Ryan Brinkman

Dr. Ryan Brinkman’s research is focused on flow cytometry bioinformatics: developing automated data analysis methods for large, high-dimensional datasets. Early work centered on creating the data standards and a free, open source computational infrastructure to support high throughput computational statistical analysis of flow data. Building on flowClust (the first robust automated gating approach), recent efforts have concentrated around developing complete analysis pipelines that cover all the steps from FCS data pre-processing to diagnosis and discovery. The R/BioConductor flow analysis platform now supports diverse collaborative research and patient care projects in cancer and immunology.

Brinkman is also active in the community as chair of ISAC’s Data Standards Task Force, ISAC Councilor, organizer of the Flow Informatics and Computational Cytometry Society (FICCS.org), and coordinating the Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP.flowsite.org) Project. Brinkman is a Michael Smith Foundation for Health Research Scholar, a Terry Fox Foundation New Investigator, and a past ISAC Scholar.

Recent Publications

Aghaeepour N, Finak G; FlowCAP Consortium; DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods. 2013 Mar;10(3):228-38. doi: 10.1038/nmeth.2365. Epub 2013 Feb 10. (PubMed abstract)

Aghaeepour N, Chattopadhyay PK, Ganesan A, O’Neill K, Zare H, Jalali A, Hoos HH, Roederer M, Brinkman RR. Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. Bioinformatics. 2012 Apr 1;28(7):1009-16. doi: 10.1093/bioinformatics/bts082. Epub 2012 Feb 29. (PubMed abstract)

Spidlen J, Moore W, Parks D, Goldberg M, Bray C, Bierre P, Gorombey P, Hyun B, Hubbard M, Lange S, Lefebvre R, Leif R, Novo D, Ostruszka L, Treister A, Wood J, Murphy RF, Roederer M, Sudar D, Zigon R, Brinkman RR. Data File Standard for Flow Cytometry, version FCS 3.1. Cytometry A. 2010 Jan;77(1):97-100. doi: 10.1002/cyto.a.20825. (PubMed abstract)

Aghaeepour N, Nikolic R, Hoos HH, Brinkman RR. Rapid cell population identification in flow cytometry data. Cytometry A. 2011 Jan;79(1):6-13. doi: 10.1002/cyto.a.21007. (PubMed abstract)

Zare H, Shooshtari P, Gupta A, Brinkman RR. Data reduction for spectral clustering to analyze high throughput flow cytometry data. BMC Bioinformatics. 2010 Jul 28;11:403. doi: 10.1186/1471-2105-11-403. (PubMed abstract)