Bourquin-web.jpgJean-Pierre Bourqin
Abteilung Onkologie, Universitäts-Kinderspital Zürich
Comprehensive Cancer Center Zurich
Children’s Research Center Kinderspital Zurich
Life Science Zurich

Topic: Towards personalized approaches for relapsed and refractory childhood leukemia

Jean-Pierre Bourquin is the elected chair of the largest division in pediatric Hematology/Oncology in Switzerland and directing a large translational research effort within the Comprehensive Cancer Center Zurich at the at the Children’s Research Centre at the University Children’s Hospital in Zurich. He is a physician scientist with an active clinical and translational research program. Since 2019, he chairs the resistant disease committee of the international BFM Study Group, which is the central organization in Europe that leads the development of new treatments for childhood leukemia and have initiated a Scientific Working Group for functional  precision hematology for  the European Society of Hematoloty in 2019.

His research focus is on transcriptional dependencies and mechanisms of drug  resistance in childhood acute lymphoblastic leukemia (ALL). Over the last decade the Bourquin group has built and characterized a large repository of patient-derived xenografts within the framework of our international clinical studies. This constitutes a comprehensive model and a renewable resource to address mechanistic research directly in the relevant cancer cells. Using this model they have developed a functional screening platform for precision medicine that will be implement in clinical trials within the international BFM study group (application of drug response profiling to individualize treatment components for relapsed and refractory ALL). Using this model, they are dissecting different aspects of the biology of resistant disease. We have a program to define the leukemia microenvironment, are dissecting the function of relevant fusion transcription factors such as TCF3-HLF, which defines a paradigm of resistant ALL and highjacks a stem cell program driven by the master regulator transcription factor HLF, and are exploring new phenotypes that emerge from our comprehensive modelling approach. Relevant for this application, we have identified a signature that is highly associated with de novo resistance to chemotherapy in ALL (persistence of minimal residual disease). A key feature is the aberrant expression of the cell surface protein gp180, also called Vanin-2 or VNN2. This gene is only expressed in the hematopoietic system and markes a very early fetal stem cell compartment that also expresses HLF. VNN2 is also expressed in subsets of cord blood and adult hematopoietic stem cells, and in a later wave in differentiated myelomonocytic cells and lymphoid cells. In a prospective study, we confirm association of VNN2 by flow cytometry with MRD persistence in different genetic subgroups at risk. Given the association of VNN2 with stemness and inflammation, we seek to identify the underlying program with the aim to identify common actionable principles in resistant disease.


  • Huang Y, Mouttet B, Warnatz HJ, Risch T, Rietmann F, Frommelt F, Ngo QA, Dobay PM1, Marovca B, Jenni S, Tsai YC, Matzk S, Amstislavskiy S, Schrappe  M, Stanulla M, Gstaiger M, Bornhauser B, Yaspo ML and Bourquin J-P. The leukemogenic TCF3-HLF complex rewires enhancers driving cellular identity and self-renewal conferring EP300 vulnerability. Cancer Cell, accepted 5.9.2019.

  • Frismantas V, Dobay MP, Rinaldi A, Tchinda J, Dunn SH, Kunz J, Richter-Pechanska P, Marovca B, Pail O, Jenni S, Diaz-Flores E, Chang BH, Brown TJ, Collins RH, Uhrig S, Balasubramanian GP, Bandapalli OR, Higi S, Eugster S, Voegeli P, Delorenzi M, Cario G, Loh ML, Schrappe M, Stanulla M, Kulozik AE, Muckenthaler MU, Saha V, Irving JA, Meisel R, Radimerski T, Stackelberg von A, Eckert C, Tyner JW, Horvath P, Bornhauser BC, Bourquin J-P. Ex vivo drug response profiling detects recurrent sensitivity patterns in drug-resistant acute lymphoblastic leukemia. Blood. 2017 Mar 16;129(11):e26–e37.

