CompCancer Seminar 15.05.2024 - Francesco Iorio

For the seminar on the 15th of May at 11 am Viola Hollek invited Francesco Iorio from the Human Technopole (Milano, Italy), to give us a talk on his recent work. If you are interested in joining write an e-Mail to compcancer at charite dot de to receive the zoom link.

Dr. Francesco Iorio, a Research Group Leader in Computational Biology at the Human Technopole in Milan, with a rich background in computer science and a Ph.D. from the University of Salerno and the TeleThon Institute of Genetics and Medicine, has dedicated his career to advancing the fields of drug discovery and computational pharmacogenomics. His post-doctoral research at the prestigious EMBL-European Bioinformatics Institute and the Wellcome Sanger Institute has paved the way for innovative computational frameworks to predict and dissect drug sensitivity in cancer. He’s presenting his latest work published in Cancer Cell on constructing a map of cancer dependencies, integrating comprehensive multi-omics data with CRISPR-Cas9 screens across 930 cancer cell lines. This work illuminates the intricate relationships between molecular markers and cancer vulnerabilities and opens new avenues for drug development against cancer.


Save the date: Colloquium 2024

We are pleased to announce our CompCancer Colloquium!

This time with two different topics, taking place each time at 4 pm (mostly) on Wednesdays at HU Campus Nord.
The posters will follow once all the speakers have confirmed, however, please save already the following dates in your calendar:

Evolving Cancer Genomes:
Tue, 28.05.24         Isidro Cortes Ciriano  (EMBL-EBI, UK)
Wed, 10.07.24        Kisten Kübler   (BIH, DE)
Wed, 18.09.24        Francesca Ciccarelli (Francis Crick Institute, UK)

Modelling and Systems Biology:
Wed, 21.08.24       Laurence Calzone (Institut Curie, FR)
Wed, 23.10.24       Francis Levi (Université Paris-Saclay, FR)
Wed, 20.11.24       Andrea Ciliberto (IFOM, IT)



Colloquium 03.04.2024 - Marc Abrahams

For our first colloquium this year Marc Abrahams will give a talk about the IgNobel prize and Annals of Improbable Research!

Marc founded the Ig Nobel Prize Ceremony in 1991, and serves as master of ceremonies. The prizes — for achievements that make people LAUGH, then THINK — are handed out by genuine, bemused Nobel laureates in a gala event held every year at Harvard University

He co-founded and edits the magazine Annals of Improbable Research (AIR), and has written This is Improbable, The Ig Nobel Prizes, and other books.


When? April 3rd 2024 at 4 pm

Where? HU Campus North, Philipstr. 13, House 18, Lecture Hall 2  (Location)


We are looking forward to see you there for this exciting talk!

CompCancer Seminar 06.12.2023 - Dana Pe’er


For the seminar on the 6th of December Sofya Marchenko invited Dana Pe’er from the Sloan Kettering Institute (New York, USA), to give us a talk on her recent work. If you are interested in joining write an e-Mail to compcancer at charite dot de to receive the zoom link.

Because of the time difference, the literature seminar will take place virtually on zoom at 3 pm (Berlin- time).


Dr. Dana Pe’er is chair and professor in Computational and Systems Biology Program at Sloan Kettering Institute and a researcher in computational systems biology. She was previously a professor at columbia  Department of Biological Sciences. Pe’er’s research focuses on understanding the organization, function and evolution of molecular networks, particularly how genetic variations alter the regulatory network and how these genetic variations can cause cancer. Dana Pe’er investigates cellular development – in particular, how healthy cells shape their identities and build and repair organs, how cancer cells abandon those identities and hijack those processes, and how tissue environments influence an individual cell’s fate. Pe’er’s lab combines mathematical approaches with a range of emerging technologies that enable large-scale analyses of single cells. They are developing computational frameworks to characterize cell-state compositions and tissue-level dynamics and seeking to answer a variety of questions related to the causes and consequences of plasticity in development, regeneration, and cancer. For example, Pe’er wants to understand intratumoral heterogeneity which is essential for predicting cancer behavior and identifying molecular vulnerabilities.

Her Talk is titled „Beyond Cells: Gene programs and tissue context”. In which she will among others talk about methods and results from her very recent publication in Nature Biotechnology „Supervised discovery of interpretable gene programs from single-cell data” (



CompCancer Seminar 10.08.2023 - Niklas J. Lang

Our PhD student Karina Tristan invited Niklas J. Lang (MD candidate) to present at the CompCancer Literature Seminar, which will take place Thursday, 10th August, at 10 am.


It will be held in person at:

Maud Menten Hall

Philippstraße 13, Haus 18

10115 Berlin, Germany

[Google Maps link:]

If you are interested in joining online write an e-Mail to compcancer at charite dot de to receive the zoom link.


Paper: Ex vivo tissue perturbations coupled to single cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis 

Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivocytokine and drug perturbations of human precision-cut lung slices (hPCLS) with scRNAseq and induced a multi-lineage circuit of fibrogenic cell states in hPCLS, which we show to be highly similar to the in vivo cell circuit in a multi-cohort lung cell atlas from pulmonary fibrosis patients. Using micro-CT staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the ex vivo hPCLS model provides evidence that the basaloid cell state was derived from alveolar type-2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in the hPCLS model and anti-fibrotic drug treatments showed highly cell type specific effects. Our work provides an experimental framework for perturbational single cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration and pathology. We further demonstrate that hPCLS offers novel avenues for scalable, high-resolution drug testing to accelerate anti-fibrotic drug development and translation.

Niklas Lang's Bio:

Mr. Niklas Lang is a final-year medical student at LMU Munich (GER). He obtained his M.Sc. in Bioinformatics from the University of Edinburgh (UK) in 2020. He is now an MD candidate in the Lab of Dr. Herbert Schiller at the Institute of Lung Health and Immunity at Helmholtz Munich and the Comprehensive Pneumology Center of the LMU Klinikum. His research interest lies in understanding the spatiotemporal dynamics of cell circuits that orchestrate lung fibrogenesis through the lens of single-cell genomics.



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The research training group CompCancer (RTG2424) is a DFG funded PhD programme in Berlin, focussing on computational aspects of cancer research.

Contact: compcancer at charite dot de