SCOG Workshop Computational Single Cell Genomics, March 2019, Munich

Watch the workshop sessions following the links. Thanks to the Chan Zuckerberg Initiative for sponsoring the recordings.

Christoph BockCeMM Research Center, ViennaCRISPR single-cell sequencing: Toward functional biology in high throughput
Joachim SchultzeDZNE, BonnFrom single cells to patients: A LifeTime journey
Sam RiesenfeldBroad Institute of MIT and Harvard, BostonUsing topic models to analyze the transcriptional spectrum of innate lymphoid cells
Clément CochainComprehensive Heart Failure Center, WürzburgTime series single-cell analysis of cardiac myeloid cells after acute myocardial infarction in mice
Heiko LickertHelmholtz MunichDeciphering mechanisms of β-cell failure and regeneration by single cell RNA Sequencing
Peter KharchenkoHarvard Medical School, BostonWiring together large single-cell RNA-seq collections
Vahid ShahrezaeiImperial College LondonBayesian gene expression recovery, imputation and normalisation for single cell RNA-sequencing data
Amit FrishbergTel Aviv UniversityCell composition analysis of bulk genomics using single-cell data
David FischerHelmholtz Munichdiffxpy: Scalable differential expression analysis for single-cell RNA-seq data
Angela GoncalvesDKFZ HeidelbergDetermining KIR repertoires using single cell transcriptomics
Maria Colomé-TatchéHelmholtz MunichEpiscanpy: epigenomic single cell analysis
Sara AibarVIB-KU LeuvenExploiting single-cell transcriptomics and epigenomics to reconstruct gene-regulatory networks

Helmholtz Horizons 2018

The Helmholtz Horizons Symposium 2018, hosted by the President of the Association, highlights scientific breakthroughs of Helmholtz’s established researchers, showcases talented early career researchers, and gives a platform to the entrepreneurs and innovators, who ensure that Helmholtz research has societal impact.

Visit the Helmholtz Horizons Website.

Video production: BIOCOM

Fabian Theis: ‘The Digital (R)Evolution in Science’ – Berlin, 2018 talking about ‘Learning cell lineages using artificial intelligence’.

Christin Sünkel @ Helmholtz Horizons 2018: ‘The Digital (R)Evolution in Science’ – Berlin, 2018

“Single Cells in Time and Space”

Single cell RNA sequencing allows us to study all genes that are being used in a single cell. However powerful this method is, it leaves us with thousands of data points for each cell and we study thousands of cells per experiment. Hence, there is a big need to develop computational methods that can deal with this kind of “big data”.

In her presentation Christin also introduces the LifeTime initiative for a new FET-Flagship which is coordinated  by Nikolaus Rajewsky, Head of the Berlin Institute for Medical Systems Biology at the  Max-Delbrück Center for Molecular Medicine.

Christin Sünkel studied biochemistry and molecular biology at the University of Bayreuth. As a student intern at the Rockefeller University in New York City, in the laboratory of Thomas Tuschl she worked on the role of certain RNA-binding proteins. Her studies were supported by the Studienstiftung des deutschen Volkes. For her master thesis she moved to the laboratory of Nikolaus Rajewsky at Max-Delbrück Center for Molecular Medicine / Berlin Institute for Medical Systems Biology in Berlin to develop in vitro methods for the study of circular RNAs. Now she is pursuing her PhD in Nikolaus Rajewsky’s lab focusing on the function of circular RNAs and on the development of a method to study single cell gene expression in a spatial context. Her PhD work is supported by the Boehringer Ingelheim Fonds, Signgene and MDC BOOST.

Single Cell Data Analysis - Overview

This video has been made for bioinformatics students in Cairo University, Egypt; to discuss the main Single Cell Data Analysis challenges.

Hemberg lab course:

Abdelrahman Mahmoud @ DKFZ – Heidelberg, 2018.