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people

Cindy van Velthoven

Associate Investigator

teams /
Allenite

Cindy van Velthoven joined the Allen Institute as part of a large effort to define cell types in the developing and adult mouse brain. Here she develops and applies computational tools to identify cell types in various mouse brain regions and characterize changes in gene regulation associated with development or experimental perturbations.
Prior to joining the Allen Institute, she completed her postdoctoral training in the lab of Tom Rando at Stanford University where she studied post-transcriptional mechanisms involved in regulating stem cell quiescence. She used various transcriptional and translational profiling techniques to probe the earliest activation changes in quiescent stem cells in vivo. Cindy received her Ph.D. in neuroscience from Utrecht University, The Netherlands, where she examined the use of stem cells to repair the neonatal brain after ischemic injury. Prior to that Cindy earned a M.S. in pathobiology from Radboud University Nijmegen, the Netherlands.

research focus

My main interest is in understanding how a cell navigates the cell fate determination process. During development, cells must proliferate, differentiate, and signal to each other to ensure correct organization within structures. Gene expression, regulated by transcription factor networks, aides in coordinating growth, shape, and function of cells. Using their epigenomic and transcriptional profiles, we can distinguish cell types and increase our understanding of cell fate determination.

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news
Scientists complete first drafts of developing mammalian brain cell atlases
New research reveals how early brains form and the critical periods that could help diagnose and treat brain disease.
multimedia
Key players in brain aging
New research identifies age-related damage on a cellular level.
news
Unraveling the Complexity of the Mammalian Brain
Scientists used advanced, single-cell genomics and spatial mapping technologies to reveal this complex and rich cellular landscape.

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featured publications

publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
publication / 2024
Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
eLife
publication / 2023
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Nature
publication / 2023
A guide to the BRAIN Initiative Cell Census Network data ecosystem
PLoS biology
publication / 2021
A multimodal cell census and atlas of the mammalian primary motor cortex
Nature
publication / 2021
Isoform cell-type specificity in the mouse primary motor cortex
Nature
publication / 2021
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Nature
publication / 2021
Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
eLife
publication / 2021
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Cell
publication / 2021
Enhancer viruses for combinatorial cell-subclass-specific labeling
Neuron
publication / 2021
Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network
Neuron
publication / 2020
Common cell type nomenclature for the mammalian brain
eLife
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