Haiqing Xiong, Qianhao Wang, Chen C. Li, He A. Single-cell joint profiling of multiple epigenetic proteins and gene transcription. Sci. Adv., 2024; 5;10(1); Full Text


Haiqing Xiong, Runyu Wang, He A. Single-cell protein-DNA interactomics and multiomics tools for deciphering genome regulation. National Science Open., 2023; 2(3): 20220057; Full Text

Youdong Zhang, Xin Li, Shu Gao, Yuanhui Liao, Yingjie Luo, Min Liu, Yunkun Bian, Haiqing Xiong, Yanzhu Yue, He A. Genetic reporter for live tracing fluid flow forces during cell fate segregation in mouse blastocyst development. Cell Stem Cell., 2023; 30(8): 1110-1123; Full Text


Li C, Wu B, Li Y, Liu Y, Wang J, Xie J, Xu X, Tian X, Ye Z, Guan J, Chen J, Xie S, Zhang B, Cai B, Wang Q, Yu H, Lan T, Man C, Kang X, Qian P, Perry J, He A, Jiang L, Zhao M. Loss of sphingosine kinase 2 promotes the expansion of hematopoietic stem cells by improving their metabolic fitness. Blood., 2022; 140(15): 1686–1701; Full Text

Lei Z, Meng H, Liu L, Zhao H, Rao X, Yan Y, Wu H, Liu M, He A, Yi C. Mitochondrial base editor induces substantial nuclear off-target mutations. Nature., 2022; 606(7915): 804-811. Full Text

Li C C, Zhang G, Du J, Li Z, Ni Y, Zhou J, Li Y, Hou S, Zheng X, Lan Y, Liu B, He A. Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos. Nat Commun., 2022; 13(1): 1-13. Full Text

Li X, Yue Y, Zhang Y, Liao Y, Wang Q, Bian Y, Na J, He A. Continuous live imaging reveals a subtle pathological alteration with cell behaviors in congenital heart malformation. Fundamental Research, 2022, 2(1): 14-22. Full Text


Xiong H, Luo Y, Wang Q, Yu X, He A. Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions. Nat Methods, 2021;18(6): 652-660. Full Text


Xiong H and He A. Single-Cell Transcriptomic Analysis of Cardiac Progenitor Differentiation. Curr Cardiol Rep. 2020;22:38. Full Text

Yue Y, Zong W, Li X, Li J, Zhang Y, Wu R, Liu Y, Cui J, Wang Q, Bian Y, Yu X, Liu Y, Tan G, Zhang Y, Zhao G, Zhou B, Chen L, Xiao W, Cheng H and He A. Long-term, in toto live imaging of cardiomyocyte behaviour during mouse ventricle chamber formation at single-cell resolution. Nat Cell Biol. 2020;22:332-340. Full Text

Hu X, Deng Q, Ma L, Li Q, Chen Y, Liao Y, Zhou F, Zhang C, Shao L, Feng J, He T, Ning W, Kong Y, Huo Y, He A, Liu B, Zhang J, Adams R, He Y, Tang F, Bian X and Luo J. Meningeal lymphatic vessels regulate brain tumor drainage and immunity. Cell Res. 2020;30:229-243. Full Text


Wang Q, Xiong H, Ai S, Yu X, Liu Y, Zhang J and He A. CoBATCH for High-throughput Single-cell Epigenomic Profiling. Mol Cell. 2019. Full Text

Ai S, Xiong H, Li CC, Luo Y, Shi Q, Liu Y, Yu X, Li C and He A. Profiling chromatin states using single-cell itChIP-seq. Nat Cell Biol. 2019. Full Text

Xiong H, Luo Y, Yue Y, Zhang J, Ai S, Li X, Wang X, Zhang YL, Wei Y, Li H, Hu X, Li C and He A. Single-Cell Transcriptomics Reveals Chemotaxis Mediated Intra-Organ Crosstalk During Cardiogenesis. Circ Res. 2019. Full Text

Li Y, Ai S, Yu X, Li C, Li X, Yue Y, Wei Y, Li CY# and He A. Replication-Independent Histone Turnover Underlines the Epigenetic Homeostasis in Adult Heart. Circ Res. 2019. Full Text

Liu L, Cai J, Wang H, Liang X, Zhou Q, Ding C, Zhu Y, Fu T, Guo Q, Xu Z, Xiao L, Liu J, Yin Y, Fang L, Xue B, Wang Y, Meng ZX, He A, Li JL, Liu Y, Chen XW and Gan Z. Coupling of COPII vesicle trafficking to nutrient availability by the IRE1alpha-XBP1s axis. Proc Natl Acad Sci U S A. 2019;116:11776-11785. Full Text

