Webcasts and Publications From Clinical Systems Biology

Book Chapters

• Toole JT, Rice MA Jr., Craddock TJA, Nierenberg B, Klimas NG, Fletcher MA, Zysman J, Morris M, Broderick G. Breaking away: the role of homeostatic drive in perpetuating depression. In: Yan Q. (Ed.), Psychoneuroimmunology: Methods and Protocols 2nd Ed. (Methods in Molecular Biology), Springer, New York, NY, 2018; 1781: 121-144.
• Toole JT, Rice MA jr., Nierenberg B, Craddock TJA, Fletcher MA, Klimas NG, Zysman J, Morris M, Broderick G. Increasing Resilience to Traumatic Events: Simulating the Protective Role of Well-Being. In: Yan Q. (Ed.), Psychoneuroimmunology: Methods and Protocols 2nd Ed. (Methods in Molecular Biology), Springer, New York, NY, 2018; 1781: 87-100.
• Broderick G, Fletcher MA, Gallgher M, Barnes Z, Vernon SD, Klimas NG. Exploring the Diagnostic Potential of Immune Biomarker Coexpression in Gulf War Illness. In: Yan Q. (Ed.), Psychoneuroimmunology: Methods and Protocols (Methods in Molecular Biology), Springer, New York, NY, 2012 (2017 Ed. 2), Part II, Chap. 8: 145-164.
• Fletcher MA, Barnes Z, Broderick G, Klimas NG. Psychoneuroimmunology and Natural Killer Cells: The Chromium Release Whole Blood Assay. In: Yan Q. (Ed.), Psychoneuroimmunology: Methods and Protocols (Methods in Molecular Biology), Springer, New York, NY, 2012 (2017 Ed. 2), Part III, Chap. 16: 313-324.

Journal Publications

2018

• Ashbrook DG, Hing B, Michalovicz LT, Kelly KA, Miller JV, De Vega W, Miller DB, Broderick G, O’Callaghan J, McGowan PO. Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War Illness. J Neuroinflammation. 2018 Mar 17;15(1):86.
• Sedghamiz H, Morris M, Craddock TJA, Whitley D, Broderick G. High-fidelity discrete modeling of the HPA axis: A study of regulatory plasticity in biology. BMC Sys Biol. 2018, 12: 76.
• Craddock TJA, Michalovicz L, Kelly KA, Rice MA Jr., Miller DB, Klimas NG, Morris M, O’Callaghan J, Broderick G. A Logic Model of Neuronal-Glial Interaction Suggests Altered Homeostatic Regulation in the Perpetuation of Chronic Neuroinflammation. Frontiers in Cellular Neuroscience. 2018, 12: 336.
• Jaundoo R, Bohmann J, Gutierez G, Klimas NG, Broderick G, Craddock TJA. Using a Consensus Docking Approach to Predict Adverse Drug Reactions in Combination Drug Therapies in Gulf War Illness. Int J Mol Sci. 2018, 19: 3355.
• Shinn E, Broderick G, Harris B, Fellman B, Urbauer D, Moulder S, Paterson D, Archer J, Hernandez L, Johnson A, Symmans WF. Simulating time-dependent patterns of breast cancer patients' nonadherence from adjuvant oral endocrine therapy. JCO Clinical Cancer Informatics, 2018, In Press.

2017

• Sedghamiz H, Chen W, Rice M Jr., Whitley D, Broderick G. Selecting Optimal Models Based on Efficiency and Robustness in Multi-valued Biological Networks, 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE), 2017, 00(0): 200-205.(https://www.computer.org/csdl/proceedings/bibe/2017/1324/00/132401a200-abs.html)
• Barker T, Russo SA, Barker G, Rice MA Jr, Jeffrey MG, Broderick G, Craddock TJA. A case matched study examining the reliability of using ImPACT to assess effects of multiple concussions. BMC Psychol. 2017 Apr 28; 5(1):14.
• Cook DB, Light AR, Light KC, Broderick G, Shields MR, Dougherty RJ, Meyer JD, VanRiper S, Stegner AJ, Ellingson LD, Vernon SD. Neural consequences of post-exertion malaise in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Brain Behav Immun. 2017 May; 62:87-99.

