmacogenomics. 2006 Apr;7(3):407-19. PMID: 16610951
  • Gene expression correlates of unexplained fatigue. Whistler T, Taylor R, Craddock RC, Broderick G, Klimas N, Unger ER. Pharmacogenomics. 2006 Apr;7(3):395-405. PMID: 16610950
  • The Realistic Modelling of Biological Systems: A Workshop Synopsis. Broderick G, Rubin E. ComPlexUs.  2006; 3:217–230.

2005

  • A life-like virtual cell membrane using discrete automata. Broderick G, Ru'aini M, Chan E, Ellison MJ. In Silico Biol. 2005;5(2):163-78. PMID: 15972012
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