Single Cell Genomics

Single Cell GenomicsSingle Cell Genomics

Single Cell Genomics

  • Research programme page
  • Members

Coordinator: Lars Velten


The human body consists of trillions of cells, but a mutation in one of them can cause cancer. This example demonstrates that biology is not a process driven by averages and highlights the importance of single cell-level studies. The last years have seen a rapid expansion of the field of single-cell genomics, which enables the massively parallel profiling of tissues and even entire organisms at the single-cell level. These abilities have enabled paradigm shifts in many fields of biological sciences, ranging from evolutionary biology over stem cell biology to cancer research. With its strong capacities in genomics and computational biology, the CRG is well positioned to take a leading role in this dynamically developing area of research.

This transversal research area brings together scientists from the different research programs to exchange know-how and develop synergies. It forms an integral part of a wider network of researchers employing single cell genomics methods in Barcelona.


  • Courses@CRG | Computational analysis of single-cell RNA and multi-ome data

Dates: 14th-18th March 2022

Organizer: Lars Velten

More information soon on the section Events and/or Courses

  • Trimestral Barcelona-wide single cell data club, jointly organized with IRB and CNAG-CRG.

Contact: Sergi Beneyto,

Upcoming data club: 1st July 2021, 14:00 - 16:00 h
Wayme Michael Stallaert, The University of North Carolina Chapel, USA
Anamaria Elek, Centre for Genomic Regulation (CRG), Spain
Connection details coming soon

  • Next events: September 2021 (date to be confirmed) and December 2021 (date to be confirmed).




We develop single cell genomic technology to study cancer stem cells in leukaemia and gene regulation in healthy haematopoiesis.
The Unit is currently being involved and generating single cell data using cortical brain organoids from diseased vs wt samples. We expect to participate in further projects involving single cell analyses.
We use single-cell technologies (chromatin accessibility, transcriptome and DNA methylation) to better understand epigenetic and gene expression events in early tumour formation, focusing on lymphomas (cancers that arise from normal immune cells). 
We have recently discovered that C/EBPa is an organiser of the decision between pluripotency and trophectoderm fates. We are currently performing a single cell analysis of trophectoderm induction by C/EBPa in ESCs.
Profiling the epigenetic signature at single cell resolution will greatly contribute to uncover cell identity and to highlight the epigenetic differences between cell populations upon different processes and along disease progression. We have developed a high-resolution method to profile histone modifications from ultra-low input samples and are currently working in the implementation on a method to profile histone modifications from single cells in multi-well plates and in a droplet-based manner. A second project focuses on QTL mapping in single cells.
We are the Single Cell Genomics team at the CNAG-CRG developing experimental and computational single-cell and spatial genomics tools for cell atlasing and immuno-oncology.
We employ single-cell genomics methods to study the diversity and evolution of cell type programs across the animal tree of life.
My group studies the origins and outcomes of inter-individual heterogeneity in aging populations, which we peruse using a combination of transcriptomics, molecular genetics, statistical modelling and math.