life decoders

*co-first author, #Corresponding author, members of our group are underlined.

2024

45. Tian, R.* , Yu, Z. , Xue, Z. , Wu, J., Wu, L. , Cai, S. , Gao, B. , He, B., Zhao, Y., Yao, J., Lu, L., Liu, W.# , 2024. Evaluation of T Cell Receptor Construction Methods from scRNA-Seq Data. Genomics, Proteomics & Bioinformatics . link

44. Xue, Z.* , Wu, L.* , Tian, R. , Gao, B. , Zhao, Y., Bing, H., Zhao, B. , Li, Y. , Zhu, K., Wang, L., Yao, J.#, Liu, W.# & Lu, L.#, 2024. Integrative mapping of human CD8+ T cells in inflammation and cancer. Nature Methods . link

43. Zhang, J.*, Tian, R.* , Liu, J.*, Yuan, J.*, Zhang, S., Chi, Z., Yu, W., Yu, Q., Wang, Z., Chen, S., Li, M., Yang, D., Hu, T., Deng, Q., Lu, X., Yang, Y., Zhou, R., Zhang, X., Liu, W.# , and Wang, D.#, 2024. A two-front nutrient supply environment fuels small intestinal physiology through differential regulation of nutrient absorption and host defense. Cell p6251-6271.e20 link

42. Chen, Y.*, Yan, Y.*, Tian, R. , Sheng, Z., Li, L., Chen, J., Liao, Y., Wen, Y., Lu, J., Liu, X., Sun, W., Wu, H., Liao, Y., Zhang, X., Chen, X., An, C., Zhao, K., Liu, W. , Gao, J., Hay, D. C., Ouyang, H.# 2024. Chemically programmed metabolism drives a superior cell fitness for cartilage regeneration. Science Advances , 10(37): eadp4408. link

41. Su, Y.* , Yu, Z. , Jin, S. , Ai, Z. Yuan, R. , Chen, X. , Xue, Z. , Guo, Y. , Chen, D., Liang, H., Liu, Z., Liu, W.# , 2024. Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data. Nature Communications , 15, 3972 link

40. Guo, Y.* , Xue, Z.* , Gong, M. , Jin, S. , Wu, X. , Liu, W.# , 2024.CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements. Mobile DNA , 3. link

2023

39. Tian, R.* , Xue, Z.* , Ruan, D.* , Chen, P., Xu, Y., Dai, C., Shen, W., Ouyang, H.#, Liu, W.# , Lin, J.# , 2023. MSdb: An integrated expression atlas of human musculoskeletal system. iScience , 26(6). link

2022

38. Ai, Z.*, Xiang, X.* , Xiang, Y.*, Szczerbinska, I.*, Qian, Y.*, Xu, X., Ma, C., Su, Y. , Gao, B. , Shen, H., Ramli, M., Chen, D., Liu, Y., Hao, J., Ng, H., Zhang, D. #, Chan, Y. #, Liu, W.# , Liang, H.# 2022. Kruppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency. Cell Reports , 40, 111240. link

37. Wang, L.*, You, X.*, Ruan, D.* , Shao, R., Dai, H., Shen, W., Xu, G., Liu, W.# , Zou, W. # 2022. TET enzymes regulate skeletal development through increasing chromatin accessibility of RUNX2 target genes. Nature communications. Nature Communications , 13, 4709. link

36. Xiang,X.* , Tao,Y., DiRusso,J., Hsu, F.M., Zhang, J. , Xue, Z. , Pontis,J., Trono,D., Liu, W.# , Clark,A. #, 2022. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections, Nature Communications , 13, 463. link

35. Lin, J.* , Yang,Y., Zhou, W., Dai, C. , Chen,X., Xie,Y., Han,S., Liu,H., Hu,Y., Tang,C., Bunpetch,V., Zhang,D., Chen,Y., Zou,X., Chen,D., Liu, W.# , Ouyang,H. #, 2022. Single cell analysis reveals inhibition of angiogenesis attenuates the progression of heterotopic ossification in Mkx−/− mice, Bone research , 10, 4. link

