Single Cell Data

Tätigkeiten der Projektgruppe

(October 2021) 

On Sept 28, 2021, the GMDS project group on single-cell data organized its second workshop, this time as part of the annual (virtual) GMDS conference. Thus, many of the participants and the speakers contributing the short talks had to pay the congress fee, in return for being able to attend many other omics-related, bioinformatics and biostatistics events distributed over the entire week. Overall, we had 35 attendants. From the application area perspective, we focussed on ageing and stem cell research, and the GSCN sponsored two speakers. Towards the end, the contributed talk by Benedikt Obermayer could not be done due to wifi failure, but it will be redone Jan 5, 2022 as part of the lunch seminars organized by the comprehensive cancer center Rostock/Greifswald. We are also planning a workshop in 2022, likely as part of the next GMDS meeting, which is intended to be a “real meeting” in Kiel. The session was not recorded this time, but for the slides, the presenters may be contacted. Highlights of the program were the introductory talks on aging and stem cell research and single-cell data, by João Pedro de Magalhães and Antonio del Sol, and by Martin Treppner on deep learning methods with a focus on designing single-cell experiments. Further talks focussed on cell competition in the embryo (Antonio Scialdone), identifying proliferating cardiomyocytes by integrative cluster analysis (Anne-Marie Galow), identifying rare cell types by synthetic oversampling (Markus Wolfien), and intercellular communication and aging (Cyril Lagger). At the end, Angela Pisco from the Chan Zuckerberg Biohub gave an invited lecture on the Tabula Muris Senis data, comprehensively describing the hallmarks of aging by single-cell transcriptomics. This and all the other talks gave rise to lively discussions and a lot of valuable insights were gained; we look forward to the next workshop for sure. 
Martin Treppner (Freiburg) and Georg Fuellen (Rostock).


(September 2021) You are cordially invited to our Sept 28 workshop at the GMDS TMF conference!

(February 2021)  We had a very interesting workshop on Feb 10, 2021, with 55 participants!

We plan to follow-up on this topic at a workshop that is part of the upcoming GMDS conference in September 2021, where we will also have presentations and discussions on other topics of interest regarding single-cell data. Stay tuned!

Here are the recordings and slides of the Feb 10 event:

  • Harald Binder (Freiburg) presentation as video or PDF
  • Katharina Schmid, Matthias Heinig (Munich) presentation as video or PDF
  • Kenong Su (Emory University, USA) presentation as video or PDF


(Dezember 2020) Wir laden ein zur ersten Veranstaltung:

"Power Analyses for single-cell Data" small workshop

Date & Venue: Wednesday Febr 10, 1615-18h, Zoom-meeting

You are cordially invited to a small virtual workshop on
"Power Analyses for single-cell Data". The meeting is intended
to bring together bioinformaticians, statisticians, experimentalists and clinicians
who are wondering how many samples are needed for robust single-cell based insights,
specifically (but not limited to) transcriptomics.


For the meeting,  please register here:

The preliminary program runs as follows:

1615-1630: Introduction

1630-1655: Harald Binder (Freiburg): "Deep generative models for designing single cell sequencing experiments"

1655-1720: Katharina Schmid, Matthias Heinig (Munich): "Design and power analysis for multi-sample single cell genomics experiments"

1720-1745: Kenong Su (Emory University, USA): "Simulation, Power Evaluation, and Sample Size Recommendation for Single Cell RNA-seq" (see the link for the abstract)

1745-1800: Discussion

We would be happy about your participation,
and forwarding of this announcement to interested parties.


(November 2020) Innerhalb des Fachbereich "Medizinische Bioinformatik & Systembiologie" gibt es seit 2020 eine Projektgruppe "Single Cell Data", zunächst geleitet von Georg Fuellen mit Unterstützung durch Harald Binder. Erste Aktivitäten sind ein Workshop zum Thema, mit Unterstützung des German Stem Cell Network, dieser wurde verschoben auf die Tagung in Kiel im September 2021. Bis dahin soll ein zoom-basiertes 1h-Meeting stattfinden in der zweiten Februarwoche 2021, zu "Power Analyses for single-cell Data", mit 2-3 Vorträgen/Softwarevorstellungen, zu scpower vom Helmholtz München und zu „Deep Generative Models“ aus Freiburg.


Tätigkeiten vom 1. Januar 2020 bis 31. Dezember 2020

Innerhalb des Fachbereichs "Medizinische Bioinformatik & Systembiologie" gibt es seit 2020 eine Projektgruppe "Single-Cell data", zunächst geleitet von Georg Fuellen mit Unterstützung durch Harald Binder. Erste Aktivität war ein Workshop zum Thema, "Power Analyses for single-cell Data", via Zoom im Februar 2021. Das Treffen war gedacht, um Bioinformatiker, Statistiker, Experimentatoren und Kliniker zusammenzubringen, die sich fragen, wie viele Proben für robuste Single-Cell-basierte Erkenntnisse benötigt werden, speziell (aber nicht beschränkt auf) Transkriptomik.

Trotz einer Konkurrenzveranstaltung zur gleichen Zeit gab es 55 interessierte Teilnehmer und eine Menge interessanter Diskussionen über die 3 sehr informativen Vorträge. Deren Aufzeichnungen und auch die Folien sind erhältlich unter , und zwar von Harald Binder zu "Deep generative models for designing single cell sequencing experiments", von Katharina Schmid zu "Design and power analysis for multi-sample single cell genomics experiments" und von Kenong Su aus den USA zu "Simulation, Power Evaluation, and Sample Size Recommendation for Single Cell RNA-seq".

Mit Unterstützung des German Stem Cell Network soll ein größerer -- zunächst für 2020 geplanter -- Workshop nun auf der GMDS/TMF-Tagung im September 2021 stattfinden.v