About Josef Spidlen

Josef is a staff scientist at BC Cancer Agency. He received his MSc in computer science and his PhD in biomedical informatics from the Charles University in Prague. He started his career at the Institute of Computer Science, Academy of Sciences of the Czech Republic, where he spent 5 years conducting research in the field of medical informatics. In 2005, Josef joined the Terry Fox Laboratory at the BC Cancer Agency in Vancouver, Canada. Since then, his research has been mainly 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 most cytometry data file standards. Currently, Josef is the lead developer of FlowRepository - ISAC's web-based repository of flow cytometry datasets. Josef has a great deal of experience with Big data analysis and with a full scale of software engineering technologies as a team leader, consultant and developer.

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Josef Spidlen - Curriculum Vitae

Staff Scientist, Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
+1 (604) 675-8000, ex. 7755

Education

Charles University in Prague, First Faculty of Medicine2002 - 2005
Ph.D. in Medical Informatics and Biomedicine
Charles University in Prague, Faculty of Mathematics and Physics1996 - 2002
M.Sc. in Computer Science, Major in Information Technologies and Databases

Work Experience

Terry Fox Laboratory, BC Cancer Agency, BC, Canada2014 -
Staff Scientist
Research in automated flow cytometry data analysis methods, development of software tools and libraries, development of FlowRepository
Terry Fox Laboratory, BC Cancer Agency, BC, Canada2009 - 2013
Research Associate
Development and research of flow cytometry data analysis tools and standards, development of GenePattern modules, development of R libraries, development of FlowRepository
Terry Fox Laboratory, BC Cancer Agency, BC, Canada2005 - 2008
Postdoctorate Fellow
Development of flow cytometry data standards and analysis tools
Institute of Computer Science, Academy of Sciences of the Czech Republic, Czech Republic2001 - 2005
Researcher
Research in the field of medical informatics, electronic health record, and telemedicine
Institute of Computer Science, Academy of Sciences of the Czech Republic, Czech Republic2001 - 2005
Researcher
Research in the field of medical informatics, electronic health record, and telemedicine
IPPS Ltd, Czech Republic2000 - 2005
Software Developer and Consultant
Design and development of information systems
Reuters Ltd, Great Britain1998 - 1999
Contractor for Software Development
Development of financial tools and a trading platform
Intergram Ltd, Czech Republic1996 - 2000
Software Developer and Data Wrangler
Data conversions, processing and analysis

Membership

International Society for Analytical Cytology (ISAC)
Flow Informatics and Computational Cytometry Society (FICCS)

IT Experience

Brainbench certificates (C Programmer, C++ Programmer, Object-Oriented Developer, Oracle 7 DBA, TCP/IP Administrator, High IT Aptitude Performer, RDBMS Concepts)
Database design, ER Modeling, SQL (MS SQL, Oracle, MySQL, Informix)
Programming: Java, Ruby, R, C, C++, C#, Javascript, PHP, Rails, .NET, Eclipse, Netbeans, Visual Studio
XML Development (XSD, RDF, OWL)
Web Development (HTML, CSS, JSON, Javascript, PHP, RoR, Haml, Sass, Tomcat)