2021

34. Ruan,D.* , Tang,C.*, Fei,Y*, Qian,S., Xiang,X. ,Xu,J., Huang,Z., Chen,X., Heng,B., Yin,Z., Chen,W., Liu, W. , Shen,W.#, Ouyang,H.#; 2021. Early-Stage Primary Anti-inflammatory Therapy Enhances the Regenerative Efficacy of Platelet-Rich Plasma in a Rabbit Achilles Tendinopathy Model, The American journal of sports medicine , 49(12): 3357-3371. link

33. Wu, L.* , Xue, Z.* , Jin, S. , Zhang, J. , Guo, Y. , Bai, Y., Jin, X., Wang, C., Wang, L., Liu, Z., Wang, J.Q., Lu, L.#, Liu, W.# , 2021. huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level, Nucleic Acids Research , gkab867. link

32. Jin, S.* , Xue, Z.* , Zhang, J. , Wang, Z., Zhang, J., Chen, D.#, Liu, W.# , Lin, J.# , 2021. Identification of SRSF3 target mRNAs using inducible TRIBE. Biochemical and Biophysical Research Communications. link

31. Hancock GV, Liu, W. , Peretz,L, Chen,D, Gell,J., Collier,AJ, Zamudio,JR, Plath,K, Clark,AT.#, 2021. Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development. Stem Cell Res 55:102493. link

30. Liu, W. *# , J. Gallego-Bartolomé*, Y. Zhou , Z. Zhong, M. Wang, S. P. Wongpalee, J. Gardiner, S. Feng, P. H. Kuo and S. E. Jacobsen.#, 2021. Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase. Nature Communications 12(1): 3130. link

29. Guo, Y. , Xue, Z. , Yuan, R. , Li, J., Pastor, W. & Liu, W.# , 2021. RAD: a web application to identify region associated differentially expressed genes. Bioinformatics , btab075. link

28. Zhong, Z., Feng, S., Duttke, S.H., Potok, M.E., Zhang, Y. , Gallego-Bartolomé, J., Liu, W.# & Jacobsen, S.E.#, 2021. DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis. Proceedings of the National Academy of Sciences . 118(5), e2023347118. link

2020

27. Yuan, C.*, Pan, Z.*, Zhao, K.*, Li, J., Sheng, Z., Yao, X., Liu, H., Zhang, X., Yang, Y., Yu, D., Zhang, Y., Xu, Y., Zhang, Z., Huang, T., Liu, W. & Ouyang, H.#, 2020. Classification of four distinct osteoarthritis subtypes with a knee joint tissue transcriptome atlas. Bone Research , 8, 38 link

26. Cinkornpumin, J.K., Kwon, S.Y., Guo, Y. , Hossain, I., Sirois, J., Russett, C.S., Tseng, H., Okae, H., Arima, T., Duchaine, T.F., Liu, W. & Pastor, W.A.#, 2020. Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome. Stem Cell Reports . link

25. Gell, J. J.*, Liu, W. , Sosa, E., Chialastri, A., Hancock, G., Tao, Y., Wamaitha, S. E., Bower, G., Dey, S. S., Clark, A. T.#, 2020. An Extended Culture System that Supports Human Primordial Germ Cell-like Cell Survival and Initiation of DNA Methylation Erasure. Stem Cell Reports , 14(3), 433-446. link

2019

24. Wongpalee, S. P.*, Liu, S.*, Gallego-Bartolomé, J.*, Leitner, A., Aebersold, R., Liu, W. , Yen L., Nohales, M. A., Kuo, P. H., Wohlschlegel J. A., Feng, S., Kay, S. A., Zhou, Z.#, Jacobsen, S. E#, 2019. CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Nature Communications , 10(1), 3916. link

