Team

Staff Profiles

Cindy van Velthoven, Ph.D.

Associate Director, Single Cell Genomics

Cindy.vanVelthoven@alleninstitute.org

​​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

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.

Expertise

  • ​Stem Cell Biology
  • Transcriptomics

Research Programs

  • Cell Types

Selected Publications

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
September 2, 2021

Bakken TE, van Velthoven CT, Menon V, Hodge RD, Yao Z, Nguyen TN, Graybuck LT, Horwitz GD, Bertagnolli D, Goldy J, Yanny AM, Garren E, Parry S, Casper T, Shehata SI, Barkan ER, Szafer A, Levi BP, Dee N, Smith KA, Sunkin SM, Bernard A, Phillips J, Hawrylycz MJ, Koch C, Murphy GJ, Lein E, Zeng H, Tasic B

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Cell
May 17, 2021

Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H.

Enhancer viruses for combinatorial cell-subclass-specific labeling

Neuron
March 23, 2021

Graybuck LT, Daigle TL, Sedeño-Cortés AE, Walker M, Kalmbach B, Lenz GH, Morin E, Nguyen TN, Garren E, Bendrick JL, Kim TK, Zhou T, Mortrud M, Yao S, Siverts LA, Larsen R, Gore BB, Szelenyi ER, Trader C, Balaram P, van Velthoven CTJ, Chiang M, Mich JK, Dee N, Goldy J, Cetin AH, Smith K, Way SW, Esposito L, Yao Z, Gradinaru V, Sunkin SM, Lein E, Levi BP, Ting JT, Zeng H, Tasic B.

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Nature
October 6, 2021

Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA

A multimodal cell census and atlas of the mammalian primary motor cortex

Nature
October 6, 2021

BRAIN Initiative Cell Census Network (BICCN)

Isoform cell-type specificity in the mouse primary motor cortex

Nature
October 6, 2021

Booeshaghi AS, Yao Z, van Velthoven C, Smith K, Tasic B, Zeng H, Pachter L

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

Neuron
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

eLife
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