‌‌‌ Michael J. Zilliox ‌ is an Assistant Professor in the Department of Public Health Sciences and Scientific Director of the Loyola Genomics Facility.   The Loyola Genomics Facility is located on the Health Sciences campus.  

mizilliox@LUC.edu  ‌

Also contact:
Gina R. Kuffel
Loyola Genomics Facility, Laboratory Manager
Phone: 708-216-8270
Email: gkuffel@LUC.edu

Current research programs
The Microbiome and Disease
Transcriptome Atlas and Biomarker Discovery

Active Funding 
1P01 CA154778 Nishimura (PI)  
                  09/21/11-08/31/17                             2.4 calendar months
NIH/NCI                                                        $2,667,213
TCR Gene Modified T Cells for Adoptive Immunotherapy
The overall goal of this Program is to understand how the biology of TCR transduced mouse and human T cells compares to normal T cells bearing the same TCR. This information will enable us to modify how TCR transduced T cells are used to improve the overall outcome of cancer patients.
Role: Co-Investigator

R01CA191317 (Le Poole)                               08/01/2015-07/31/2020                   0.36 calendar months
Separating autoimmunity and anti-tumor immunity      
Role: Co-Investigator           

P20DK108268 (Wolfe)                                  12/01/15-11/30/17                              1.20 calendar months
NIH/NIDDK                                                  $200,000
The Female Urinary Microbiome: Adjacent Microbiomes and Clinical Associations
This proposal compares the urinary microbiome with the vaginal and perianal microbiomes and builds a database to make urinary microbiome available to other researchers.
Role: Co-Investigator        

R01DK104718 (LB/Wolfe)                             09/01/15-8/31/20                              2.40 calendar months
NIH/NIDDK                                                  $499,922                              
The Female Urinary Microbiome and Urinary Incontinence
The goal of this proposal is to study the urinary microbiome in control women and those with urge urinary incontinence and stress urinary incontinence.
Role: Co-Investigator

R01 (Irizarry)                                                 07/-1/16-6/30/21                               2.16 calendar months
NIH                                                                 $25,000
Preprocessing and Analysis Tools for High-throughput Technologies. This proposal develops new statistical algorithms for high-throughput technologies.
Role: Co-Investigator

