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He Lab at UCSF

Computational Spatial and Single-Cell Multi-Omics

About Our Lab

My research group is innovating analytical and experimental workflows of transcriptomic and chromatin analyses in single cells and within spatial contexts of the tissue, to dissect the intricate relationships between genes, cells and tissues.

Our research group mainly follows three directions:

  1. Construct ultra-high resolution cell atlases of healthy and altered tissues and organoids using advanced computational methods and in-depth -omic profiling methods in single-cells and in space.
  2. Develop computational workflows and algorithms to enable more robust and sensitive discoveries of novel cell populations, tissue niches, as well as cis- and trans-acting regulators in the gene regulatory network.
  3. Dissect gene regulatory networks in single-cells by perturbations of organoids.

Research Highlights

Mouse embryo transcriptome

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

Nature (2020)

Cross-tissue bulk RNA-seq study of organogenesis; Rest/NRSF regulated H3K27me3 de-repression; House-keeping gene transcriptional and post-transcriptional regulation; scRNA-seq of mouse limb development; Gene regulatory network inference from multi-omic sequencing data. GitHub

He P*, Williams BA*, et al.
Human fetal lung cell atlas

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

Cell (2022)

Comprehensive map of 144 human fetal lung cell populations; scRNA-seq and scATAC-seq; Proximal and distal niches with distinct fibroblasts; Organoid gain-of-function screen; Novel NEUROD1+ GHRL+ neuroendocrine lineage that mirrors Type-N small cell lung cancer. GitHub

He P*, Lim K*, Sun D*, et al.
Human embryonic limb atlas

A human embryonic limb cell atlas resolved in space and time

Nature (2023)

Spatiotemporal mapping of human limb development using scRNA-seq and Visium; Whole-tissue atlasing; Mice and humans integrated cell atlas; Spatial axies regulators; digit regulators. GitHub

Zhang B*, He P*, Lawrence JEG*, Wang S*, et al.
Lung immune cell development

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

Science Immunology (2023)

Temporal single-cell mapping of immune cells in the lung; scBCR/abTCR/gdTCR-seq and lymphoid lineage inference; B-1 cells and myeloids in the lung; Myeloid-epithelial interaction via IL1ß and IL13; Organoid scRNA-seq after cytokine induction. GitHub

Barnes JL*, Yoshida M*, He P*, et al.

Lab Members

Dr. Peng He

Dr. Peng He

Principal Investigator

Caltech (PhD)
Cambridge (MA)
U of Hong Kong (BSc)

Dr. Jianwen Xie

Dr. Jianwen Xie

Affiliate Assistant Professor

UCLA (PhD, MSc)
Jinan U (BEng)

Dr. Konstantinos Stasinos

Dr. Konstantinos Stasinos

Postdoctoral Researcher

Queen Mary (PhD)
U of Athens (MD)
Oxford (MSc)

Dr. Yuefei Zhu

Dr. Yuefei Zhu

Postdoctoral Researcher

Columbia (PhD)
Fudan (MSc, BSc)

Yujie (York) Zhang

Yujie (York) Zhang

Graduate Student

Harvard (MSc)
UCSD (BSc)
Co-advised with Dr. Theodoris

Ana-Maria Guerrero

Ana-Maria Guerrero

Facility Manager

Managing laboratory infrastructure and resources

Jennifer Paloma

Jennifer Paloma

Administrative Assistant

Managing administrative operations

Wenjiang Zhou

Wenjiang Zhou

Remote Visitor

Imperial College London (MSc)
CUHK-Shenzhen (BSc)

Other Trainees and Past Lab Members

Name Previous Role Institution Current Position
Won Jun Kim Undergraduate Research Assistant Caltech MD-PhD student at Tri-I
John Lawrence Clinical PhD Student Sanger PhD student at Sanger
Hanchen Wang PhD Student Cambridge Postdoc at Genentech with Aviv Regev
Simon Murray Bioinformatics Apprentice Sanger Bioinformatics Apprentice at Sanger
Austin Reed Research Assistant CRUK PhD student at CRUK
Dan Zhang Remote Visitor Visiting student at Sanger
Weimin Lin Remote Visitor Visiting student at Cambridge
Sid Mahesh BMI student (thesis committee) UCSF
Wanjun Gu BMI student (thesis committee) UCSF
Sara Smith BMI student (QBC journal club) UCSF
Jerry Wang BMS student (thesis committee) UCSF
Madison Lotstein BMS student (thesis committee) UCSF

Publications (reverse chronological)

Considerations for building and using integrated single-cell atlases
Nat 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 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 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, 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
WebAtlas pipeline for integrated single-cell and spatial transcriptomic data
Nat Methods (2024)
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
A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast
Nat Genet (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
Early human lung immune cell development and its role in epithelial cell fate
Sci Immunol (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, 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 (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, 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
Maternally inherited siRNAs initiate piRNA cluster formation
Mol 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
Nat Genet (2023)
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
Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease
Cell Stem Cell (2023)
Lim K, Donovan APA, Tang W, Sun D, He P, Pett JP, Teichmann SA, Marioni JC, Meyer KB, Brand AH, Rawlins EL
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, He X, Barker RA, Teichmann SA, Marioni JC, Meyer KB, Rawlins EL
SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling
EMBO J (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 (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, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Nat Med (2022)
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
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
PMID: 32728245; PMCID: PMC7410830
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 JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM
PMID: 32728248; PMCID: PMC7410827
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 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
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
PMID: 32701060; PMCID: PMC7417190
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
PMID: 29555645; PMCID: PMC5921965
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
PMID: 25575081; PMCID: PMC4291542

Contact Us

Join Our Lab!

We are currently seeking enthusiastic researchers at any levels especially:

Dry or Wet Postdocs

• Graduate Students (through BMS and BMI programs)

Dry or Wet Research Assistants

If you're interested in joining our team, please reach out!

peng.he在ucsf.edu