Staff Profiles

Cindy van Velthoven, Ph.D.

Senior Scientist

​​Cindy joined the Allen Institute as part of the Mouse Cell Types program in September 2018. Here, she contributes to projects related to cell type identification and develops new techniques to characterize the cells. ​Before joining the Institute, she completed her postdoctoral training in the lab of Tom Rando at Stanford University. She studied post-transcriptional mechanisms involved in regulating stem cell quiescence. Cindy 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 studied the use of stem cells to repair the neonatal brain after ischemic injury. Cindy earned a M.S. in pathobiology from Radboud University Nijmegen, the Netherlands.


Research Interests

My main interest is in understanding how a developing 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 transcriptional profiles, we can distinguish cell types and increase our understanding of cell fate determination.


  • ​Stem Cell Biology
  • Transcriptomics

Research Programs

  • Cell Types

Selected Publications

Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

December 7, 2020

Whitesell JD, Liska A, Coletta L, Hirokawa KE, Bohn P, Williford A, Groblewski PA, Graddis N, Kuan L, Knox JE, Ho A, Wakeman W, Nicovich PR, Nguyen TN, van Velthoven CTJ, Garren E, Fong O, Naeemi M, Henry AM, Dee N, Smith KA, Levi B, Feng D, Ng L, Tasic B, Zeng H, Mihalas S, Gozzi A, Harris JA.

Common cell type nomenclature for the mammalian brain

December 29, 2020

Miller JA, Gouwens NW, Tasic B, Collman F, van Velthoven CT, Bakken TE, Hawrylycz MJ, Zeng H, Lein ES, Bernard A.

Transcriptional Profiling of Quiescent Muscle Stem Cells In Vivo.

Cell Reports
November 14, 2017

van Velthoven CTJ, Morree A, Egner IM, Brett JO, Rando TA