Ma C, Niu R, Huang T, Shao LW, Peng Y, Ding W, Wang Y, Jia G, He C, Li CY, He A and Liu Y. N6-methyldeoxyadenine is a transgenerational epigenetic signal for mitochondrial stress adaptation. Nat Cell Biol. 2019;21:319-327. Full Text

An NA, Ding W, Yang XZ, Peng J, He BZ, Shen QS, Lu F, He A, Zhang YE, Tan BC, Chen JY and Li CY. Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates. Genome Biol. 2019;20:24. Full Text


Li Y, Li C, Li S, Peng Q, An NA, He A# and Li CY#. Human exonization through differential nucleosome occupancy. Proc Natl Acad Sci U S A. 2018;115:8817-8822. Full Text

Zhang M, Dong Y, Hu F, Yang D, Zhao Q, Lv C, Wang Y, Xia C, Weng Q, Liu X, Li C, Zhou P, Wang T, Guan Y, Guo R, Liu L, Geng Y, Wu H, Du J, Hu Z, Xu S, Chen J, He A, Liu B, Wang D, Yang YG and Wang J. Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes. Nat Immunol. 2018;19:279-290. Full Text


Zhou P, Gu F, Zhang L, Akerberg BN, Ma Q, Li K, He A, Lin Z, Stevens SM, Zhou B and Pu WT. Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq. Elife. 2017;6. Full Text

Zhang S-J, Wang C, Yan S, Fu A, Luan X, Li Y, Sunny Shen Q, Zhong X, Chen J-Y, Wang X, Chin-Ming Tan B, He A and Li C-Y. Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. Mol Biol Evol. 2017;34:2453-2468. Full Text

Yang Y, Liu B, Xu J, Wang J, Wu J, Shi C, Xu Y, Dong J, Wang C, Lai W, Zhu J, Xiong L, Zhu D, Li X, Yang W, Yamauchi T, Sugawara A, Li Z, Sun F, Li X, Li C, He A, Du Y, Wang T, Zhao C, Li H, Chi X, Zhang H, Liu Y, Li C, Duo S, Yin M, Shen H, Belmonte JCI and Deng H. Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency. Cell. 2017;169:243-257.e25. Full Text

Wang F, Song W, Zhao H, Ma Y, Li Y, Zhai D, Pi J, Si Y, Xu J, Dong L, Su R, Zhang M, Zhu Y, Ren X, Miao F, Liu W, Li F, Zhang J, He A, Shan G, Hui J, Wang L and Yu J. The RNA-binding protein QKI5 regulates primary miR-124-1 processing via a distal RNA motif during erythropoiesis. Cell Res. 2017;27:416-439. Full Text

Han X, Li P, Yang Z, Huang X, Wei G, Sun Y, Kang X, Hu X, Deng Q, Chen L, He A, Huo Y, Li D, Betzig E and Luo J. Zyxin regulates endothelial von Willebrand factor secretion by reorganizing actin filaments around exocytic granules. Nat Commun. 2017;20:24. Full Text

Ai S, Yu X, Li Y, Peng Y, Li C, Yue Y, Tao G, Li C-Y, Pu WT and He A. Divergent Requirements for EZH1 in Heart Development Versus Regeneration. Circ Res. 2017;121:106-112. Full Text

Ai S, Peng Y, Li C, Gu F, Yu X, Yue Y, Ma Q, Chen J, Lin Z, Zhou P, Xie H, Prendiville TW, Zheng W, Liu Y, Orkin SH, Wang D-Z, Yu J, Pu WT# and He A#. EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent. Elife. 2017;6. Full Text


Lin Z, Guo H, Cao Y, Zohrabian S, Zhou P, Ma Q, VanDusen N, Guo Y, Zhang J, Stevens SM, Liang F, Quan Q, van Gorp PR, Li A, Dos Remedios C, He A, Bezzerides VJ, Pu WT. Acetylation of VGLL4 Regulates Hippo-YAP Signaling and Postnatal Cardiac Growth. Dev Cell. 2016. Full Text

Xiao C, Gao L, Hou Y, Xu C, Chang N, Wang F, Hu K, He A, Luo Y, Wang J, Peng J, Tang F, Zhu X, Xiong JW. Chromatin-remodelling factor Brg1 regulates myocardial proliferation and regeneration in zebrafish. Nat Commun. 2016;7:13787. Full Text


Prendiville TW, Guo H, Lin Z, Zhou P, Stevens SM, He A, VanDusen N, Chen J, Zhong L, Wang D-Z, Gao G and Pu WT. Novel Roles of GATA4/6 in the Postnatal Heart Identified through Temporally Controlled, Cardiomyocyte-Specific Gene Inactivation by Adeno-Associated Virus Delivery of Cre Recombinase. PLoS One. 2015;10:e0128105. Full Text