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Publications

Spidlen J, Brinkman RR. Use FlowRepository to Share Your Clinical Data upon Study Publication. Cytometry: Part B - Clinical Cytometry 2016 (in press).
Fletez-Brant K, Spidlen J, Brinkman RR, Roederer M, Chattopadhyay PK. flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data. Cytometry A (2016) doi: 10.1002/cyto.a.22837
AbstractWiley Online Library
Full textPDF (733 kB)
Spidlen J, Moore W, ISAC Data Standards Task Force, Brinkman R. ISAC's Gating-ML 2.0 Data Exchange Standard for Gating Description. Cytometry A (2015) doi: 10.1002/cyto.a.22690. PMID:25976062.
AbstractWiley Online Library
Full textPDF (99 kB)
Spidlen J, Bray C, ISAC Data Standards Task Force, Brinkman RR. ISAC's Classification Results File Format. Cytometry A (2015) doi: 10.1002/cyto.a.22586. PMID:25407887.
AbstractWiley Online Library
Full textPDF (99 kB)
O'Neill K, Aghaeepour N, Spidlen J, Brinkman R. Flow Cytometry Bioinformatics. PLoS Comput Biol (2013) 9(12). e1003365. doi:10.1371/journal.pcbi.1003365
Full textPLOS Collections
Spidlen JBarsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y, Liefeld T, Reich M, Mesirov JP, Wilkinson P, Scheuermann RH, Sekaly RP, Brinkman RR. GenePattern Flow Cytometry Suite. Source Code Biol Med (2013) Jul 3; 8(1):14.
AbstractSCFBM
Full textPDF (962 kB)
Aghaeepour N, Finak G; FlowCAP Consortium, Dougall D, Khodabakhshi AH, Mah P, Obermoser G, Spidlen J, Taylor I, Wuensch SA, Bramson J, Eaves C, Weng AP, Iii ES, Ho K, Kollmann T, Rogers W, De Rosa S, Dalal B, Azad A, Pothen A, Brandes A, Bretschneider H, Bruggner R, Finck R, Jia R, Zimmerman N, Linderman M, Dill D, Nolan G, Chan C, Khettabi FE, O'Neill K, Chikina M, Ge Y, Sealfon S, Sugár I, Gupta A, Shooshtari P, Zare H, De Jager PL, Jiang M, Keilwagen J, Maisog JM, Luta G, Barbo AA, Májek P, Vilček J, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, McLachlan GJ, Wang K, Naim I, Sharma G, Nikolic R, Pyne S, Qian Y, Qiu P, Quinn J, Roth A; DREAM Consortium, Meyer P, Stolovitzky G, Saez-Rodriguez J, Norel R, Bhattacharjee M, Biehl M, Bucher P, Bunte K, Di Camillo B, Sambo F, Sanavia T, Trifoglio E, Toffolo G, Dimitrieva S, Dreos R, Ambrosini G, Grau J, Grosse I, Posch S, Guex N, Keilwagen J, Kursa M, Rudnicki W, Liu B, Maienschein-Cline M, Manninen T, Huttunen H, Ruusuvuori P, Nykter M, Schneider P, Seifert M, Strickert M, Vilar JM, 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):228-238.
Full textPDF (1 MB)
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.
Full textPDF (9.3 MB)
Spidlen J, Novo D. ICEFormat - The Image Cytometry Experiment Format. Cytometry A, 2012 Dec; 81(12):1015-1018.
AbstractWiley Online Library
Full textPDF (96 kB)
Spidlen J, Breuer K, Rosenberg C, Kotecha N, Brinkman R. FlowRepository - A Resource of Annotated Flow Cytometry Datasets Associated with Peer-reviewed Publications. Cytometry A, 2012 Sep; 81(9):727-731.
AbstractWiley Online Library
Full textPDF (661 kB)
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, July 2012.
AbstractWiley Online Library
Full textWiley Online Library
Full textPDF (1.2 MB)
Spidlen J, Bray C, Brinkman R. FCS 3.1 Implementation Guidance. Cytometry A, 2012 Jun; 81(6):523-526.
AbstractWiley Online Library
Full textPDF (191 kB)
Spidlen J, Shooshtari P, Kollmann T, Brinkman R. Flow cytometry data standards. BMC Research Notes, 2011 Mar 7; 4(1):50.
AbstractBMC Research Notes
Full textBMC Research Notes
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 R, Roederer M, Sudar D, Zigon R, Brinkman R. Data File Standard for Flow Cytometry, version FCS 3.1. Cytometry A, 2010; 77(1): pp.97-100.
AbstractWiley Online Library
Full textPDF (191 kB)
Qian Y, Tchuvatkina O, Spidlen J, Wilkinson P, Gasparetto M, Jones A, Manion F, Scheuermann R, Sekaly R, Brinkman R. FuGEFlow: data model and markup language for flow cytometry. BMC Bioinformatics, 2009; 10:184.
AbstractPubMed
Full textBMC Bioinformatics
Hahne F, Le Meur N, Brinkman R, Ellis B, Haaland P, Sarkar D, Spidlen J, Strain E, Gentleman R. flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinformatics, 2009; 10(1):106.
AbstractPubMed
Full textBMC Bioinformatics
Spidlen J, Leif R, Moore W, Roederer M, Brinkman R. Gating-ML: XML-based Gating Descriptions in Flow Cytometry. Cytometry A, 2008; 73(12):pp.1151-1157.
AbstractWiley Online Library
Full textPDF (285 kB)
*Lee J, *Spidlen J (*contributed equally), Boyce K, Cai J, Crosbie N, Dalphin Mark, Furlong Jeff, Gasparetto Maura, Goldberg Michael, Goralczyk Elizabeth M., Hyun Bill, Jansen Kirstin, Kollmann Tobias, Kong Megan, Leif Robert, McWeeney Shannon, Moloshok Thomas D., Moore Wayne, Nolan Garry, Nolan John, Nikolich-Zugich Janko, Parrish David, Purcell Barclay, Qian Yu, Selvaraj Biruntha, Smith Clayton, Tchuvatkina Olga, Wertheimer Anne, Wilkinson Peter, Wilson Christopher, Wood James, Zigon Robert, the International Society for Advancement of Cytometry Data Standards Task Force, Scheuermann Richard H., and Brinkman Ryan R. MIFlowCyt: The Minimum Information about a Flow Cytometry Experiment. Cytometry A, 2008; 73(10): pp.926-30.
AbstractWiley Online Library
Full textPDF (107 kB)
Spidlen J, Gentleman R, Haaland P, Langille M, Le Meur N, Ochs M, Schmitt C, Smith C, Treister A, Brinkman R: Data Standards for Flow Cytometry. OMICS. 2006; 10(2), pp.209-214.
AbstractPubMed
Full textPubMed Central
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Spidlen J, Hanzlicek P, Riha A, Zvarova J. Flexible Information Storage in MUDR-II EHR. Int J Med Inform, 2006; 75 (3-4): pp. 201-208.
AbstractPubMed
Full textElsevier
Full textPDF (440 kB)
Nagy M, Spidlen J., Synchronization of Data Models to Support Continuous Health Care. Proceedings of Medical Informatics Europe, 2006, Maastricht.
Full textPDF (724 kB)
Spidlen J, Pies M, Teuberova Z, Nagy M, Hanzlicek P, Zvarova J, Dostalova T. MUDRLite - An Electronic Health Record Applied to Dentistry by the Usage of a Dental-cross Component. IFMBE Proceedings, 2005, Vol. 11, ISSN 1727-1983. pp. 1077-1081.
Full textPDF (94 kB)
Preckova P, Spidlen J, Zvarova J. Usage of International Nomeclatures and Metathesauruses in Shared Healthcare in the Czech Republic. Acta Medica Informatica, Vol. 13, No. 4, 2005, pp. 201-205.
Full textPDF (1 MB)
Spidlen J. J2ME Usage in Telemedicine Applications Development for Classical Mobile Phones. Physician and Technology, 35 (3), ISSN: 0301-5491, 2004, pp. 55–62.
AbstractPDF (88 kB)
Full text (Czech)PDF (330 kB)