2016

• Russell L, Broderick G, Taylor R, Fernandes H, Harvey J, Barnes Z, Smylie AL, Collado F, Balbin E, Katz BZ, Klimas NG, Fletcher MA. Illness Progression in Chronic Fatigue Syndrome: a Shifting Immune Baseline. BMC Immunology, 2016, 17: 3.
• Rice M, del Rosario R, Craddock TJA, Barnes ZM, Klimas NG, Fletcher MA, Zysman J, Broderick G. Gulf War Illness: is There Lasting Damage to Endocrine-immune Circuitry? Sys Biomed 2016, 2(4): 80-89.
• Harvey JM, Bowie A, Katz BZ, O’Gorman MRG, Taylor R, Fletcher MA, Klimas NG, Broderick G. Tracking Post-infectious Fatigue in Clinic using Routine Clinical Lab Tests. BMC Pediatrics 2016, 16:54. 

2015

• Vashishtha S, Broderick G, Craddock TJA, Fletcher MA, Klimas NG. Inferring Broad Regulatory Biology from Time Course Data: Have We Reached an Upper Bound under Constraints Typical of In Vivo Studies?  PLoS ONE 2015, 10(5): e0127364.
• Craddock TJA, Harvey JM, Nathanson L, Barnes ZM, Klimas NG, Fletcher MA, Broderick G. Using gene expression signatures to identify novel treatment strategies in gulf war illness. BMC BMC Med Genomics. 2015 Jul 9; 8(1): 36.
• Craddock TJA, del Rosario R, Rice M , Zysman J, Fletcher MA, Klimas NG, Broderick G. Achieving Remission in Gulf War Illness: A Simulation-Based Approach to Treatment Design. PLoS ONE 2015 10(7): e0132774.

2014

• Craddock TJA, Fritsch P, Rice MA Jr, del Rosario RM, Miller DB, Fletcher MA, Klimas NG, Broderick G. A Role for Homeostatic Drive in the Perpetuation of Complex Chronic Illness: Gulf War Illness and Chronic Fatigue Syndrome. PLoS One 2014, 9(1): e84839.

2013

• Broderick G, Ben-Hamo R, Vashishtha S, Efroni S, Nathanson L, Barnes Z, Fletcher MA, Klimas NG. Altered Immune Pathway Activity under Exercise Challenge in Gulf War Illness: An Exploratory Analysis. Brain Behav Immun. 2013, 28: 159-169.
• Smylie AL, Broderick G, Fernandes H, Razdan S, Barnes Z, Collado F, Sol C, Fletcher MA, Klimas NG. A Comparison of Sex-specific Immune Signatures in Gulf War Illness and Chronic Fatigue Syndrome. BMC Immunol 2013, 14:29.
• Fritsch P, Craddock TJ, del Rosario RM, Rice MA, Smylie A, Folcik VA, de Vries G, Fletcher MA, Klimas NG, Broderick G. Succumbing to the laws of attraction: Exploring the sometimes pathogenic versatility of discrete immune logic. Sys Biomed 2013, 1(3):1.

2012

• Broderick G, Katz BZ, Fernandes H, Fletcher MA, Klimas NG, Smith FA, O’Gorman MRG, Vernon SD, Taylor R. Cytokine Expression Profiles of Immune Imbalance in Post-mononucleosis Chronic Fatigue. J Transl Med. 2012, 10: 191.

2011

• Folcik VA, Broderick G, Mohan S, Block B, Ekbote C, Doolittle J, Khoury M, Davis L, Marsh CB. Using an agent-based model to analyze the dynamic communication network of the immune response. Theor Biol Med Model, 2011 Jan 19; 8:1.
• Broderick G, Kreitz A, Fuite J, Fletcher MA, Vernon SD, Klimas N. A pilot study of immune network remodeling under challenge in Gulf War Illness. Brain Behav Immun. 2011 Feb; 25(2): 302-13.
• Carruthers BM, van de Sande MI, De Meirleir KL, Klimas NG, Broderick G et al. Myalgic encephalomyelitis: International Consensus Criteria. J Intern Med. 2011 Oct; 270(4): 327-38.

