Deniz Cizmeci

Deniz Cizmeci

Postdoctoral Fellow of Computational Immunology

Ragon Institute of MGH, MIT and Harvard, USA







Network Associate


Research Keywords:

Computational immunology, machine learning, bioinformatics



Deniz left VALIDATE and is now doing her post-doctoral fellowship at Harvard. Deniz has a solid background in computational biology, complemented by experience in infectious disease research. Prior to joining the VALIDATE team she worked as a bioinformatician at Imperial College London analysing transcriptomic responses across preclinical animal platforms to identify novel biomarkers of vaccine safety and reactogenecity. Deniz completed her PhD at the University of Exeter. Her doctorate project employed an interdisciplinary approach to investigating host-pathogen interactions during infection with Burkholderia pseudomallei.

Deniz’s role at VALIDATE was to ensure that VALIDATE maximises outputs and lessons learned from the immunology and vaccine-related data available across the Network. She was responsible for setting up the VALIDATE data sharing portal and integrating data sets for cross-pathogen, cross-species and/or cross-country analyses and modelling that will advance vaccine R&D for our focus pathogens.


Related Websites: 




McKay PF, Cizmeci D, Aldon Y, Maertzdorf J, Weiner J, Kaufmann SH, Lewis DJ, van den Berg RA, Del Giudice G, Shattock RJ. Identification of potential biomarkers of vaccine inflammation in mice. Elife. 2019 May 14;8. pii: e46149. doi: 10.7554/eLife.46149. [Epub ahead of print] PubMed PMID: 31084714.

Cheeseman HM, Day S, McFarlane LR, Fleck S, Miller A, Cole T, Sousa-Santos N, Cope A, Cizmeci D, Tolazzi M, Hwekwete E, Hannaman D, Kratochvil S, McKay PF, Chung AW, Kent SJ, Cook A, Scarlatti G, Abraham S, Combadiere B, McCormack S, Lewis DJ, Shattock RJ. Combined Skin and Muscle DNA Priming Provides Enhanced Humoral Responses to a Human Immunodeficency Virus Type 1 Clade C Envelope Vaccine. Hum Gene Ther. 2018 Sep;29(9):1011-1028. doi: 10.1089/hum.2018.075. PubMed PMID: 30027768; PubMed Central PMCID: PMC6214652.

Pinder CL, Kratochvil S, Cizmeci D, Muir L, Guo Y, Shattock RJ, McKay PF. Isolation and Characterization of Antigen-Specific Plasmablasts Using a Novel Flow Cytometry-Based Ig Capture Assay. J Immunol. 2017 Dec 15;199(12):4180-4188. doi: 10.4049/jimmunol.1701253. Epub 2017 Nov 8. PubMed PMID: 29118244; PubMed Central PMCID: PMC5720343.

Kratochvil S, McKay PF, Kopycinski JT, Bishop C, Hayes PJ, Muir L, Pinder CL, Cizmeci D, King D, Aldon Y, Wines BD, Hogarth PM, Chung AW, Kent SJ, Held K, Geldmacher C, Dally L, Santos NS, Cole T, Gilmour J, Fidler S, Shattock RJ. A Phase 1 Human Immunodeficiency Virus Vaccine Trial for Cross-Profiling the Kinetics of Serum and Mucosal Antibody Responses to CN54gp140 Modulated by Two Homologous Prime-Boost Vaccine Regimens. Front Immunol. 2017 May 24;8:595. doi: 10.3389/fimmu.2017.00595. eCollection 2017. PubMed PMID: 28596770; PubMed Central PMCID: PMC5442169.

Cizmeci D, Dempster EL, Champion OL, Wagley S, Akman OE, Prior JL, Soyer OS, Mill J, Titball RW. Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection. Sci Rep. 2016 Aug 3;6:30861. doi: 10.1038/srep30861.PubMed PMID: 27484700; PubMed Central PMCID: PMC4971488.

Cizmeci D, Arkun Y. Regulatory networks and complex interactions between the insulin and angiotensin II signalling systems: models and implications for hypertension and diabetes. PLoS One. 2013 Dec 31;8(12):e83640. doi: 10.1371/journal.pone.0083640. eCollection 2013. PubMed PMID: 24400038; PubMed Central PMCID: PMC3882141.