  • McComb S, Aguadé-Gorgorió J, Harder L, Marovca B, Cario G, Eckert C, Schrappe M, Stanulla M, Stackelberg von A, Bourquin J-P, Bornhauser BC. Activation of concurrent apoptosis and necroptosis by SMAC mimetics for the treatment of refractory and relapsed ALL. Sci Transl Med. 2016 May 18;8(339):339ra70–0. Equal last author

  • Fischer U, Forster M, Rinaldi A, Risch T, Sungalee S, Warnatz H-J, Bornhauser B, Gombert M, Kratsch C, Stütz AM, Sultan M, Tchinda J, Worth CL, Amstislavskiy V, Badarinarayan N, Baruchel A, Bartram T, Basso G, Canpolat C, Cario G, Cavé H, Dakaj D, Delorenzi M, Dobay MP, Eckert C, Ellinghaus E, Eugster S, Frismantas V, Ginzel S, Haas OA, Heidenreich O, Hemmrich-Stanisak G, Hezaveh K, Höll JI, Hornhardt S, Husemann P, Kachroo P, Kratz CP, Kronnie GT, Marovca B, Niggli F, McHardy AC, Moorman AV, Panzer-Grümayer R, Petersen BS, Raeder B, Ralser M, Rosenstiel P, Schäfer D, Schrappe M, Schreiber S, Schütte M, Stade B, Thiele R, Weid NVD, Vora A, Zaliova M, Zhang L, Zichner T, Zimmermann M, Lehrach H, Borkhardt A, Bourquin J-P, Franke A, Korbel JO, Stanulla M, Yaspo M-L. Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options. Nat Genet. 2015 Sep;47(9):1020–9. Equal last author and corresponding.

Hyun-Dong Chang
Schwiete-Laboratory for Microbiota and Inflammation, Deutsches Rheuma-Forschungszentrum (DRFZ) Berlin, a Leibniz Institute, Berlin, Germany

T cells, Microbiota, Chronic Inflammation

Hyun-Dong Chang studied biology at the Free University Berlin and at the University of California, San Diego (UCSD). During his PhD thesis at the German Rheumatism Research Center (DRFZ) Berlin, he studied the regulation of cytokine expression in T cells. His research focused on the establishment and maintenance of a functional memory in T cells, in particular the molecular basis and prerequisites of epigenetic and functional imprinting of T cells for cytokine expression and the molecular adaptations of T cells to chronic inflammation allowing them to function and persist in inflamed tissue. He is the scientific leader of the flow cytometry core facility of the DRFZ and past president of the German Society for Cytometry (DGfZ). As the group leader of the Schwiete-Laboratory for Microbiota and Inflammation at the DRFZ, his current research activities focus on understanding the role of the intestinal microbiota in the prevention, triggering and maintenance of chronic inflammation.


  • Maschmeyer P, Petkau G, Siracusa F, Zimmermann J, Zügel F, Kühl AA, Lehmann K, Schimmelpfennig S, Weber M, Haftmann C, Riedel R, Bardua M, Heinz GA, Tran CL, Hoyer BF, Hiepe F, Herzog S, Wittmann J, Rajewsky N, Melchers FG, Chang HD, Radbruch A, Mashreghi MF. Selective targeting of pro-inflammatory Th1 cells by microRNA-148a-specific antagomirs in vivo. J Autoimmun 89:41-52, 2018

  • Cossarizza A*, Chang HD*, Radbruch A*, et al. Guidelines for the use of flow cytometry and cell sorting in immunological studies. Eur J Immunol 47:1584-1797, 2017.

  • Zimmermann J, Hübschmann T, Schattenberg F, Schumann J, Durek P, Riedel R, Friedrich M, Glauben R, Siegmund B, Radbruch A, Müller S, Chang HD. High-resolution microbiota flow cytometry reveals dynamic colitis-associated changes in fecal bacterial composition. Eur J Immunol 46:1300-3, 2016.

  • Zimmermann J, Kühl AA, Weber M, Grün JR, Löffler J, Haftmann C, Riedel R, Maschmeyer P, Lehmann K, Westendorf K, Mashreghi MF, Löhning M, Mack M, Radbruch A, Chang HD. T-bet expression by Th cells promotes type 1 inflammation but is dispensable for colitis. Mucosal Immunol. 9(6):1487-1499, 2016. 

  • Niesner U, Albrecht I, Janke M, Doebis C, Loddenkemper C, Lexberg MH, Eulenburg K, Kreher S, Koeck J, Baumgrass R, Bonhagen K, Kamradt T, Enghard P, Humrich JY, Rutz S, Schulze-Topphoff U, Aktas O, Bartfeld S, Radbruch H, Hegazy AN, Löhning M, Baumgart DC, Duchmann R, Rudwaleit M, Häupl T, Gitelman I, Krenn V, Gruen J, Sieper J, Zeitz M, Wiedenmann B, Zipp F, Hamann A, Janitz M, Scheffold A, Burmester GR, Chang HD, Radbruch A. Autoregulation of Th1-mediated inflammation by twist1. J Exp Med 205:1889-901, 2008. 

  • Lexberg MH, Taubner A, Förster A, Albrecht I, Richter A, Kamradt T, Radbruch A, Chang HD. Th memory for interleukin-17 expression is stable in vivo. Eur J Immunol 38:2654-64, 2008. 

Andrea Cossarizza
Director of the School of Specialization in Clinical Pathology, University of Modena and Reggio Emilia School of Medicine, Italy
President of the ISAC

Topic: Single cell analysis in monitoring the immunotherapy of cancer

Professor of Pathology and Immunology at the University of Modena and Reggio Emilia and ISAC President,  has been working on HIV infection, aging and longevity, mitochondria and apoptosis, and on these topics has published more than 320 papers in peer-reviewed journals.

He has >30 years of experience in Immunology, and in particular in the development and use of original cytometric approaches for sophisticated and innovative analysis. His longstanding research commitments are centered into identifying the molecular and cellular basis of the involvement of the immune system in several diseases and infections, such as HIV/AIDS, hepatitis, and sepsis. His interests also embrace different physiopathological conditions, that include those of neurodegenerative origin (multiple sclerosis, Alzheimer disease, amyothrophic lateral sclerosis) or human aging, either physiological (with the model of healthy centenarians) and pathological (Down’s syndrome), along with inflammaging. During the past decade he has built expertise in the clinical application of new methods for the identification of rare cellular subsets to patients affected by HIV infection and to patients undergoing liver transplantation, as well as in patients suffering of multiple sclerosis or patients during septic shock. Such methods are now allowing a new and fine characterization of the functional activities of these cells. Prof. Cossarizza has published more than 300 full papers on peer-reviewed international journals, authored >90 papers or chapters on books or conference proceedings and presented >450 communications to conferences and meetings. His papers have received >19,000 citations.

Paula C. Fernandez, MD/PhD
FAMH Hämatologie

Topic: T-cell Lymphomas

After studying Medicine and Biology in Switzerland, she first focused on basic research working in cell signaling and gene regulation before changing to a clinical diagnostic laboratory. Currently she heads the Flow/Stem-cell laboratory at the Kantonsspital Aarau, Switzerland, which provides diagnostic services in hemato-oncology and cryopreserves autologous stem cell transplants. In addition, she is active in teaching clinical flow cytometry nationally and internationally, was involved in the national, and currently serves the European Society for Clinical Cell Analysis as president. She is interested in the standardization of immunophenotyping in diagnostics and an affiliated laboratory of the EuroFlow Consortium.

Selected publications

  • Flores-Montero J, Kalina T, Corral-Mateos A, Sanoja-Flores L, Pérez-Andrés M, Martin-Ayuso M, Sedek L, Rejlova K, Mayado A, Fernández P, van der Velden V, Bottcher S, van Dongen JJM, Orfao A. Fluorochrome choices for multi-color flow cytometry. J Immunol Methods. 2019 Jun 7. pii: S0022-1759(19)30132-2. doi: 10.1016/j.jim.2019.06.009. 

  • Kalina T, Brdickova N, Glier H, Fernandez P, Bitter M, Flores-Montero J, van Dongen JJ, Orfao A;Frequent issues and lessons learned from EuroFlow QA; Frequent issues and lessons learned from EuroFlow QA. Frequent issues and lessons learned from EuroFlow QA.; J Immunol Methods. 2018 Sep 17. pii: S0022-1759(17)30140-0. doi: 10.1016/j.jim.2018.09.008

  • Nováková M, Glier H, Brdičková N, Vlková M, Santos AH, Lima M, Roussel M, Flores-Montero J,  Szczepanski T, Böttcher S, van der Velden VHJ, Fernandez P, Mejstříková E, Burgos L, Paiva B, van Dongen JJM, Orfao A, Kalina T. How to make usage of the standardized EuroFlow 8-color protocols possible for instruments of different manufacturers; J Immunol Methods. 2017 Nov 20. pii: S0022-1759(17)30139-4. doi: 10.1016/j.jim.2017.11.007

