profile_picture
Jonas Simon Fleck
Scientist, Roche Institute of Human Biology
jonas_simon dot fleck at roche dot com

I’m a postdoctoral scientist with Gray Camp at the Institute of Human Biology in Basel. I’m collaborating with Aviv Regev to develop predictive ML models for high-thoughput perturbation screens in organoids and with Fabian Theis to assemble integrated single-cell genomic atlases of various organoid systems.

I recently graduated from ETH Zürich with a Ph.D. in Computational & Systems Biology. During my PhD in the lab of Barbara Treutlein I applied and developed statistical and machine learning methods to decipher the gene regulatory logic of cell fate decisions in brain organoids. My PhD work was also supported by a Boehringer Ingelheim Fonds fellowship.

Before that, I worked as a Master student in the group of Georg Zeller at EMBL Heidelberg, where I developed a method for prediction of biosynthetic gene clusters from metagenomic assemblies using conditional random fields.

I am excited about the intersection of high-throughput biology and machine learning and I am convinced that it will revolutionize biology towards a more predictive science. I am always open for collaborations and new ideas, so feel free to reach out to me via email or social media.

Outside of science I enjoy eating and making tasty things, dabbling in graphic design, climbing rocks and building blinking glucose lamps.

Interests

  • (Single-cell) genomics
  • Machine learning
  • Predictive biology
  • Organoids
  • Stem cell engineering

Academia

ETH Zürich
2019 - 2022
Ph.D. Computational & Systems Biology
Ruprecht-Karls University of Heidelberg
2016 - 2018
M.Sc. Molecular Biotechnology / Bioinformatics
Ruprecht-Karls University of Heidelberg
2012 - 2016
B.Sc. Biosciences

Publications

Single-cell epigenomic reconstruction of developmental trajectories in human neural organoid systems from pluripotency, 2024, bioRxiv (accepted in Nat Neurosci)
Fides Zenk* , Jonas Simon Fleck* , Sophie Martina Johanna Jansen , Bijan Kashanian , Benedikt Eisinger , Małgorzata Santel , Jean Dupre , J. Gray Camp , Barbara Treutlein
An integrated transcriptomic cell atlas of human neural organoids, 2023, bioRxiv
Zhisong He* , Leander Dony* , Jonas Simon Fleck* , Artur Szałata , Katelyn X. Li , Irena Slišković , Hsiu-Chuan Lin , Malgorzata Santel , Alexander Atamian , Giorgia Quadrato , Jieran Sun , Sergiu P. Paşca , J. Gray Camp , Fabian Theis , Barbara Treutlein
Single-cell brain organoid screening identifies developmental defects in autism, 2023, Nature
Chong Li* , Jonas Simon Fleck* , Catarina Martins-Costa , Thomas R. Burkard , Marlene Stuempflen , Ábel Vertesy , Angela Maria Peer , Christopher Esk , Ulrich Elling , Gregor Kasprian , Nina S. Corsini , Barbara Treutlein , Juergen A. Knoblich
What is a cell type?, 2023, Science
Jonas Simon Fleck , J Gray Camp , Barbara Treutlein
Multimodal spatiotemporal phenotyping of human organoid development, 2023, Nature Biotechnology
Philipp Wahle* , Giovanna Brancati* , Christoph Harmel* , Zhisong He* , Gabriele Gut , Aline Santos , Qianhui Yu , Pascal Noser , Jonas Simon Fleck , [...] , Lucas Pelkmans , Barbara Treutlein , J. Gray Camp
Inferring and perturbing cell fate regulomes in human brain organoids, 2022, Nature
Jonas Simon Fleck* , Sophie Martina Johanna Jansen* , Damian Wollny , Fides Zenk , Makiko Seimiya , Akanksha Jain , Ryoko Okamoto , Malgorzata Santel , Zhisong He , J. Gray Camp , Barbara Treutlein
Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration, 2022, Science
Katharina Lust* , Ashley Maynard* , Tomás Gomes* , Jonas Simon Fleck , J. Gray Camp , Elly M. Tanaka , Barbara Treutlein
Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases, 2022, Cell Stem Cell
Jonas Simon Fleck* , Fátima Sanchís-Calleja* , Zhisong He , Malgorzata Santel , Michael James Boyle , J. Gray Camp , Barbara Treutlein
Accurate de novo identification of biosynthetic gene clusters with GECCO, 2021, bioRxiv
Laura M. Carroll* , Martin Larralde* , Jonas Simon Fleck* , Ruby Ponnudurai , Alessio Milanese , Elisa Cappio , Georg Zeller
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer, 2019, Nature Medicine
Jakob Wirbel* , Paul Theodor Pyl* , Ece Kartal , Konrad Zych , Alireza Kashani , Alessio Milanese , Jonas Simon Fleck , [...] , Peer Bork , Georg Zeller 
Organoid single-cell genomic atlas uncovers human-specific features of brain development, 2019, Nature
Sabina Kanton* , Michael James Boyle* , Zhisong He* , Malgorzata Santel , Anne Weigert , Fátima Sanchís-Calleja , Patricia Guijarro , Leila Sidow , Jonas Simon Fleck , [...] , Svante Pääbo , Barbara Treutlein , J. Gray Camp 

Projects

snapseed - GPU-accelerated celltype annotation
Pando - Multiome GRN inference
VoxHunt - reference mapping of organoid single-cell data
GECCO - Gene Cluster prediction using Conditional Random Fields
LatentLego - flexible latent spaces for single cells