Chen J-Y, Shen QS, Zhou W-Z, Peng J, He BZ, Li Y, Liu C-J, Luan X, Ding W, Li S, Chen C, Tan BC-M, Zhang YE, He A and Li C-Y. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet. 2015;11:e1005391. Full Text

Before 2015

Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang D-Z, Li K, Wang J, Wanders RJA, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK and Pu WT. Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nat Med. 2014;20:616-23. Full Text

Wang F, Zhu Y, Guo L, Dong L, Liu H, Yin H, Zhang Z, Li Y, Liu C, Ma Y, Song W, He A, Wang Q, Wang L, Zhang J, Li J and Yu J. A regulatory circuit comprising GATA1/2 switch and microRNA-27a/24 promotes erythropoiesis. Nucleic Acids Res. 2014;42:442-57. Full Text

Prendiville TW, Ma Q, Lin Z, Zhou P, He A and Pu WT. Ultrasound-guided Transthoracic Intramyocardial Injection in Mice. J Vis Exp. 2014. Full Text

He A , Gu F, Hu Y, Ma Q, Yi Ye L, Akiyama JA, Visel A, Pennacchio LA and Pu WT. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. Nat Commun. 2014;5:4907. Full Text

Aronson BE, Rabello Aronson S, Berkhout RP, Chavoushi SF, He A and Pu WT, Verzi MP and Krasinski SD. GATA4 represses an ileal program of gene expression in the proximal small intestine by inhibiting the acetylation of histone H3, lysine 27. Biochim Biophys Acta. 2014. Full Text

Zhou P, Zhang Y, Ma Q, Gu F, Day DS, He A, Zhou B, Li J, Stevens SM, Romo D and Pu WT. Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification. Proc Natl Acad Sci U S A. 2013;110:15395-400. Full Text

Prendiville TW, Ma Q, Lin Z, Zhou P, He A, Huang T and Gong W. Alteration of innate immunity by donor IL-6 deficiency in a presensitized heart transplant model. PLoSOne. 2013;8:e77559. Full Text

Zhou P, He A, and Pu WT. Regulation of GATA4 Transcriptional Activity in Cardiovascular Development and Disease. Curr Top Dev Biol. 2012;100:143-69. Full Text

Ounzain S, Kobayashi S, Peterson RE, He A, Motterle A, Samani NJ, Menick DR, Pu WT, Liang Q and Chong NW. Cardiac expression of ms1/STARS, a novel gene involved in cardiac development and disease, is regulated by GATA4. Mol Cell Biol. 2012;32:1830-43. Full Text

He A, Shen X, Ma Q, Cao J, von Gise A, Zhou P, Wang G, Marquez VE, Orkin SH and Pu WT. PRC2 directly methylates GATA4 and represses its transcriptional activity. Genes Dev. 2012;26:37-42. Full Text

He A, and Pu WT. Mature Cardiomyocytes Recall Their Progenitor Experience Via Polycomb Repressive Complex 2. Circulation Research. 2012;111:162-164. Full Text

He A , Ma Q, Cao J, von Gise A, Zhou P, Xie H, Zhang B, Hsing M, Christodoulou DC, Cahan P, Daley GQ, Kong SW, Orkin SH, Seidman CE, Seidman JG and Pu WT. Polycomb Repressive Complex 2 Regulates Normal Development of the Mouse Heart. Circ Res. 2012;110:406-15. Full Text

Seok HY, Tatsuguchi M, Callis TE, He A, Pu WT and Wang DZ. miR-155 inhibits expression of the MEF2A protein to repress skeletal muscle differentiation. J Biol Chem. 2011;286:35339-46. Full Text

Kuttippurathu L, Hsing M, Liu Y, Schmidt B, Maskell DL, Lee K, He A, Pu WT and Kong SW. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics. 2011;27:715-7. Full Text

He A, Kong SW, Ma Q and Pu WT. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A. 2011;108:5632-7. Full Text

He A and Pu WT. Genome-wide location analysis by pull down of in vivo biotinylated transcription factors. Curr Protoc Mol Biol. 2010;Chapter 21:Unit 21.20. Full Text

Ikeda S, He A, Kong SW, Lu J, Bejar R, Bodyak N, Lee KH, Ma Q, Kang PM, Golub TR and Pu WT. MicroRNA-1 negatively regulates expression of the hypertrophy-associated calmodulin and Mef2a genes. Mol Cell Biol. 2009;29:2193-204. Full Text

He A, Zhu L, Gupta N, Chang Y and Fang F. Overexpression of micro ribonucleic acid 29, highly up-regulated in diabetic rats, leads to insulin resistance in 3T3-L1 adipocytes. Mol Endocrinol. 2007;21:2785-94. Full Text

He A, Liu X, Liu L, Chang Y and Fang F. How many signals impinge on GLUT4 activation by insulin? Cell Signal. 2007;19:1-7. Full Text