User:Jspidlen

Josef Spidlen PhD



 * Research Associate, Senior Software Engineer, Bioinformatician
 * Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
 * http://spidlen.cz/
 * http://spidlen.ca/

Profile
Josef received his MSc degree in computer science and his PhD degree in biomedical informatics from Charles University in Prague, Faculty of Mathematics and Physics, and First Faculty of Medicine, respectively. He started his career at the Institute of Computer Science, Academy of Sciences of the Czech Republic, where he spent five years conducting research in the field of medical informatics. In 2005, he joined the Terry Fox Laboratory at the BC Cancer Agency in Vancouver, Canada. Since then, his research has been focused on developing tools for automated high throughput flow cytometry data analysis. In addition, Josef contributed to the standardization in flow cytometry as the main author of the Flow Cytometry Data File Standard (FCS 3.1), the gating description standard (Gating-ML), the image cytometry experiment format (ICEFormat) and the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt). Since 2011, Josef has also been the lead developer of FlowRepository - a public databank of flow cytometry datasets maintained by the International Society for Advancement of Cytometry (ISAC).

Featured publications

 * Spidlen J., Breuer K., Brinkman R.: Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) Compliant Manuscript Using the International Society for Advancement of Cytometry (ISAC) FCS File Repository (FlowRepository.org). Current Protocols in Cytometry Unit 10.18, 2012.
 * Spidlen J., Breuer K., Rosenberg C., et al.: FlowRepository - A Resource of Annotated Flow Cytometry Datasets Associated with Peer-reviewed Publications. Cytometry Part A 2012 Sep;81(9):727-731.
 * Spidlen J., Moore W., Parks D., et al.: Data File Standard for Flow Cytometry, Version FCS 3.1. Cytometry A 77(1): 97–100, 2010.
 * Spidlen J., Bray C., Brinkman R.: FCS 3.1 Implementation Guidance. Cytometry Part A 2012 Jun;81(6):523-526.
 * Spidlen J., Novo D.: ICEFormat - The Image Cytometry Experiment Format. Cytometry Part A 2012 Dec;81(12):1015-1018.
 * Spidlen J., Shooshtari P., Kollmann T., Brinkman R.: Flow cytometry data standards. BMC Research Notes 2011 Mar 7; 4(1):50.
 * Spidlen J., Leif R., Moore W., et al.: Gating-ML: XML-based Gating Descriptions in Flow Cytometry. Cytometry A 73(12): 1151-1157, 2008.
 * Lee J., Spidlen J., Keith B., et al.: MIFlowCyt: The Minimum Information about a Flow Cytometry Experiment. Cytometry A. 73(10): 926-930, 2008.
 * Spidlen J., Brinkman R.: MIFlowCyt: Guidelines for Systems Biology in W. Dubitzky, O. Wolkenhauer, K. Cho & H. Yokota (eds.), Encyclopedia of Systems Biology, DOI 10.1007/978-1-4419-9863-7, Springer Science + Business Media, LLC 2012.
 * Qian Y., Tchuvatkina O., Spidlen J., et al.: FuGEFlow: data model and markup language for flow cytometry. BMC Bioinformatics 2009; 10:184
 * Spidlen J., Gentleman R., Haaland P., et al.: Data Standards for Flow Cytometry. OMICS. 2006 Summer; 10(2), pp.209-214.
 * Hahne F., LeMeur N., Brinkman R., et al.: flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinformatics 10(1), 2009.
 * Spidlen J., Hanzlicek P., Riha A., Zvarova J.: Flexible Information Storage in MUDR-II EHR. Int J Med Inform. 2006 Mar-Apr; 75 (3-4): pp. 201-208.