23. Chen, D.*, Sun, N.*, Hou, L.*, Kim, R., Faith, J., Aslanyan, M., Tao Y., Zheng Y., Fu J., Liu W. , Manolis K.#, Clark, A#, 2019. Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors. Cell Reports ,29(13), 4568-4582.e4565. link

22. Lin, F.*, Meng, X.*, Guo, Y. , Cao, W., Liu, W. , Xia, Q., Hui, Z., Chen, J., Hong, S., Zhang, X., Wu, C., Wang, D., Wang, J., Lu, L., Qian W., Wei, L., Wang, L.#,2019. Epigenetic initiation of the TH17 differentiation program is promoted by Cxxc finger protein 1. Science Advances ,5,eaax1608 link

21. Potok, M.E.*, Wang, Y.*, Xu, L., Zhong, Z., Liu, W. , Feng, S., Naranbaatar, B., Rayatpisheh, S., Wang, Z., Wohlschlegel, J.E., Ausin, I.#, Jacobsen, S.E.#, 2019. Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A. Z deposition. Nature Communications ,10(1), p3352 link

20. Nohales, M.A., Liu, W. , Duffy, T., Nozue, K., Sawa, M., Pruneda-Paz, J.L., Maloof, J.N., Jacobsen, S.E.# and Kay, S.A.#, 2019. Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock. Developmental Cell , 49(6), pp.840-851. link

19. Gallego-Bartolome, J.*, Liu, W.* , Kuo, P.H., Feng, S., Ghoshal, B., Gardiner, J., Zhao, J.M.C., Park, S.Y., Chory, J. and Jacobsen, S.E.#, 2019. Co-targeting RNA polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis. Cell , 176(5), pp.1068-1082. link

18. Papikian, A., Liu, W. , Gallego-Bartolomé, J. and Jacobsen, S.E.#, 2019. Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems. Nature Communications , 10(1), p.729. link

17. Stoddard, C.I., Feng, S., Campbell, M.G., Liu, W. , Wang, H., Zhong, X., Bernatavichute, Y., Cheng, Y., Jacobsen, S.E.# and Narlikar, G.J.#, 2019. A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase. Molecular Cell , 73(1), pp.73-83. link

2018

16. Chen, D.*, Liu, W.* , Zimmerman, J., Pastor, W.A., Kim, R., Hosohama, L., Ho, J., Aslanyan, M., Gell, J.J., Jacobsen, S.E. and Clark, A.T., 2018. The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation. Cell Reports , 25(13), pp.3591-3602. link

15. Harris, C.J.*, Scheibe, M.*, Wongpalee, S.P., Liu, W. , Cornett, E.M., Vaughan, R.M., Li, X., Chen, W., Xue, Y., Zhong, Z. and Yen, L., 2018. A DNA methylation reader complex that enhances gene transcription. Science , 362(6419), pp.1182-1186. link

14. Pastor, W.A., Liu, W. , Chen, D., Ho, J., Kim, R., Hunt, T.J., Lukianchikov, A., Liu, X., Polo, J.M., Jacobsen, S.E.# and Clark, A.T.#, 2018. TFAP2C regulates transcription in human naive pluripotency by opening enhancers. Nature Cell Biology , 20(5), p.553. link

13. Liu, W.* , Duttke, S.H.*, Hetzel, J., Groth, M., Feng, S., Gallego-Bartolome, J., Zhong, Z., Kuo, H.Y., Wang, Z., Zhai, J., Chory, J., Jacobsen, S.E.#, 2018. RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis. Nature Plants , 4(3), p.181. link

12. Gallego-Bartolomé, J.*, Gardiner, J.*, Liu, W.* , Papikian, A.*, Ghoshal, B., Kuo, H.Y., Zhao, J.M.C., Segal, D.J. and Jacobsen, S.E.#, 2018. Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain. Proceedings of the National Academy of Sciences , 115(9), pp.E2125-E2134. link

