Josef Spidlen

Josef Spidlen

Director of Bioinformatics

Education Postdoctorate Fellow, 2005 - 2008, BC Cancer Agency, BC, Canada Ph.D. in Biomedical Informatics, 2002-2005, Charles University in Prague, First Faculty of Medicine, Czech Republic M.Sc. in Computer Science, 1996-2002, Charles University in Prague, Faculty of Mathematics and Physics, Czech Republic

Scientific Interest and Avenues for Collaboration My scientific interest and research are focused on the development and application of software tools for single cell sequencing and automated high-throughput cytometry data analysis. My formal training is in computer science and software engineering, which I have been applying in the fields of medical informatics and computational biology. I am the author and maintainer of several R packages, and the author of several flow cytometry data analysis tools, including most of the modules in the GenePattern Flow Cytometry Suite, and the FlowClean FlowJo plugin. I am also the main author of most recent ISAC data standards, a.k.a. file formats, such as FCS, Gating-ML, CLR, ICEFormat, and for the past 5 years, I was the chief developer of FlowRepository - the largest open source database of public flow cytometry data. In the Fall of 2016, after 11 years at the BC Cancer Agency, I joined the FlowJo, LLC team to help bring advancements of computational biology to researchers without programming skills. Currently, I am mostly focused on creating tools and algorithms for tertiary single cell sequencing data analysis, and I am designing and implementing novel approaches in our SeqGeq™ application. I am always excited to engage in collaborations, especially when it comes to improving FlowJo® or SeqGeq™ to address data analysis challenges to gain novel biological insights.

Participation / Support of ISAC ISAC Data Standards Task Force: first author of most ISAC data standards. FlowRepository Steering Committee: Chief developer of FlowRepository 2012-2016. Member of the CYTO 2016 Parallel Session Committee. Attended many past CYTO conferences, taught at workshops, helped by chairing sessions and judging posters.