Selected publications

  • Thomas-White, K.J., Hilt, E.E., Fok, C., Pearce, M.M., Mueller, E.R., Kliethermes, S., Jacobs, K., Zilliox, M.J., Brincat, C., Price, T.K., Kuffel, G., Schreckenberger, P., Gai, X., Brubaker, L., Wolfe, A.J.  2016.  Incontinence medication response relates to the female urinary microbiota.  Int. Urogynecol. J. 27:723-733.
  • Yang, S.F., Bier-Laning, C.M., Adams, W., Zilliox, M.J.  2016.  Candidate biomarkers for HPV-negative head and neck cancer identified via gene expression barcode analysis.  Otolaryngology- Head and Neck Surgery 155:416-422.  
  • Malki, K., Shapiro, J.W., Price, T.K., Hilt, E.E., Thomas-White, K., Sircar, T., Rosenfeld, A.B., Kuffel, G., Zilliox, M.J., Wolfe, A.J., Putonti, C.  2016.  Genomes of gardnerella strains reveal an abundance of prophages within the bladder microbiome.  PLoS One. 11:e0166757.
  • Lynch TL 4th, Ismahil MA, Jegga AG, Zilliox MJ, Troidl C, Prabhu SD, Sadayappan S.  2016.  Cardiac inflammation in genetic dilated cardiomyopathy caused by MYBPC3 mutation.  J. Mol. Cell Cardiol. 102:83-93.
  • Plichta, J.K., Holmes, C.J., Nienhouse, V., Puszynski, M., Gao, X., Dong, Q., Lin, H., Sinacore, S., Zilliox, M., Toh, E., Nelson, DE, Gamelli, R.I., and Radek, K.A.. Cutaneous burn injury modulates urinary antimicrobial peptide responses and the urinary microbiome. Critical Care Medicine. Accepted, September 25, 2016.
  • The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence Pearce, M. M.; Hilt, E. E.; Rosenfeld, A. B.; Zilliox, M. J.; Thomas-White, K.; Fok, C.; Kliethermes, S.; Schreckenberger, P. C.; Brubaker, L.; Gai, X.; Wolfe, A. J., mBio
  • The Gene Expression Barcode 3.0: improved data processing and mining tools McCall, M. N.; Jaffee, H. A.; Zelisko, S. J.; Sinha, N.; Hooiveld, G.; Irizarry, R. A.; Zilliox, M. J., Nucleic acids research
  • Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder Hilt, E. E.; McKinley, K.; Pearce, M. M.; Rosenfeld, A. B.; Zilliox, M. J.; Mueller, E. R.; Brubaker, L.; Gai, X.; Wolfe, A. J.; Schreckenberger, P. C., Journal of clinical microbiology
  • ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data Wu, G., Yustein, J.T., McCall, M.N., Zilliox, M.J., Irizarry, R.A. Zeller, K., Dang, C.V. and Ji, H., Bioinformatics (Oxford, England)
  • Comparative analysis of simian immunodeficiency virus gag-specific effector and memory CD8+ T cells induced by different adenovirus vectors Tan, W. G.; Jin, H. T.; West, E. E.; Penaloza-MacMaster, P.; Wieland, A.; Zilliox, M. J.; McElrath, M. J.; Barouch, D. H.; Ahmed, R., Journal of virology
  • Identification of novel markers for mouse CD4(+) T follicular helper cells Iyer, S. S.; Latner, D. R.; Zilliox, M. J.; McCausland, M.; Akondy, R. S.; Penaloza-Macmaster, P.; Hale, J. S.; Ye, L.; Mohammed, A. U.; Yamaguchi, T.; Sakaguchi, S.; Amara, R. R.; Ahmed, R., European journal of immunology
  • Phenotype function, and gene expression profiles of programmed death-1(hi) CD8 T cells in healthy human adults, Duraiswamy, J.; Ibegbu, C. C.; Masopust, D.; Miller, J. D.; Araki, K.; Doho, G. H.; Tata, P.; Gupta, S.; Zilliox, M. J.; Nakaya, H. I.; Pulendran, B.; Haining, W. N.; Freeman, G. J.; Ahmed, R., Journal of immunology (Baltimore, Md.: 1950)
  • The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes McCall, M. N.; Uppal, K.; Jaffee, H. A.; Zilliox, M. J.; Irizarry, R. A., Nucleic acids research
  • A gene expression bar code for microarray data Zilliox, M. J.; Irizarry, R. A., Nature methods
  • Gene expression changes in peripheral blood mononuclear cells during measles virus infection Zilliox, M. J.; Moss, W. J.; Griffin, D. E., Clinical and vaccine immunology : CVI
  • Gene expression patterns in dendritic cells infected with measles virus compared with other pathogens Zilliox, M. J.; Parmigiani, G.; Griffin, D. E., Proceedings of the National Academy of Sciences of the United States of America
  • Adjuvant danger signals increase the immune response to porcine reproductive and respiratory syndrome virus Foss, D. L.; Zilliox, M. J.; Meier, W.; Zuckermann, F.; Murtaugh, M. P., Viral immunology
  • Bacterially induced activation of interleukin-18 in porcine intestinal mucosa Foss, D. L.; Zilliox, M. J.; Murtaugh, M. P., Veterinary immunology and immunopathology
  • Experimental autoimmune myocarditis in A/J mice is an interleukin-4-dependent disease with a Th2 phenotype Afanasyeva, M.; Wang, Y.; Kaya, Z.; Park, S.; Zilliox, M. J.; Schofield, B. H.; Hill, S. L.; Rose, N. R., The American journal of pathology
  • Differential regulation of macrophage interleukin-1 (IL-1) IL-12, and CD80-CD86 by two bacterial toxins, Foss, D.L., Zilliox, M.J., and Murtaugh, M.P., Infection & Immunity
  • In vitro and in vivo bioactivity of single-chain interleukin-12 Foss, D.L, Moody, M.D., Murphy Jr., K.P., Pazmany, C., Zilliox, M.J., and Murtaugh, M.P., Scandinavian journal of immunology
  • Efficient assembly of rat hepatocyte spheroids for tissue engineering applications Wu, F.J., Friend, J.R., Hsiao, C.C., Zilliox, M.J., Ko, W.J., Cerra, F.B., and Hu, W.S., BIOTECHNOLOGY AND BIOENGINEERING