Staff Profiles

Nelson Johansen, Ph.D.

Scientist I

Nelson joined the at the Allen Institute in August 2021 as a Scientist working on the Human Cell Types team. His research is focused on developing analytical tools and methods to characterize the epigenetics defining cell types in the human brain in part to construct more specific viral gene therapies.  Previously, he completed a PhD in Computer Science from the University of California, Davis in Gerald Quon’s group where he developed machine learning methods in critical areas of single cell biology to better understand the molecular definitions of cell type and state. His research touched on a wide range of applications including characterizations of malaria parasites, identifying cross-species cell type homologies and spatial deconvolution. Prior to that, Nelson received his BSc in Computer Science from the University of California, Davis.


Research Interests

Currently Nelson's research focuses on building deep generative models to integrate epigenetic, DNA sequence and molecular measurements, in order to better understand how changes in molecular biology, reflected in high dimensional transcriptomic data, might fundamentally link with alternative cellular characterizations. The Allen Institute provides a wealth of high-resolution taxonomies and molecular atlas for the human, mouse and NHP brains which clearly define cellular state. Leveraging these works and efforts with the BICCN as well as 4DN Nelson aims to identify cell type specific epigenic mechanisms that can be used as guides for viral gene therapies for neurodegenerative disease in humans as well as other species. Additionally, he is interested in the application of machine learning, especially deep learning, to domains such as agriculture.


  • Computational biology
  • Machine Learning
  • Genomics

Research Programs:

  • Human Cell Types

Selected Publications

Conserved cell types with divergent features in human versus mouse cortex

August 21, 2019

Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES