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1.Peng, G*., Cui, G., Ke, J. and Jing, N. (2020) Using Single-Cell and Spatial Transcriptomes to Understand Stem Cell Lineage Specification During Early Embryo Development. Annu Rev Genomics Hum Genet,doi: 10.1146/annurev-genom-120219-083220
2.Kim, H.J., Osteil, P., Humphrey, S.J., Cinghu, S., Oldfield, A.J., Patrick, E., Wilkie, E.E., Peng, G., Suo, S., Jothi, R., Tam, P.P.L. and Yang, P. (2020) Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning. Nucleic Acids Res48,1828-1842.
3.Zhang, K., Yu, F., Zhu, J., Han, S., Chen, J., Wu, X., Chen, Y., Shen, T., Liao, J., Guo, W., Yang, X., Wang, R., Qian, Y., Yang, J., Cheng, L., Zhao, Y., Hui, C.C., Li, J., Peng, G., He, S., Jing, N. and Tang, K. (2020) Imbalance of Excitatory/Inhibitory Neuron Differentiation in Neurodevelopmental Disorders with an NR2F1 Point Mutation. Cell Rep 31,107521.
4.He, D.D., Tang, X.T., Dong, W., Cui, G., Peng, G., Yin, X., Chen, Y., Jing, N. and Zhou, B.O. (2020) C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors. Stem Cell Reports doi: 10.1016/j.stemcr.2020.03.001
5.Peng G*, Suo S, Cui G, Yu F, Wang R, Chen J, Chen S, Liu Z, Chen G, Qian Y, Tam PPL, Han JJ*, Jing N* (2019) Molecular architecture of lineage allocation and tissue organization in early mouse embryo. Nature,572:528–532
6.Niu Y, Sun N, Li C, Lei Y, Huang Z, Wu J, Si C, Dai X, Liu C, Wei J, Liu L, Feng S, Kang Y, Si W, Wang H, Zhang E, Zhao L, Li Z, Luo X, Cui G, Peng G, Izpisúa Belmonte JC, Ji W, Tan T (2019) Dissecting primate early post-implantation development using long-term in vitro embryo culture. Science,366: doi:10.1126/science.aaw5754
7.Cui G, Jing N, Peng G* (2019) Comments on ‘Molecular architecture of lineage allocation and tissue organization in early mouse embryo’. Journal of Molecular Cell Biology,doi:10.1093/jmcb/mjz101
8.Yang X, Hu B, Liao J, Qiao Y, Chen Y, Qian Y, Feng S, Yu F, Dong J, Hou Y, Xu H, Wang R, Peng G, Li J, Tang F, Jing N (2019) Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development. Cell Research,29: 911–926
9.Zhou Y, Wang X, Song M, He Z, Cui G, Peng G, Dieterich C, Antebi A, Jing N, Shen Y (2019) A secreted microRNA disrupts autophagy in distinct tissues of Caenorhabditis elegans upon ageing. Nature Communications,10: 4827
10. Yu W, Ma X, Xu J, Heumüller AW, Fei Z, Feng X, Wang X, Liu K, Li J, Cui G, Peng G, Ji H, Li J, Jing N, Song H, Lin Z, Zhao Y, Wang Z, Zhou B, Zhang L (2019) VGLL4 plays a critical role in heart valve development and homeostasis. PLoS Genetics,15: e1007977
11. Song W, Wang R, Jiang W, Yin Q, Peng G, Yang R, Yu QC, Chen J, Li J, Cheung TH, Jing N, Zeng YA (2019) Hormones induce the formation of luminal-derived basal cells in the mammary gland. Cell Research,29: 206–220
12. Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PPL, Jing N, Deng Q (2019) Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development. Cell Reports,26: 2593–2607.e3
13. Liu Q, Liu K, Cui G, Huang X, Yao S, Guo W, Qin Z, Li Y, Yang R, Pu W, Zhang L, He L, Zhao H, Yu W, Tang M, Tian X, Cai D, Nie Y, Hu S, Ren T, Qiao Z, Huang H, Zeng YA, Jing N, Peng G*, Ji H*, Zhou B* (2019) Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction. Nature Genetics,51: 728–738