2010 and prior

• Broderick G, Fuite J, Kreitz A, Vernon SD, Klimas N, Fletcher MA. Formal Analysis of Cytokine Networks in Chronic Fatigue Syndrome. Brain Behav Immun, 2010 Oct; 24(7): 1209-17.
• Fletcher MA, Zeng XR, Maher K, Levis S, Barry H, Antoni M, Broderick G, Klimas NG. Biomarkers in chronic fatigue syndrome: Evaluation of natural killer cell function and dipeptyl peptidase IV. PLoS ONE, 25 May, 2010; 10.1371/journal.pone.0010817.
• Nakamura T, Schwander SK, Donnelly R, Ortega F, Togo F, Broderick G, Yamamoto Y, Cherniack NS, Rapoport D, Natelson BH. Cytokines across the night in chronic fatigue syndrome with and without Fibromyalgia. Clin Vaccine Immunol. 2010 Apr; 17(4): 582-7.
• Fletcher MA, Rosenthal M, Antoni M, Ironson G, Zeng XR, Barnes Z, Harvey JM, Hurwitz B, Levis S, Broderick G, Klimas NG. Plasma neuropeptide Y: a biomarker for symptom severity in chronic fatigue syndrome. Behav Brain Funct, 2010 Dec 29; 6(1): 76.
• Ben-Zvi A, Vernon SD, Broderick G. Model-based Therapeutic Correction of Hypothalamic Pituitary Adrenal Axis Dysfunction. PLoS Comput Biol, 2008; 5(1): e1000273. doi:10.1371/journal.pcbi.1000273.
• Aspler AL, Bolshin C, Vernon SD, Broderick G. Evidence of Inflammatory Immune Signaling in Chronic Fatigue Syndrome: A Pilot Study of Gene Expression in Peripheral Blood. Behav Brain Funct, 2008 Sep 26; 4(1): 44. doi:10.1186/1744-9081-4-44. [18 citations, May, 2011]
• Fuite J,Vernon SD, Broderick G. Neuroendocrine and Immune Network Re-modeling in Chronic Fatigue Syndrome: An Exploratory Analysis. Invited submission, Genomics 2008; 92(6): 393-399. doi:10.1016/j.ygeno.2008.08.008 (issue cover). 
• Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M. Extraction of elementary rate constants from global network analysis of E. coli central metabolism. BMC Systems Biology, 2008; 2: 41, doi:10.1186/1752-0509-2-41.
• Ridgway D, Broderick G, Ru’aini M, Winter P, Lopez-Campistrous A, Ellison MJ. Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys J, 2008 May 15; 94(10): 3748-59.
• Mueller TF, Einecke G, Reeve J, Sis B, Mengel M, Jhangri G, Bunnag S, Cruz, J, Wishart D, Meng C, Broderick G, Kaplan B, Halloran PF. Microarray analysis of rejection in human kidney transplants using pathogenesis-based transcripts sets. Am J Transplant, 2007; 7(12): 2712-2722.
• Famulski KS, Broderick G, Einecke G, Hayl K, Cruz J, Sis B, Mengel M Halloran PF. Transcriptome analysis reveals heterogeneity in the injury response of kidney transplants. Am J Transplant, 2007; 7: 1–13.
• Einecke G, Broderick G, Sis B, Halloran PF. Early loss of renal transcripts in kidney allografts: relationship to morphologic changes and alloimmune effector mechanisms. Am J Transplant, 2007; 7(5): 1121–1130.
• Broderick G, Craddock RC, Whistler T, Taylor R, Klimas N, Unger ER. Identifying illness parameters in fatigue syndromes using classical projection methods. Pharmacogenomics, 2006; 7(3): 407-419.
• Whistler T, Craddock RC, Taylor R, Broderick G, Klimas N, Unger ER. Gene expression correlates of fatigue. Pharmacogenomics, 2006; 7(3): 395-405.   
• Craddock RC, Taylor R, Broderick G, Whistler T, Klimas N, Unger ER. Exploration of statistical dependence between illness parameters using the Entropy Correlation Coefficient.  Pharmacogenomics, 2006; 7(3): 421-428.
• Broderick G, Ru’aini M, Chan E, Ellison MJ. A Life-like Virtual Cell Membrane Using Discrete Automata. Invited Paper, In Silico Biology, 2004; 5: 0016.
• Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Weiner JH, Ellison MJ. Localization, Annotation & Comparison of the Escherichia coli K-12 Proteome under Two States of Growth. Mol Cell Proteomics, 2005 May 19; 10.1074/mcp.D500006-MCP200.