Research Summary

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.

Education

Postdoc, 06/2024 - Single-cell, spatial and computational genomics, Sanger Institute and EMBL-EBI
PhD, 06/2019 - Functional genomics and computational biology, California Institute of Technology
BSc, 06/2012 - Statistics, Biochemistry and Computer Science, University of Hong Kong

Honors & Awards

  • 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

Selected Publications

  1. 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 I, Memi F, Cakir B, Predeus AV, Horsfall D, Murray S, Prete M, Mazin P, He X, Meyer KB, Haniffa M, Barker RA, Bayraktar O, Chédotal A, Buckley CD, Teichmann SA. A multi-omic atlas of human embryonic skeletal development. Nature. 2024 Nov; 635(8039):657-667.  View on PubMed
  2. 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. A prenatal skin atlas reveals immune regulation of human skin morphogenesis. Nature. 2024 Oct 16.  View on PubMed
  3. 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. WebAtlas pipeline for integrated single-cell and spatial transcriptomic data. Nat Methods. 2024 Aug 19.  View on PubMed
  4. 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. A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nat Genet. 2024 Apr; 56(4):652-662.  View on PubMed
  5. Xu C, Prete M, Webb S, Jardine L, Stewart BJ, Hoo R, He P, Meyer KB, Teichmann SA. Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell. 2023 12 21; 186(26):5876-5891.e20.  View on PubMed
  6. 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. Early human lung immune cell development and its role in epithelial cell fate. Sci Immunol. 2023 Dec 15; 8(90):eadf9988.  View on PubMed
  7. 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 embryonic limb cell atlas resolved in space and time. Nature. 2024 Nov; 635(8039):668-678.  View on PubMed
  8. Luo Y, He P, Kanrar N, Fejes Toth K, Aravin AA. Maternally inherited siRNAs initiate piRNA cluster formation. Mol Cell. 2023 Nov 02; 83(21):3835-3851.e7.  View on PubMed
  9. 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. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat Genet. 2023 01; 55(1):66-77.  View on PubMed
  10. 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. 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.  View on PubMed
  11. Lim K, Donovan APA, Tang W, Sun D, He P, Pett JP, Teichmann SA, Marioni JC, Meyer KB, Brand AH, Rawlins EL. 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.  View on PubMed
  12. 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. SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. EMBO J. 2022 11 02; 41(21):e111338.  View on PubMed
  13. 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. Mapping the developing human immune system across organs. Science. 2022 06 03; 376(6597):eabo0510.  View on PubMed
  14. 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. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med. 2021 03; 27(3):546-559.  View on PubMed
  15. 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. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710.  View on PubMed
  16. 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. Perspectives on ENCODE. Nature. 2020 07; 583(7818):693-698.  View on PubMed
  17. 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. The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature. 2020 07; 583(7818):760-767.  View on PubMed
  18. Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. Elife. 2020 07 23; 9.  View on PubMed
  19. Li G, So AY, Sookram R, Wong S, Wang JK, Ouyang Y, He P, Su Y, Casellas R, Baltimore D. Epigenetic silencing of miR-125b is required for normal B-cell development. Blood. 2018 04 26; 131(17):1920-1930.  View on PubMed
  20. Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ. Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell. 2015 Jan 08; 16(1):88-101.  View on PubMed

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