Staff Profiles

Elise Shen

Research Associate II

Elise joined Neuroanatomy team at the Allen Institute in 2018. She is currently researching single neuron reconstruction and classification at a whole-brain level using virtual reality. She received her B.S. in Biology-Neurobiology at the University of Texas at Austin, where she worked in the Center for Learning and Memory. Her points of focus included developing image analysis methods paired with surgery techniques for in-vivo injections and imaging surgeries in immature and mature mice for long-term cerebellar studies using two-photon microscopy. Elise earned her M.S. in Biomedical Engineering from National Taiwan University, where she studied an in-vivo fornix deep brain stimulation surgery in triple-transgenic Alzheimer’s disease mice using DT-MRI, PET, behavioral, and immunohistochemical assessments of therapy efficacy.

Prior to the Allen Institute, she worked at Baylor College of Medicine and Texas Children’s Hospital for a CRO, where she performed NGS and RNA-seq analysis and biostatistics in order to improve an immunotherapy for neuroblastoma.


Research Interests

Elise's research interests include neurodegenerative diseases, cancer, and image reconstruction and analysis. She ultimately wants to combine image reconstruction and analysis with her biomedical engineering background for robotic surgery and artificial intelligence diagnosis applications.


  • Multimodal Image Acquisition and Analysis
  • Small-animal surgery development
  • Bioinformatics

Research Programs

  • Neuroanatomy

Selected Publications

Hierarchical organization of cortical and thalamic connectivity

October 30, 2019

Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Choi H, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feiner A, Feng D, Gaudreault N, Gerfen CR, Graddis N, Groblewski PA, Henry AM, Ho A, Howard R, Knox JE, Kuan L, Kuang X, Lecoq J, Lesnar P, Li Y, Luviano J, McConoughey S, Mortrud MT, Naeemi M, Ng L, Oh SW, Ouellette B, Shen E, Sorensen SA, Wakeman W2, Wang Q2, Wang Y, Williford A, Phillips JW, Jones AR, Koch C, Zeng H

IL-21 Selectively Protects CD62L+ NKT Cells and Enhances Their Effector Functions for Adoptive Immunotherapy

Journal of Immunology
October 1, 2018

Ngai H, Tian G, Courtney AN, Ravari SB, Guo L, Liu B, Jin J, Shen ET, Di Pierro EJ, Metelitsa LS

Central Thalamic Deep-Brain Stimulation Alters Striatal-Thalamic Connectivity in Cognitive Neural Behavior

Frontiers in Neural Circuits
January 13, 2016

Lin HC, Pan HC, Lin SH, Lo YC, Shen ET, Liao LD, Liao PH, Chien YW, Liao KD, Jaw FS, Chu KW, Lai HY, Chen YY