14. Osteil P, Studdert JB, Goh HN, Wilkie EE, Fan X, Khoo PL, Peng G, Salehin N, Knowles H, Han JJ, Jing N, Fossat N, Tam PPL (2019) Dynamics of Wnt activity on the acquisition of ectoderm potency in epiblast stem cells. Development,146, doi:10.1242/dev.172858
15. Xue Y, Liu D, Cui G, Ding Y, Ai D, Gao S, Zhang Y, Suo S, Wang X, Lv P, Zhou C, Li Y, Chen X, Peng G, Jing N, Han JJ, Liu F (2019) A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis. Cell Reports,27: 1567–1578.e5
16. Friedman CE, Nguyen Q, Lukowski SW, Helfer A, Chiu HS, Miklas J, Levy S, Suo S, Han JJ, Osteil P, Peng G, Jing N, Baillie GJ, Senabouth A, Christ AN, Bruxner TJ, Murry CE, Wong ES, Ding J, Wang Y, Hudson J, Ruohola-Baker H, Bar-Joseph Z, Tam PPL, Powell JE, Palpant NJ (2018) Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation. Cell Stem Cell,23: 586–598.e8
17. Peng G, Han JJ (2018) Regulatory network characterization in development: challenges and opportunities. F1000Res,7:
18. Cui G, Suo S, Wang R, Qian Y, Han JJ, Peng G*, Tam PPL*, Jing N* (2018) Mouse gastrulation: Attributes of transcription factor regulatory network for epiblast patterning. Dev Growth Differ,60: 463–472
19. Christodoulou N, Kyprianou C, Weberling A, Wang R, Cui G, Peng G, Jing N, Zernicka-Goetz M (2018) Sequential formation and resolution of multiple rosettes drive embryo remodelling after implantation. Nature Cell Biology, 20: 1278–1289
20. Sibbritt, T., Ip, C. K., Khoo, P. L., Wilkie, E., Jones, V., Sun, J. Q. J., Shen, J. X., Peng, G., Han, J. J., Jing, N., Osteil, P., Ramialison, M., Tam, P. P. L., and Fossat, N. (2018). A gene regulatory network anchored by LIM homeobox 1 (LHX1) for embryonic head development. Genesis 56: e23246
21. Liu C, Wang, R, He Z, Osteil P, Yang X, Chen J, Peng G, Tam P, Jing N (2018), Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells. Stem Cell Reports 11, 43-57.
22. Yang X, Hu B, Hou Y, Qiao Y,, Wang R, Chen Y, Qian Y, Feng S, Chen J, Liu C, Peng G, Tang F and Jing N (2018). Silencing of developmental genes by H3K27me3 and DNA methylation reflects the discrepant plasticity of embryonic and extraembryonic lineages. Cell Research 28(5):593-596.
23. Han, X#, Luo, S#, Peng G#, Lu, JY, Cui G, Liu L, Yan P, Yin Y, Liu W, Wang R, Chang Z, Na J, Jing N*, and Shen X* (2018). Mouse knockout models reveal largely dispensable but context-dependent functions of lncRNAs during development. Journal of Molecular Cell Biology.10:175-178.
24. Liu, C., Peng, G., and Jing, N. (2018). TGF-β signaling pathway in early mouse development and embryonic stem cells. Acta Biochim Biophys Sin.50, 68-73.
25. Peng G (2017) Looking Back: Single-Cell Analysis, Empowering Stem Cell Studies (2017) Cell Stem Cell 20: 758 (Commentary)
26. Peng G, Tam P & Jing N (2017) Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies. National Science Review.doi:10.1093/nsr/nwx093
27. Peng G* & Jing N* (2017) The genome-wide molecular regulation of mouse gastrulation embryo. Science China Life Science.doi:10.1007/s11427-016-0285-3
28. Zamir L, Singh R, Nathan E, Patrick R, Yifa O, Yahalom-Ronen Y, Arraf AA, Schultheiss TM, Suo S, Han J-DJ, Peng G, Jing N, Wang Y, Palpant N, Tam PP, Harvey RP & Tzahor E (2017) Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta. elife 6, e20994.