11. Zhang, Y.*, Harris, C.J.*, Liu, Q.*, Liu, W. , Ausin, I., Long, Y., Xiao, L., Feng, L., Chen, X., Xie, Y., Chen, X., Zhan, L., Feng, S., Li, J.J., Wang, H.#, Zhai, J.#, Jacobsen, S.E.#, 2018. Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. Proceedings of the National Academy of Sciences , 115(5), pp.E1069-E1074. link

2017

10. Clark, A.T.#, Gkountela, S., Chen, D., Liu, W. , Sosa, E., Sukhwani, M., Hennebold, J.D. and Orwig, K.E., 2017. Primate primordial germ cells acquire transplantation potential by Carnegie stage 23. Stem Cell Reports , 9(1), pp.329-341. link

9. Chen, D., Liu, W. , Lukianchikov, A., Hancock, G.V., Zimmerman, J., Lowe, M.G., Kim, R., Galic, Z., Irie, N., Surani, M.A., Jacobsen, S.E., Clark, A.T.# 2017. Germline competency of human embryonic stem cells depends on eomesodermin. Biology of Reproduction , 97(6), pp.850-861. link

2016

8. Ausin, I., Feng, S., Yu, C., Liu, W. , Kuo, H.Y., Jacobsen, E.L., Zhai, J., Gallego-Bartolome, J., Wang, L., Egertsdotter, U., Street, N.R., Jacobsen, S.E.#, Wang, H.#, 2016. DNA methylome of the 20-gigabase Norway spruce genome. Proceedings of the National Academy of Sciences , 113(50), pp.E8106-E8113. link

7. Li, S., Yen, L., Pastor, W.A., Johnston, J.B., Du, J., Shew, C.J., Liu, W. , Ho, J., Stender, B., Clark, A.T. and Burlingame, A.L., Daxinger, L.#, Patel, D.J#, Jacobsen, S.E.#, 2016. Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin. Proceedings of the National Academy of Sciences , 113(35), pp.E5108-E5116. link

6. Harris, C.J.*, Husmann, D.*, Liu, W. , El Kasmi, F., Wang, H., Papikian, A., Pastor, W.A., Moissiard, G., Vashisht, A.A., Dangl, J.L., Wohlschlegel, J.A., Jacobsen, S.E.#, 2016. Arabidopsis AtMORC4 and AtMORC7 form nuclear bodies and repress a large number of protein-coding genes. PLoS Genetics , 12(5), p.e1005998. link

5. Pastor, W.A.*, Chen, D.*, Liu, W.* , Kim, R., Sahakyan, A., Lukianchikov, A., Plath, K., Jacobsen, S.E.# and Clark, A.T.#, 2016. Naive human pluripotent cells feature a methylation landscape devoid of blastocyst or germline memory. Cell Stem Cell , 18(3), pp.323-329. link

2015

4. Zhai, J.*, Bischof, S.*, Wang, H., Feng, S., Lee, T.F., Teng, C., Chen, X., Park, S.Y., Liu, L., Gallego-Bartolome, J., Liu, W. , Henderson, I.R., Meyers, B.C., Ausin, I.#, Jacobsen, S.E.#, 2015. A one precursor one siRNA model for Pol IV-dependent siRNA biogenesis. Cell , 163(2), pp.445-455. link

2014

3. Pastor, W.A.*, Stroud, H.*, Nee, K., Liu, W. , Pezic, D., Manakov, S., Lee, S.A., Moissiard, G., Zamudio, N., Bourc’his, D. and Aravin, A.A., Clark, A.T.#, Jacobsen, S.E.#, 2014. MORC1 represses transposable elements in the mouse male germline. Nature Communications , 5, p.5795. link

