2020-Today Group Leader at the Centre for Genomic Regulation (CRG), Barcelona, Spain
2016-2019 Research Staff Scientist, European Molecular Biology Laboratory, Heidelberg (Germany)
2012-2016 Ph.D. in Genomics, European Molecular Biology Laboratory, Heidelberg (Germany)
2012 M.Sc. in Cancer Biology, German Cancer Research Center, Heidelberg (Germany)

Summary

The hematopoietic system supplies our bodies with hundreds of millions of new blood cells per day and constitutes one of the most sophisticated regenerative systems in biology. Ultimately, this massive cellular output traces back to about 100,000 unique stem cells. Key questions driving our research are: How is this differentiation process encoded in the genome? And: How is it altered in ageing and disease? 

To answer these questions, we strive to innovate cutting-edge genomics technology. We were the first to characterize human hematopoiesis by single-cell RNA-seq  (Velten et al., 2017) and we pioneered spatial transcriptomics in the bone marrow (Baccin et al., 2020). Recently, we have focused on clonal dynamics in leukemia (Beneyto-Calabuig et al., 2023) and ageing (Scherer et al., Nature 2025). To that end, we have developed a unique method, based on epi-mutations, to trace isogenic stem cell clones in humans and characterize age-dominant stem cell clones at the molecular level. These capabilities open the door to potential diagnostic and therapeutic applications. 

To gain a handle on the genomic encoding of these programs, we embraced Massively Parallel Reporter Assays (MPRAs) and Perturb-Seq screens. Recently, we have used fully synthetic DNA constructs to decode the design rules of cell-state-specific enhancers (Frömel et al., Cell 2025). Based on these rules, we constructed an AI-based model capable of designing new enhancer sequences with user-defined specificity patterns. Ongoing work focuses on the dissection of gene regulatory networks, and a deeper dissection of regulatory programs underlying the stem cell identity in homeostasis, healthy ageing and leukemia formation. 

News

‘Barcodes’ written into our DNA reveal how blood ages (21/05/2025)
A new study in the journal Nature explains how age reshapes the blood system. In both humans and mice, a few stem cells, or “clones”, outcompete their neighbours and gradually take over blood production.

AI-designed DNA controls genes in healthy mammalian cells for first time (08/05/2025)
A study published in the journal Cell marks the first reported instance of generative AI designing synthetic molecules that can successfully control gene expression in healthy mammalian cells.

Differentiation landscape of acute myeloid leukemia charted with new tool (24/04/2023)
Researchers have developed a new method to distinguish between cancerous and healthy stem cells and progenitor cells from samples of patients with acute myeloid leukaemia (AML), a disease driven by malignant blood stem cells that have historically been difficult to identify.

CRG researchers selected for EMBO Young Investigator programme (22/11/2022)
CRG researchers Lars Velten and Arnau Sebe Pedros are two of 24 life scientists to be selected for this year’s EMBO Young Investigator Programme.

Researchers at the CRG receive €4.5m to study cancer, reproduction and blood formation (01/01/2022)
Lars Velten, Group Leader at the CRG, will combine deep learning and single-cell screening techniques to create new models of gene regulation in the human blood-forming system. 

Cell atlas of human blood formation paves way for improved diagnostics (29/11/2021)
Researchers at the Centre for Genomic Regulation (CRG) in Barcelona, EMBL Heidelberg, the German Cancer Research Center and the Berlin Institute of Health have created the most detailed atlas of gene expression of human blood and bone marrow cells to date.

Single cell sequencing opens new avenues for eradicating leukemia at its source (01/03/2021).
We have published our method to identify and characterize leukemic stem cells by single cell genomics.

€2.45 m to investigate leukaemia causes and therapies (11/03/2020).
Together with partners from the University Clinics Heidelberg and the Max Delbrück Center for Molecular Medicine (Berlin), we form part of the LeukoSyStem consortium that was awarded with a prestigious junior research alliance grant by the German government.

Job Openings

We are very interested in applications of prospective postdocs and PhD students with an interest in hematopoietic stem cell biology, gene regulation, single cell genomics, single cell genetic screens and/or machine learning.

Funding acknowledgements

The project "Single cell genomics for synthetic biology of gene regulatory element" (PID2019-108082GA-I00 / AEI / 10.13039/501100011033) has received funding from the National Research Agency (Agencia Estatal de Investigación, AEI), from the Spanish Ministry of Science and Innovation.

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This project "Artificial intelligence for synthetic funtional genomics of blood- AI4SYN_101041399" has received funding from the European Union’s Horizon EIC-ESMEA Pathfinder program under grant agreement No 101046620.

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The project 'Nuevos enfoques para combatir la hematopoyesis clonal, una etapa temprana en el desarrollo de la leucemia mieloide aguda' has received funding from the Asociación Española contra el Cáncer, under the call 'Ayuda LAB AECC 2022'
Period: 01/12/2022 to 30/11/2025