29. Chen J, Suo S, Tam PP, Han J-DJ*, Peng G* & Jing N* (2017) Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nature Protocols 12,566–580.
30. Song L, Chen J, Peng G, Tang K & Jing N (2016) Dynamic Heterogeneity of Brachyury in Mouse Epiblast Stem Cells Mediates Distinct Response to Extrinsic Bone Morphogenetic Protein (BMP) Signaling. Journal of Biological Chemistry 291,15212–15225.
31. Peng G#, Suo S#, Chen J#, Chen W, Liu C, Yu F, Wang R, Chen S, Sun N, Cui G, Song L, Tam PPL, Han J-DJ & Jing N (2016) Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Developmental Cell 36,681–697.
32. Peng G &Jing N (2016) Early embryo development and lineage determination. Chinese Bulletin of Life Sciences.
33. Tang K, Peng G, Qiao Y, Song L & Jing N (2015) Intrinsic regulations in neural fate commitment. Development, Growth&Differentiation.57, 109–120.
34. Li L, Song L, Liu C, Chen J, Peng G, Wang R, Liu P, Tang K, Rossant J & Jing N (2015) Ectodermal progenitors derived from epiblast stem cells by inhibition of Nodal signaling. Journal of Molecular Cell Biology7,455–465.
35. Liu P, Dou X, Peng G, Han J-DJ & Jing N (2015) Genome-wide analysis of histone acetylation dynamics during mouse embryonic stem cell neural differentiation. Genomic Data5,15–16.
36. Song L, Sun N, Peng G, Chen J, Han J-DJ & Jing N (2015) Genome-wide ChIP-seq and RNA-seq analyses of Pou3f1 during mouse pluripotent stem cell neural fate commitment. Genomic Data 5,375–377.
37. Liu P, Dou X, Liu C, Wang L, Xing C, Peng G, Chen J, Yu F, Qiao Y, Song L, Wu Y, Yue C, Li J, Han J-DJ, Tang K & Jing N (2015) Histone deacetylation promotes mouse neural induction by restricting Nodal-dependent mesendoderm fate. Nature Communications 6,6830.
38. Zhu Q, Song L, Peng G, Sun N, Chen J, Zhang T, Sheng N, Tang W, Qian C, Qiao Y, Tang K, Han J-DJ, Li J & Jing N (2014) The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways. elife 3, 2.
39. Li G, Bahn JH, Lee J-H, Peng G, Chen Z, Nelson SF & Xiao X (2012) Identification of allele-specific alternative mRNA processing via transcriptome sequencing. Nucleic Acids Research 40,e104–e104.
40. Bahn JH, Lee J-H, Li G, Greer C, Peng G & Xiao X (2012) Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Research 22,142–150.
41. Lee J-H, Gao C, Peng G, Greer C, Ren S, Wang Y & Xiao X (2011) Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circulation Research 109,1332–1341.
42. Kong L, Choi RCY, Xie HQ, Wang X, Peng G, Xie Z, Tsim KWK & Jing N (2011) Expression of the IgSF protein Kirre in the rat central nervous system. Life Sciences 88,590–597.
43. Zhang Y-Q#, Guo N#, Peng G#, Wang X, Han M, Raincrow J, Chiu C-H, Coolen LM, Wenthold RJ, Zhao Z-Q, Jing N& Yu L (2009) Role of SIP30 in the development and maintenance of peripheral nerve injury-induced neuropathic pain. Pain 146,130–140.
44. Peng G#, Han M#, Du Y, Lin A, Yu L, Zhang Y & Jing N (2009) SIP30 is regulated by ERK in peripheral nerve injury-induced neuropathic pain. Journal of Biological Chemistry 284,30138–30147.
(*: corresponding author)
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