2013

2. Jiang, Y., Chen, L., Zhang, S., Tong, T., Zhang, W., Liu, W. , Xu, G., Tuan, R.S., Heng, B.C., Crawford, R. and Xiao, Y.,Ouyang, H.W.#, 2013. Incorporation of bioactive polyvinylpyrrolidone–iodine within bilayered collagen scaffolds enhances the differentiation and subchondral osteogenesis of mesenchymal stem cells. Acta Biomaterialia , 9(9), pp.8089-8098. link

2012

1. Zhang, S., Jiang, Y.Z., Zhang, W., Chen, L., Tong, T., Liu, W. , Mu, Q., Liu, H., Ji, J., Ouyang, H.W. and Zou, X.#, 2012. Neonatal desensitization supports long-term survival and functional integration of human embryonic stem cell-derived mesenchymal stem cells in rat joint cartilage without immunosuppression. Stem Cells and Development , 22(1), pp.90-101. link

2024/09

• Welcome the joining of our new visiting master student Luyao Zhang, Hongchen Zhu. 欢迎新成员张璐瑶, 朱洪辰加入实验室！

2024/05

• All members of the lab went to the Shanghai Disneyland for retreat 实验室全体正式成员在上海迪士尼乐园进行愉快的团建！

2023/11

• Congrats Ruonan Tian for winning National scholarship for postgraduate students. 恭喜实验室生物信息学专业博士研究生田若楠获得2023年研究生国家奖学金！

2023/09

• Welcome the joining of our new visiting master student Yuhui Chen, Linnan Guo and Weikai Shi. 欢迎新成员陈雨卉，国林楠和石玮凯加入实验室！

2022/12

• Welcome the joining of our new visiting Ph.D. student Ziyang Li. Ziyang is currently the Ph.D. student in clinical medicine from the The Second Affiliated Hospital, Zhejiang University School of Medicine. 欢迎新成员李子阳（浙大附属第二医院，博士研究生）加入实验室！

2022/11

• Congrats Xinyu Xiang for winning National scholarship for postgraduate students. 恭喜实验室生物信息学专业博士研究生相欣雨获得2022年研究生国家奖学金！

2022/6

• Lab at All-in Cafe.
  
  

  
• Congratulation to Ziwei Xue, Siqian Jin, and Xinyu Xiang for winning the First prize and third prize of the Student Crossover Innovation Competition in the Campus Poster Day. 恭喜实验室生物信息学专业博士研究生薛子为，相欣雨和科研助理金飔倩同学获得校区学术交叉创新一等奖和三等奖！

2021/12

• Welcome the joining of our new visiting master student Yiwen Xu. Yiwen is currently the master student in clinical medicine from the The Second Affiliated Hospital, Zhejiang University School of Medicine. 欢迎新成员徐艺文（浙大附属第二医院，硕士研究生）加入实验室！

2021/11

• Congrats Yixin Guo for winning National scholarship for postgraduate students. 恭喜实验室生物信息学专业博士研究生郭奕鑫获得2021年研究生国家奖学金！

2021/9

• Welcome the joining of our new Ph.D. Students Lize Wu, Ziwei Xue and our two new master students Ruonan Tian, Xinyi Chen.
• Congrats Lize Wu et al. for publishing on Nucleic Acid Research. This is a collaboration project with Dr. Lu from ZJE.
• Congrats Siqian Jin et al., for publishing on Biochemical and Biophysical Research Communications.

2021/8

• Congrats Wanlu Liu for receiving approval for funding from The General Program of National Natural Science Foundation of China
• Congrats Wanlu Liu for publishing on Stem Cell Research. This is a collaboration project with Dr. Amander T. Clark from UCLA, USA.

2021/7

• Congrats Wanlu Liu for receiving Justice, Equity, Diversity and Inclusion (JEDI) awards from the Life Science Editors Foundation (LSEF). For more information, please visit http://lifescienceeditors.org/

2021/5

• Lab hike to Jing Mountain in Hangzhou. We enjoy the outdoors.