Peng He, PhD

Assistant Professor
Department of Pathology
[email protected]
Research Description: 

My research focuses on gene regulatory networks in human tissues, leveraging single-cell and spatial assays combined with innovative computational methods. I've significantly contributed to the Encyclopedia of DNA Elements (ENCODE) project through RNA-centric approaches, and to the Human Cell Atlas (HCA) with a focus on developing limbs and lungs.
My interdisciplinary research group is dedicated to developing computational methods and profiling transcriptomic and chromatin changes. We aim to construct ultra-high resolution cell atlases of healthy and altered tissues and organoids, to dissect the intricate relationships between genes, cells and tissues.

Primary Thematic Area: 
Developmental & Stem Cell Biology
Secondary Thematic Area: 
Human Genetics
Research Summary: 
Single-cell and spatial transcriptomics and multiomics; computational biology; gene regulation in cell fate decision
Featured Publications: 

Early human lung immune cell development and its role in epithelial cell fate.

Science immunology

Barnes JL, Yoshida M, He P, Worlock KB, Lindeboom RGH, Suo C, Pett JP, Wilbrey-Clark A, Dann E, Mamanova L, Richardson L, Polanski K, Pennycuick A, Allen-Hyttinen J, Herczeg IT, Arzili R, Hynds RE, Teixeira VH, Haniffa M, Lim K, Sun D, Rawlins EL, Oliver AJ, Lyons PA, Marioni JC, Ruhrberg C, Tuong ZK, Clatworthy MR, Reading JL, Janes SM, Teichmann SA, Meyer KB, Nikolic MZ

A human embryonic limb cell atlas resolved in space and time.

Nature

Zhang B, He P, Lawrence JEG, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, Li T, Elmentaite R, Fasouli ES, Prete M, He X, Yayon N, Fu Y, Yang H, Liang C, Zhang H, Blain R, Chedotal A, FitzPatrick DR, Firth H, Dean A, Bayraktar OA, Marioni JC, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA

A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.

Cell

He P, Lim K, Sun D, Pett JP, Jeng Q, Polanski K, Dong Z, Bolt L, Richardson L, Mamanova L, Dabrowska M, Wilbrey-Clark A, Madissoon E, Tuong ZK, Dann E, Suo C, Goh I, Yoshida M, Nikolic MZ, Janes SM, He X, Barker RA, Teichmann SA, Marioni JC, Meyer KB, Rawlins EL

The changing mouse embryo transcriptome at whole tissue and single-cell resolution.

Nature

He P, Williams BA, Trout D, Marinov GK, Amrhein H, Berghella L, Goh ST, Plajzer-Frick I, Afzal V, Pennacchio LA, Dickel DE, Visel A, Ren B, Hardison RC, Zhang Y, Wold BJ