Workshop in Computational Methods for Cytometry and Single-Cell Data

1 – 3 September 2017, Heraklion, Crete


Welcome !

With great pleasure we announce the second International Workshop on Computational Methods for Single-Cell data. The event is jointly organized by the University of Crete in collaboration with the Karolinska Institutet and the University of Amsterdam under the aegis of the European Research Council (ERC – CAUSALPATH and CAFES projects).

The workshop aims to bring together computational researchers, biologists, translational clinicians, and biotechnologists performing related research. It is meant as a forum for brainstorming, exchanging work-in-progress, forging collaborations, and strategizing about the future of computational methods for single-cell data.

Our primary goal during this workshop will be to spark fruitful discussions by exchanging ideas and research findings related to the ambitious objectives of MASSCAUSAL. We hope that our enthusiasm will engage the workshop’s participants to open up the many potential challenges for research in the field and identify new possibilities for collaboration and interaction.

Workshop Topics

The topics to be addressed during the workshop are (but not limited to) the following:

  • Single cell technologies: Flow Cytometry, Mass Cytometry, Genomics, Imaging
  • Biology: Signaling pathways, Gene Networks, Immunology
  • Modeling: Systems Biology, ODEs/SDEs, Statistical Modeling, Bayesian Networks, Causal Discovery
  • Data & Software: Open/Commercial tools, Repositories, Data/Code sharing, Challenges (+ special eventRAMP)

Organizing Committee

Local Organizers

Keynote Speakers

Boris Kholodenko (Systems Biology Center, University College Dublin)
Gustavo A. Stolovitzky (IBM Research, DREAM Challenges)
Ryan Brinkman (Department of Medical Genetics, University of British Columbia, Terry Fox Laboratory) – ISAC Lecture



Ioannis Tsamardinos (University of Crete)
Jesper Tegnér (Karolinska University and King Abdullah University of Science and Technology (KAUST))
Joris M. Mooij (University of Amsterdam)
David Gomez-Cabrero (King’s College London)
Giorgos Papoutsoglou (University of Crete)
John Strouboulis (IMBB-FORTH)
Nima Aghaeepour (Stanford University)
Tom Claassen (Radboud University Nijmegen)
Balazs Kegl (CNRS Research, University of Paris-Sud, RAMP)
Wesley Herb Anderson (The KLI Institute)
Oliver Stegle (EMBL – EBI)
Michalis Aivaliotis (IMBB-FORTH)
Mark D. Robinson (Institute of Molecular Life Sciences, University of Zurich)
Leonidas Alexopoulos (Systems Biology & Bioengineering Research Laboratory, NTUA)
Sofia Triantafillou (Rehabilitation Institute of Chicago, Northwestern University)
Manfred Claassen (Institute of Molecular Systems Biology, ETH Zurich)
Nadine Peyriéras (CNRS – N&D, Institut de Neurobiologie Alfred Fessard, BioEmergences Lab)
René Doursat (Informatics Research Centre, Manchester Metropolitan University, UK)
Lakshmikanth Tadepally (National Mass Cytometry Facility, SciLifeLab, Karolinska University)
Nikolaos-Modestos Kougioulis (School of Mathematics, Aristotle University of Thessaloniki)
James Cussens (Department of Computer Science, University of York)
Anna Klimovskaia (Institute of Molecular Systems Biology, ETH Zurich)
Bryan Andrews (Intelligent Systems Program, University of Pittsburgh)
Tineke Blom (University of Amsterdam)
Sara Magliacane (University of Amsterdam)
Patrick Forre (University of Amsterdam)
Philip Versteeg (University of Amsterdam)
Angelika Schmidt (Karolinska University)
Szabolcs Elias (Karolinska University)
Klio Lakiotaki (University of Crete)
Georgios Georgakopoulos (Universiry of Crete)
Maria Markaki (University of Crete)
Vincenzo Lagani (University of Crete)
Michail Tsagris (University of Crete)
Yannis Pantazis (University of Crete)
Giorgos Borboudakis (University of Crete)
Christos Tselas (University of Crete)
Iordanis Xanthopoulos (University of Crete)
Konstantinos Tsirlis (University of Crete)


Kathrine Drake, Cytobank, Inc.
Christoph Freier, FlowJo, LLC
Pavlos Charonyktakis, Gnosis – Data Analysis


MASSCAUSAL is an invitation-only event. If you haven’t been contacted yet, but you’d like to attend, please e-mail us.

Because this year we expect the MASSCAUSAL event to be much larger, there will be a registration fee. The regular fee will be 400€ for invited senior participants and 200€ for students. Registration includes workshop, coffee breaks, everyday lunch, and conference dinner (possibly more).

Please download the following forms:

Registration Form: pdf(english)
Form for Invoice or Receipts: doc(greek), doc(english)

Please send the completed forms along with the proof of payment to Glykeria Fragioudaki by July, 28: glykeria.frag at (with cc: mar.papadaki at

Workshop Schedule

The following outline provides an overview of the schedule of the meeting. You may also download the detailed agenda from here: pdf (MASSCAUSAL_program)

Friday, 1 September

09:00 10:00 Welcome Reception
10:00 13:00 Morning Session
13:00 14:00 Lunch break
14:00 15:30 Afternoon Session
15:30 16:00 Coffee break
16:00 17:00 Afternoon Session
17:00 20:00 Afternoon Activity
21:00 Dinner

Saturday, 2 September

09:30 11:00 Morning Session
11:00 11:30 Coffee break
11:30 13:00 Morning Session
13:00 14:00 Lunch break
14:00 15:30 Afternoon Session
15:30 16:00 Coffee break
16:00 17:00 Afternoon Session
17:00 20:00 Afternoon Activity
21:00 Dinner

Sunday, 3 September

09:30 11:00 Morning Session
11:00 11:30 Coffee break
11:30 13:00 Morning Session
13:00 14:00 Lunch break


The event will take place at Hotel Amirandes, Gouves (17km East of Heraklion Airport —HER, see link)

new-amirandes-logo-ten-years-gold-17450AMIRANDES GRECOTEL EXCLUSIVE RESORT
GR-711 10 Gouves Heraklion, Crete, Greece
Tel: +30 28970 41103
Fax: +30 28970 41113
Workshop special rate: 270€ (single), 295€ (double) —use “MassCausal” as discount code or follow this link to book online


Recommended Accommodation
Other accommodation options we recommend will be at a walking distance from the venue site or in the city center from where transportation will be provided. Please note that the beginning of September is still high season period for Crete. Therefore, there is limited availability to these options.

Vlihadas str., 70014, Kato Gouves, Heraklion, Crete, Greece
Tel: +30 28970 42025
Workshop special rate (by June, 30): 171€ (single), 195€ (double) —use “MassCausal” as discount code.

26 Koroneou & Agiou Titou str., 71202 – Heraklion, Greece
Tel: (+30) 281/0282020
Fax: (+30) 281/0282022
Workshop special rate (limited availability after July, 15): 75€/85€ (classic/executive single), 85€/95€ (classic/executive double) —use “MassCausal” as discount code.


This project has received funding from the European Research Council (ERC) under the European Union’s Seventh under the European Union’s Seventh Framework Programme (FP/2007-2013) (grant agreements No 617393 and 639466)