Staff Profiles

Xiaoyin Chen, Ph.D.

Assistant Investigator

Xiaoyin joined Allen Institute for Brain Science in 2021. He is currently an Assistant Investigator leading the Barcoded Connectomics project. Xiaoyin and his team are developing and applying sequencing-based neuroanatomical approaches to understand the wiring logic of neuronal types across development and evolution.

Xiaoyin obtained his B.S in biology in Tsinghua University in Beijing, China. He then moved to New York City and did his Ph.D training with Dr. Martin Chalfie at Columbia University, where he studied mechanosensation in the nematode C. elegans. Xiaoyin then joined Tony Zador’s lab at Cold Spring Harbor Laboratory as a postdoc. In Tony’s lab, Xiaoyin developed BARseq, a sequencing-based neuroanatomical technique with cellular resolution and unparalleled throughput.

Xiaoyin was awarded the Kavli Institute Award for Distinguished Research in Neuroscience for his PhD thesis work. He was a Simons Collaboration on the Global Brain fellow and an O’Neil fellow during his postdoc work, and received a Discovery award from the Department of Defense Peer Reviewed Medical Research Program. His work in developing BARseq was featured by the NIH Director’s Blog, BRAIN Initiative Alliance, and various news media including Nature, Spectrum, Technology Networks, etc.



Research Interests

Xiaoyin is interested in understanding the wiring logic of neuronal types from a developmental and evolutionary perspective. To achieve this goal, his team is developing in situ sequencing-based tools that can interrogate various neuronal properties, such as gene expression and connectivity, with unprecedented throughput. These new tools will allow his team to interrogate the wiring among the basic units of a circuit, i.e. cell types, at an unprecedented scale, across the whole brain and across many individuals. Xiaoyin hopes that this systemic approach will not only reveal the basic organization of the normal brain with exquisite details, but also provides a path for discovering and understanding cellular and wiring defects in neuropsychiatric and neurodevelopmental diseases.


  • In situ sequencing
  • Neuroanatomy
  • Spatial transcriptomics

Research Programs

  • Cell types
  • Barcoded connectomics

Selected Publications View Publications

Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared across the cortex

Nature Neuroscience
June 24, 2021

Sun YC, Chen X, Fischer S, Lu S, Zhan H, Gillis J, Zador AM

Wiring logic of the early rodent olfactory system revealed by high-throughput sequencing of single neuron projections

May 2021

Chen, Y., Chen, X., Baserdem, B., Zhan, H., Li, Y., Davis, M.B., Kebschull, J.M., Zador, A.M., Koulakov, A.A., Albeanu, D.F.

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

PLoS Computational Biology
March 8, 2021

Chen, S., Loper, J., Chen, X., Vaughan, A., Zador, AM., Paninski, L

Cellular anatomy of the mouse primary motor cortex

October 6, 2021

Muñoz-Castañeda R, Zingg B, Matho KS, Chen X, Wang Q, Foster NN, Li A, Narasimhan A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park YG, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, Naeemi M, Xie P, Liu L, Kelly K, An X, Attili SM, Bowman I, Bludova A, Cetin A, Ding L, Drewes R, D'Orazi F, Elowsky C, Fischer S, Galbavy W, Gao L, Gillis J, Groblewski PA, Gou L, Hahn JD, Hatfield JT, Hintiryan H, Huang JJ, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Lo D, Mizrachi J, Mok S, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun YC, Tao HW, Wakemen W, Wang Y, Yao S, Yuan J, Zhan H, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Chung K, Yang XW, Peng H, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Josh Huang Z, Osten P, Harris JA, Dong HW

High-throughput mapping of long-range neuronal projection using in situ sequencing

October 17, 2019

Chen, X., Sun, Y., Zhan, H., Kebschull, JM., Fischer, S., Matho, K., Huang, ZJ., Gillis, J., and Zador, AM

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

Nucleic Acids Research
November 28, 2017

Chen, X., Sun, Y., Church, GM., Lee, JH., and Zador, AM