  • Lhermitte L, Mejstrikova E, van der Sluijs-Gelling A, Grigore G, Sedek L, Bras AE, Gaipa G, Sobral da Costa E, Novakova , Sonneveld E, Buracchi C, de Sá Bacelar T, Te Marvelde J, Trinquand A, Asnafi V, Szczepanski T, Matarraz S, Lopez A, Vidriales B, Bulsa J, Hrusak O, Kalina T, Lecrevisse Q, Martin Ayuso M, Brüggemann M, Verde J, Fernandez P, Burgos L, Paiva B, Pedreira CE, van Dongen JJ, Orfao A, van der Velden VH.; Automated database-guided expert-supervised orientation for immunophenotypic diagnosis and classification of acute leukemia; Leukemia. 2018 Apr;32(4):874-881. doi: 10.1038/leu.2017.313. Epub 2017 Nov 1

  • Glier H, Heijnen I, Hauwel M, Dirks J, Quarroz S, Lehmann T, Rovo A, Arn K, Matthes T, Hogan C, Keller P, Dudkiewicz E, Stüssi G, Fernandez P; Swiss Cytometry Society; Standardization of 8-color flow cytometry across different flow cytometer instruments: A feasibility study in clinical laboratories in Switzerland; J Immunol Methods. 2017 Jul 29. pii: S0022-1759(17)30205-3. doi: 10.1016/j.jim.2017.07.013

  • P.Fernandez, M.Solenthaler, O.Spertini, S.Quarroz, A.Rovo, PY.Lovey, L.Leoncini, S.Ruault-Jungblut, M.D’Asaro, M. Docquier, P.Descombes, T.Matthes.  Using digital RNA counting and flow cytometry to compare mRNA with protein expression in acute leukemias. PLoS One, 2012;7(11)


Zdeněk Hel

Topic: Altered Myelopoiesis in Infection and Cancer

Curriculum VitaeBio

Brian Husband
Department of Integrative Biology, College of Biological Science, University of Guelph, Ontario Canada
Professor and Associate Dean (Academic)

Topic: Advances in plant population biology through flow cytometry

Scientific interests: plant population dynamics, function and evolution of plant reproductive systems, polyploidy, pollination, mating systems, hybridization, DNA barcoding, conservation biology.  Pioneered use of flow cytometry for studying formation and evolutionary dynamics of polyploids using field and experimental approaches.

Favourite cytometry applications: pollen quality, plant siring success, population cytotype structure using genome size

Featured relevant publications:

  • Sabara, H.A., P. Kron, and B.C. Husband. 2013. Cytotype coexistence leads to triploid hybrid production in a diploid-tetraploid contact zone of Chamerion angustifolium. American J. Botany, 100:1-9.

  • Husband, B.C., S.J. Baldwin and J. Suda. 2012. The incidence of polyploidy in plants: major patterns and evolutionary processes. In, Plant Genomic Diversity Vol II, (J. Greilhuber, J. Dolezel, J.F. Wendel, Eds.) Springer-Verlag

  • Kron, P. and B.C. Husband 2012. Using flow cytometry to estimate pollen DNA content: improved methodology and applications. Annals of Botany 110:1067-1078. doi:10.1093/aob/mcs167

  • Baldwin, S.J. and B.C. Husband. 2010. Genome duplication and the evolution of conspecific pollen precedence. Proc Roy Soc. B. 278:2011-2017. doi: 10.1098/rspb.2010.2208

  • Kron, P., J. Suda, and B.C. Husband. 2007. Applications of flow cytometry to evolutionary and population biology. Annu. Rev. Ecol. Evol. Syst. 38:847-876.

Kanutte Huse
Department of Cancer Immunology, Oslo University Hospital, Norway
Head engineer at the Flow Cytometry Core Facility, responsible for their CyTOF2 mass cytometer

Topic: Immune profiling of lymph nodes from breast cancer patients by mass cytometry

She graduated in 2011 and her PhD work was on the role of TGF-β growth factors in normal and malignant B cells. As a postdoc she worked on B-cell signaling and spent a year in the lab of Jonathan Irish, Vanderbilt University, to learn mass cytometry technology and data analysis. In her current work she uses high-dimensional cytometry, phospho-flow and imaging mass cytometry to investigate tumor-infiltrating immune cells in lymphoma and other cancer types.

