Peng He, PhD

Title(s)Assistant Professor, Pathology
SchoolSchool of Medicine
PronounsHe/Him/His
ORCID ORCID Icon0000000224573554 Additional info
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    Collapse Education and Training
    Sanger Institute and EMBL-EBIPostdoc06/2024Single-cell, spatial and computational genomics
    California Institute of TechnologyPhD06/2019Functional genomics and computational biology
    University of Hong KongBSc06/2012Statistics, Biochemistry and Computer Science
    Collapse Awards and Honors
    ISSCR2022Abstract Merit Award
    ISSCR2022Travel Award
    St Edmund's College, University of Cambridge2019  - 2024Junior Research Fellowship and MA degree
    University of Hong Kong2011Overseas Research Fellowship
    University of Hong Kong & UCLA2010  - 2011Worldwide Exchange Scholarship
    University of Hong Kong2010Summer Research Fellowship
    University of Hong Kong2009  - 2012Rosita King Ho Scholarship (Full scholarship)

    Collapse Overview 
    Collapse Overview
    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.

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A prenatal skin atlas reveals immune regulation of human skin morphogenesis. Nature. 2024 Oct 16. 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, Annusver K, Miah MU, Tun WM, Moghimi P, Kwakwa KA, Li T, Basurto Lozada D, Rumney B, Tudor CL, Roberts K, Chipampe NJ, Sidhpura K, Englebert J, Jardine L, Reynolds G, Rose A, Rowe V, Pritchard S, Mulas I, Fletcher J, Popescu DM, Poyner E, Dubois A, Guy A, Filby A, Lisgo S, Barker RA, Glass IA, Park JE, Vento-Tormo R, Nikolova MT, He P, Lawrence JEG, Moore J, Ballereau S, Hale CB, Shanmugiah V, Horsfall D, Rajan N, McGrath JA, O'Toole EA, Treutlein B, Bayraktar O, Kasper M, Progatzky F, Mazin P, Lee J, Gambardella L, Koehler KR, Teichmann SA, Haniffa M. PMID: 39415002.
      View in: PubMed   Mentions:    Fields:    
    2. WebAtlas pipeline for integrated single-cell and spatial transcriptomic data. Nat Methods. 2024 Aug 19. 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. PMID: 39160302.
      View in: PubMed   Mentions:    Fields:    
    3. A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nat Genet. 2024 Apr; 56(4):652-662. 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. PMID: 38548988; PMCID: PMC11018528.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    4. Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell. 2023 12 21; 186(26):5876-5891.e20. Xu C, Prete M, Webb S, Jardine L, Stewart BJ, Hoo R, He P, Meyer KB, Teichmann SA. PMID: 38134877.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    5. Early human lung immune cell development and its role in epithelial cell fate. Sci Immunol. 2023 Dec 15; 8(90):eadf9988. 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. PMID: 38100545; PMCID: PMC7615868.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    6. A human embryonic limb cell atlas resolved in space and time. Nature. 2023 Dec 06. 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. PMID: 38057666; PMCID: PMC7616500.
      View in: PubMed   Mentions: 5     Fields:    
    7. Maternally inherited siRNAs initiate piRNA cluster formation. Mol Cell. 2023 Nov 02; 83(21):3835-3851.e7. Luo Y, He P, Kanrar N, Fejes Toth K, Aravin AA. PMID: 37875112; PMCID: PMC10846595.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    8. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat Genet. 2023 01; 55(1):66-77. 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, Prigmore E, Perera S, Knights A, Oszlanczi A, Hunter A, Vieira SF, Patel M, Lindeboom RGH, Campos LS, Matsuo K, Nakayama T, Yoshida M, Worlock KB, Nikolic MZ, Georgakopoulos N, Mahbubani KT, Saeb-Parsy K, Bayraktar OA, Clatworthy MR, Stegle O, Kumasaka N, Teichmann SA, Meyer KB. PMID: 36543915; PMCID: PMC9839452.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    9. Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease. Cell Stem Cell. 2023 01 05; 30(1):20-37.e9. Lim K, Donovan APA, Tang W, Sun D, He P, Pett JP, Teichmann SA, Marioni JC, Meyer KB, Brand AH, Rawlins EL. PMID: 36493780.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    10. A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates. Cell. 2022 Dec 08; 185(25):4841-4860.e25. 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. PMID: 36493756.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    11. SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. EMBO J. 2022 11 02; 41(21):e111338. 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. PMID: 36121125; PMCID: PMC9627674.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    12. Mapping the developing human immune system across organs. Science. 2022 06 03; 376(6597):eabo0510. 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, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA. PMID: 35549310; PMCID: PMC7612819.
      View in: PubMed   Mentions: 88     Fields:    Translation:HumansCells
    13. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med. 2021 03; 27(3):546-559. 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, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litvinuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network. PMID: 33654293; PMCID: PMC9469728.
      View in: PubMed   Mentions: 171     Fields:    Translation:HumansCells
    14. The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature. 2020 07; 583(7818):760-767. 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. PMID: 32728245; PMCID: PMC7410830.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    15. Perspectives on ENCODE. Nature. 2020 07; 583(7818):693-698. 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 JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. PMID: 32728248; PMCID: PMC7410827.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    16. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. 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 M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. PMID: 32728249; PMCID: PMC7410828.
      View in: PubMed   Mentions: 782     Fields:    Translation:HumansAnimalsCells
    17. Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. Elife. 2020 07 23; 9. Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. PMID: 32701060; PMCID: PMC7417190.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    18. Epigenetic silencing of miR-125b is required for normal B-cell development. Blood. 2018 04 26; 131(17):1920-1930. Li G, So AY, Sookram R, Wong S, Wang JK, Ouyang Y, He P, Su Y, Casellas R, Baltimore D. PMID: 29555645; PMCID: PMC5921965.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    19. Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell. 2015 Jan 08; 16(1):88-101. Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ. PMID: 25575081; PMCID: PMC4291542.
      View in: PubMed   Mentions: 86     Fields:    Translation:AnimalsCells
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