Peng He, PhD
Assistant Professor
Pathology
School of Medicine
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.
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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.
Awards
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- Abstract Merit Award, ISSCR, 2022
- Travel Award, ISSCR, 2022
- Junior Research Fellowship and MA degree, St Edmund's College, University of Cambridge, 2019-2024
- Overseas Research Fellowship, University of Hong Kong, 2011
- Worldwide Exchange Scholarship, University of Hong Kong & UCLA, 2010-2011
- Summer Research Fellowship, University of Hong Kong, 2010
- Rosita King Ho Scholarship (Full scholarship), University of Hong Kong, 2009-2012
Education & Training
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- Postdoc Single-cell, spatial and computational genomics Sanger Institute and EMBL-EBI 06/2024
- PhD Functional genomics and computational biology California Institute of Technology 06/2019
- BSc Statistics, Biochemistry and Computer Science University of Hong Kong 06/2012
Interests
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- Bioinformatics
- Human tissue
- Epigenomics
- Spatial
- Development
- Genomics
- Multi-omics
- Organogenesis
- Computational biology
- Gene regulation
- Single-cell
Websites
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- Posts on X PengHeAtlas (X.com)
- Lab website (peng-he-lab.github.io)
Publications (22)
Top publication keywords:
Embryonic DevelopmentSOX9 Transcription FactorOrganoidsLungDrosophila ProteinsAtlases as TopicGene Expression Regulation, DevelopmentalDatabases, GeneticCell DifferentiationExtremitiesEmbryo, MammalianMolecular Sequence AnnotationFetusTranscriptomeSingle-Cell Analysis
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Early human lung immune cell development and its role in epithelial cell fate.
Science immunology 2023 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, … -
A human embryonic limb cell atlas resolved in space and time.
Nature 2023 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, … -
A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.
Cell 2022 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, … -
The changing mouse embryo transcriptome at whole tissue and single-cell resolution.
Nature 2020 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 -
A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease.
The EMBO journal 2025 Lim K, Rutherford EN, Delpiano L, He P, Lin W, Sun D, Van den Boomen DJH, Edgar JR, Bang JH, Predeus A, Teichmann SA, Marioni JC, Matesic LE, Lee JH, Lehner PJ, Marciniak SJ, Rawlins EL, Dickens JA
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WebAtlas pipeline for integrated single-cell and spatial transcriptomic data.
Nature methods 2025 Li T, Horsfall D, Basurto-Lozada D, Roberts K, Prete M, Lawrence JEG, He P, Tuck E, Moore J, Yoldas AK, Babalola K, Hartley M, Ghazanfar S, Teichmann SA, Haniffa M, Bayraktar OA -
Considerations for building and using integrated single-cell atlases.
Nature methods 2024 Hrovatin K, Sikkema L, Shitov VA, Heimberg G, Shulman M, Oliver AJ, Mueller MF, Ibarra IL, Wang H, Ramírez-Suástegui C, He P, Schaar AC, Teichmann SA, Theis FJ, Luecken MD -
A multi-omic atlas of human embryonic skeletal development.
Nature 2024 To K, Fei L, Pett JP, Roberts K, Blain R, Polanski K, Li T, Yayon N, He P, Xu C, Cranley J, Moy M, Li R, Kanemaru K, Huang N, Megas S, Richardson L, Kapuge R, Perera S, Tuck E, Wilbrey-Clark A, Mulas … -
A prenatal skin atlas reveals immune regulation of human skin morphogenesis.
Nature 2024 Gopee NH, Winheim E, Olabi B, Admane C, Foster AR, Huang N, Botting RA, Torabi F, Sumanaweera D, Le AP, Kim J, Verger L, Stephenson E, Adão D, Ganier C, Gim KY, Serdy SA, Deakin C, Goh I, Steele L, … -
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast.
Nature genetics 2024 Reed AD, Pensa S, Steif A, Stenning J, Kunz DJ, Porter LJ, Hua K, He P, Twigger AJ, Siu AJQ, Kania K, Barrow-McGee R, Goulding I, Gomm JJ, Speirs V, Jones JL, Marioni JC, Khaled WT -
Automatic cell-type harmonization and integration across Human Cell Atlas datasets.
Cell 2023 Xu C, Prete M, Webb S, Jardine L, Stewart BJ, Hoo R, He P, Meyer KB, Teichmann SA -
Maternally inherited siRNAs initiate piRNA cluster formation.
Molecular cell 2023 Luo Y, He P, Kanrar N, Fejes Toth K, Aravin AA -
A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.
Nature genetics 2022 Madissoon E, Oliver AJ, Kleshchevnikov V, Wilbrey-Clark A, Polanski K, Richoz N, Ribeiro Orsi A, Mamanova L, Bolt L, Elmentaite R, Pett JP, Huang N, Xu C, He P, Dabrowska M, Pritchard S, Tuck L, … -
Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease.
Cell stem cell 2022 Lim K, Donovan APA, Tang W, Sun D, He P, Pett JP, Teichmann SA, Marioni JC, Meyer KB, Brand AH, Rawlins EL -
SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling.
The EMBO journal 2022 Sun D, Llora Batlle O, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA, Marioni JC, Jackson SP, Brand AH, Rawlins EL -
Mapping the developing human immune system across organs.
Science (New York, N.Y.) 2022 Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK, Polanski K, Yayon N, Xu C, Suchanek O, Elmentaite R, Domínguez Conde C, He P, Pritchard S, … -
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Nature medicine 2021 Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, … -
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Nature 2020 ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz … -
Perspectives on ENCODE.
Nature 2020 ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry … -
Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos.
eLife 2020 Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A -
Epigenetic silencing of miR-125b is required for normal B-cell development.
Blood 2018 Li G, So AY, Sookram R, Wong S, Wang JK, Ouyang Y, He P, Su Y, Casellas R, Baltimore D -
Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.
Cell stem cell 2015 Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