Recent publications:

  • Huse K, Wogsland CE, Polikowsky HG, Diggins KE, Smeland EB, Myklebust JH*, Irish JM*. Human germinal center B cells differ from naïve and memory B cells in CD40 expression and CD40L-induced signaling response. * denotes equal contribution. Cytometry A 2019.

  • Josefsson SE, Beiske K, Blaker YN, Førsund MS,  Østenstad B, Kimby E, Köksal H, Wälchli S, Bai B,  Smeland EB, Levy R, Kolstad A, Huse K, Myklebust JH. TIGIT and PD-1 mark intratumoral T cells with reduced effector function in B-cell non-Hodgkin lymphoma. Cancer Immunol Res 2019.

  • Josefsson SE, Huse K, Kolstad A, Beiske K, Pende D, Steen CB, Inderberg EM, Lingjærde OC, Østenstad B, Smeland EB, Levy R, Irish JM, Myklebust JH. T Cells Expressing Checkpoint Receptor TIGIT Are Enriched in Follicular Lymphoma Tumors and Characterized by Reversible Suppression of T-cell Receptor Signaling. Clin Cancer Res 2017.

  • Wogsland CE, Greenplate AR, Kolstad A, Myklebust JH, Irish JM, Huse K. Mass cytometry of follicular lymphoma tumors reveal intrinsic heterogeneity in proteins including HLA-DR and a deficit in nonmalignant plasmablast and germinal center B-cell populations. Cytometry B Clin Cytom 2017.

Dr. Shyamala Maheswaran

Massachusetts General Hospital, Boston, USA

Topic: Epithelial to Mesenchymal Transition: A dynamic Process Contributing to Genomic Diversity​

Dr. Shyamala Maheswaran’s research  is focused on defining the molecular mechanisms that drive breast cancer progression and metastasis. Breast cancer, initially confined to the primary site, eventually spreads to distal sites, including lung, liver, bone and brain, by invading into the bloodstream. Upon reaching these distal sites, the tumor cells continue to grow and evolve well after removal of the primary tumor resulting in overt metastasis and disease recurrence, the leading causes of cancer-related deaths. Using cell culture and mouse models and patient derived tissues and circulating tumor cells (CTCs) enriched from breast cancer patients’ blood, Dr. Maheswaran's laboratory characterizes the contribution of oncogenic cues, tumor microenvironment-derived signals, epithelial to mesenchymal transition and tumor heterogeneity to breast cancer progression and therapeutic responses. She collaborates closely across several disciplines including Clinicians and Engineers at MGH and is currently the Scientific Director of the Center for Cancer Risk Assessment at the Massachusetts General Hospital (MGH).


  • Comaills V, Kabeche L, Morris R, Buisson R, Yu M, Madden MW, LiCausi JA, Boukhali M, Tajima K, Pan S, Aceto N, Sil S, Zheng Y, Sundaresan T, Yae T, Jordan NV, Miyamoto DT, Ting DT, Ramaswamy S, Haas W, Zou L, Haber DA, Maheswaran S. Genomic Instability Induced by Persistent Proliferation of Cells Undergoing Epithelial-to- Mesenchymal Transition. Cell Reports 17, 2632–2647 (2016)

  • Tajima K, Yae T, Javaid S, Tam O, Comaills V, Morris R, Wittner BS, Liu M, Engstrom A, Takahashi F, Black JC, Ramaswamy S, Shioda T, Hammell M, Haber DA, Whetstine JR, Maheswaran S. SETD1A modulates cell cycle progression through a miRNA network that regulates p53 target genes. Nature Comm 2015 6:8257

  • Aceto N, Bardia A, Miyamoto DT, Donaldson MC, Wittner BS, Spencer JA, Yu M, Pely A, Engstrom A, Zhu H, Brannigan BW, Kapur R, Stott SL, Shioda T, Ramaswamy S, Ting DT, Lin CP, Toner M, Haber DA*, Maheswaran S*. Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell. 158(5):1110-22, 2014.

  • Yu M, Bardia A, Wittner BS, Stott SL, Smas ME, Ting DT, Isakoff SJ, Ciciliano JC, Wells MN, Shah AM, Concannon KF, Donaldson MC, Sequist MV, Brachtel E, Sgroi D, Baselga J, Ramaswamy S, Toner M, Haber DA, Maheswaran S. Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Composition. Science. 339(6119): 580-584, 2013.

  • Chiba N, Comaills V, Shiotani B, Takahashi F, Shimada T, Tajima K, Winokur D, Hayashida T, Willers H, Brachtel E, Vivanco MD, Haber DA, Zou L, Maheswaran S. Homeobox B9 induces epithelial-to-mesenchymal transition-associated radioresistance by accelerating DNA damage responses. Proc Natl Acad Sci U S A. 109(8):2760-5, 2012.

Ester Mejstrikova
Prague, Czech Republic

Topic: Lineage plasticity of acute leukemias

Ester Mejstrikova studied Medicine and PhD in Immunology in Prague at 1st and 2nd Faculty of Medicine. In 2001 she joined CLIP (Childhood Leukemia Investigation Prague) group as medical student. She focused on problematic of minimal residual disease assessment and mechanisms of bone marrow failure in childhood. She described lineage switch phenomenon towards monocytic lineage in B cell precursor leukemia.

Selected publications:

  • Mejstríková E, Hrusak O, Borowitz MJ, Whitlock JA, Brethon B, Trippett TM, et al. CD19-negative relapse of pediatric B-cell precursor acute lymphoblastic leukemia following blinatumomab treatment. Blood Cancer J. 2017 Dec 20 7(12):659. 

  • Novakova M, Zaliova M, Sukova M, Wlodarski M, Janda A, Fronkova E, et al. Loss of B cells and their precursors is the most constant feature of GATA-2 deficiency in childhood myelodysplastic syndrome. Haematologica. 2016 Mar 24

  • Mejstrikova E, Volejnikova J, Fronkova E, Zdrahalova K, Kalina T, Sterba J, et al. Prognosis of children with mixed phenotype acute leukemia treated on the basis of consistent immunophenotypic criteria. Haematologica. 2010 Jun;95(6):928–35. 

  • Slamova L, Starkova J, Fronkova E, Zaliova M, Reznickova L, van Delft FW, et al. CD2-positive B-cell precursor acute lymphoblastic leukemia with an early switch to the monocytic lineage. Leukemia. Nature Publishing Group; 2014 Mar;28(3):609–20. 

Bruno Paiva, Ph.D.
Flow Cytometry Core, CIMA LAB diagnostics, University of Navarra, Pamplona, Spain

Topic: Flow cytometry for comprehensive monitoring of multiple myeloma

Bruno Paiva is a research fellow of the Departments of Hematology and Immunology at the Clinica Universidad de Navarra (CUN) and Centro de Investigaciones Medicas Aplicadas (CIMA), Pamplona, Spain. Dr. Paiva is also the Director of the Flow Cytometry Core, and Scientific Coordinator of CIMA LAB diagnostics, the Laboratory Diagnostic Core of the University of Navarra. He graduated in Pharmaceutical Sciences at the University of Coimbra, Portugal, in 2007. Then, he spent a training period in Prof. Alberto Orfao’s laboratory focusing on immunophenotypic in acute myeloid leukemia. Afterwards, he joined the Immunopathology laboratory in the Hematology Department at the University Hospital of Salamanca, and started a Ph.D program under the supervision of Prof. Jesús F. San Miguel. He received his Ph.D in 2011 from the Medical School of the University of Salamanca, where he studied the clinical value of multiparameter flow cytometry immunophenotyping of plasma cells in multiple myeloma patients. Dr Paiva’s main area of work is on multiparameter flow cytometry evaluation of hematological malignancies. His main research interests focus on improving the differential diagnosis, risk stratification, and monitoring of patients with hematological malignancies, particularly monoclonal gammopathies (MGUS, smoldering and symptomatic multiple myeloma, Waldenström’s macroglobulinaemia, or amyloidosis) but also acute leukemias and lymphoproliferative disorders. Dr. Paiva is an author or co-author of several publications in peer-reviewed journals.

Josef Spidlen
Flowjo, Ashland, OR, USA

Recent advancements in computational cytometry and making those accessible to bench top scientists

Josef Spidlen received his MSc in Computer Science and his PhD in Biomedical Informatics from the Charles University in Prague. His career includes 5 years as a researcher at the Institute of Computer Science, Academy of Sciences of the Czech Republic, and over a decade as a scientist at the Terry Fox Laboratory, BC Cancer Agency in Vancouver, Canada. Josef developed many R packages and dozens of GenePattern modules for computational flow cytometry data analysis. He also led the development of FlowRepository for over 5 years; he is an active member of ISAC, an ISAC Marylou Ingram Scholar and the first author of several cytometry standards including FCS, Gating-ML and MIFlowCyt. In 2016, Josef joined FlowJo to help bring the advancements of computational biology to benchtop scientists by leading a team to drive innovation in FlowJo products. He was responsible for implementing algorithms, data handling and analytical capabilities of FlowJo as well as FlowJo's single cell sequencing data analysis tool SeqGeq. Currently, FlowJo is integrated in BD as the "Informatics Platform" of BD Life Sciences. As of February 2019, Josef has been promoted to the Senior Director, R&D of the Informatics platform leading engineering, bioinformatics, quality assurance, design and development teams to deliver science-first informatics solutions in flow cytometry and single cell multi-omics. He is accountable for setting the technical vision and direction for FlowJo's portfolio, execution on the Informatics strategy, delivering FlowJo's suite of cloud and desktop applications as well as driving development activities for new technology, strategy and computational approaches in Informatics. In his lecture, Josef will introduce recent advancements in computational cytometry and discuss how those can be used in a variety of both commercial and open source tools widely available to clinicians and researchers without computer programming skills.

Stavros Stavrakis
Department of Chemistry and Applied Biosciences at ETH Zurich, Switzerland

Website: https://demellogroup.ethz.ch/en/people?id=7

Topic: Optofluidic platforms for high-throughput and high precision measurements in flow cytometric detection

Stavros is currently a Senior Scientist in the deMello group in the Department of Chemistry and Applied Biosciences at ETH Zurich. He received his B.Sc. in Chemistry and Ph.D in Biophysical Chemistry from the University of Crete (Greece) in 2005. His research was focused on the application of time-resolved vibrational spectroscopies such as FTIR and Raman, applied to enzymatic systems. In 2007 Dr Stavrakis was awarded an Individual Outgoing Marie Curie Fellowship. As a Marie Curie fellow, he spent three years with Prof. Stephen Quake at Stanford University specializing in single molecule biophysics. The focus of his research was to develop new technologies to improve the throughput of current single molecule DNA sequencing platforms. His current research interests are focused on applications of single molecule fluorescence detection, and optofluidics in biology. Currently he has a team of postdocs and students developing novel microfluidic platforms for single molecule enzymology, high-throughput imaging flow cytometry, fast enzyme kinetic analysis, fluorescence lifetime combined with droplet microfluidics and high-throughput microfluidic single-cell screening platforms. 

Ondřej Štěpánek
Research group of Adaptive Immunity, Institute of Molecular Genetics
Czech Academy of Sciences, Prague, Czech Republic

T cells, TCR, Signaling, Adaptive Immunity, Immune Tolerance

Ondřej Štěpánek studied molecular biology at the Charles University in Prague and performed his PhD research in immunology at the Institute of Molecular Genetics. He spent more than 4 years as a postdoctoral scientist at the Department of Biomedicine in Basel in the group of Ed Palmer. His research contributed to the understanding how developing T cells discriminate between high-affinity and low-affinity self-antigens in the thymus. In 2016, he established his own group focusing on T-cell fate decisions and analysis of the TCR and other signaling pathways.


  • Drobek A, Moudra A, Mueller D, Huranova M, Horkova V, Pribikova M, Ivanek R, Oberle S, Zehn D, McCoy KD, Draber P, Stepanek O: Strong homeostatic TCR signals induce formation of self-tolerant virtual memory CD8 T cells. EMBO J 2018 37(14).

  • Palmer E, Drobek A, Stepanek O: Opposing effects of actin signaling and LFA-1 on establishing the affinity threshold for inducing effector T-cell responses in mice. Eur J Immunol 2016 46(8): 1887-901.

  • Coreceptor scanning by the T cell receptor provides a mechanism for T cell tolerance. Stepanek O, Prabhakar AS, Osswald C, King CG, Bulek A, Naeher D, Beaufils-Hugot M, Abanto ML, Galati V, Hausmann B, Lang R, Cole DK, Huseby ES, Sewell AK, Chakraborty AK, Palmer E. Cell. 2014 Oct 9;159(2):333-45.

  • Lo WL, Shah NH, Ahsan N, Horkova V, Stepanek O, Salomon AR, Kuriyan J, Weiss A: Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT. Nat Immunol 2018.