91糖心vlog传媒

1994  南京大学生物系&苍产蝉辫;学士

1997  北京大学细胞遗传系 硕士

2005  约翰霍普金斯医学院生物物理系 博士

2011  斯坦福大学发育生物学系 博士后

2012  清华大学 生命科学学院 研究员

2018?至今 首都师范大学 生命科学学院 研究员

主要研究领域与方向
实验室主要利用功能基因组学和发育遗传学手段，以线虫姊妹种为模型，探索生殖隔离的分子机制。目前重点在小杆线虫属建立遗传学和功能基因组手段与资源，探索近缘种基因调控网络的不相容性，认识种间隔离的分子细胞发育基础。为实现这一目标，我们开发和利用多种高通量实验方法，包括高效组装非模式动物的基因组、单细胞精度转录组技术和单细胞精度线虫影像分析系统，开发进化模式线虫的基因组和遗传发育资源，揭示细胞命运决定和进化的基因调控网络。

发表论文（代表性论文为黑体；*, corresponding author）

1. Li, Y., Gao, Y., Ma,J., Gao, Y., Zhou, W., Zhang, H., Shao, W. Liu, Z., Zhao, Z. and Liu, X.* (2024) Regulatory divergences in dosage compensation cause hybrid male inviability in Caenorhabditis. bioRxiv (https://doi.org/10.1101/2024.02.06.577000)

2. Li, Y., Chen, S., Liu, W., Zhao, D., Gao, Y., Hu, S., Liu, H., Li, Y., Qv L. and Liu, X.*. (2024) A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans. Nature Communications 15, 358

3. Zhao, D., Chen, S., Horie, T., Gao, Y., Bao, H. and Liu, X.* (2020) Comparison of differentiation gene batteries for migratory mechanosensory neurons across bilaterians. Evolution & Development (10.1111/ede.12331)

4. Ren, X., Li, R., Wei, X., Bi, Y., Ho, W., Ding, Q., Zhang, Z., Young, A., Tsieh, C., Zeng*, J., Liu, X.* and Zhao Z.* (2018) Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni. Nucleic Acids Research 46, 1295.

5. Li, Y., Zhao, D., Horie, T., Chen, G., Bao, H., Chen, S., Liu, W., Horie, R., Liang, T., Dong, B., Feng, Q., Tao, Q. and Liu, X.*. (2017) A Conserved Gene Regulatory Module Specifies Lateral Neural Borders Across Bilaterians. PNAS 114, E6352

6. Li, S., Dong, F., Wu, Y., Zhang, S., Zhang, C., Liu, X., Jiang, T. and Zeng, J. (2017) A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data. Nucleic Acids Research 45, e129.

7. Liu, W., Yu, E., Chen, S., Ma, X., Lu, Y. and Liu, X.*. (2017) Spatiotemporal expression profiling of long intervening noncoding RNAs in Caenorhabditis elegans. Scientific Reports 7, 5195

8. Wei, X., Xu, Z., Wang, G., Hou, J., Ma, X., Liu, H., Liu, J., Chen, B., Luo, M., Xie, B., Li, R., Ruan, J. and Liu, X.*. (2017) pBACode: a random-barcode-based high-throughput approach for BAC paired-end sequencing and physical clone mapping. Nucleic Acids Rsearch 45, e52

9. Ma, X., Zhan, G., Sleumer, M.C., Chen, S., Liu, W., Zhang, M.Q. and Liu, X.*. (2016) Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT). Nucleic Acids Rsearch 44, e156

10. Fr?kj?r-Jensen, C., Jain, N., Hanson, L., Davis, M.W., Li, Y., Zhao, D., Rebora, K., Millet, J.R., Liu, X., Kim, S.K., Dupuy, D., Jorgensen, E.M., and Fire, A. (2016). An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline. Cell 166: 343 - 357

11. Mann, F.G., Van Nostrand, E.L., Friedland, A.E., Liu, X., and Kim, S.K. (2016). Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans. PLoS Genetics 12: e1005956

12. Aerni, S.J., Liu, X., Do C.B., Gross, S.S., Nguyen, A., Guo, S.D., Long, F., Peng, H., Kim, S.K. and Batzoglou, S.(2013) Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans. Bioinformatics 29, i18-i26

13. Qu, L., Long, F., Liu, X., Kim, S., Myers, E., and Peng, H. (2011). Simultaneous recognition and segmentation of cells: application in C. elegan. Bioinformatics 27, 2895-2902

14. Liu, X., Long, F., Peng, H., Aerni, S.J., Jiang, M., Sánchez-Blanco A., Murray. J.I., Preston, E., Mericle, B., Batzoglou, S., Myers, G., and Kim, S.K. (2009). Analysis of cell fate from single-cell gene expression profiles in C. elegans. Cell 139: 623 - 633

15. Long, F., Peng, H., Liu, X., Kim, S.K., and Myers, G. (2009). A 3D digital atlas of C. elegans and its applicationto single-cell analyses. Nature Methods 6: 667 - 672

16. Long, F., Peng, H., Liu, X., Kim, S.K., and Myers, G. (2008). Automatic Recognition of Cells (ARC) for 3D images of C. elegans. Recomb.

17. Peng, H., Long, F., Liu, X., Kim, S.K., and Myers, E.W. (2008). Straightening Caenorhabditis elegans images. Bioinformatics 24, 234-242

18. Tang, L., Liu, X. and Clarke, N.D. (2006) Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression. BMC Genomics 7: 215

19. Liu, X., C.K. Lee, N.D. Clarke, and J.D. Lieb (2006) Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res. 16: 1517 – 1528

20. Liu, X., Noll, D.M., Lieb, J.D., and Clarke, N.D. (2005) DIP-chip: Rapid and accurate determination of DNA-binding specificity. Genome Res. 15: 421 – 427

21. Han, Y., Lassen, K., Monie, D., Sedaghat, A.R., Shimoji, S., Liu, X., Pierson, T.C., Margolick, J.B., Siliciano, R.F. and Siliciano, J.D. (2004) Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J. Virology 78: 6122

22. Liu, X. and Clarke, N. D. (2002) Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J. Mol. Biol. 323:1-8.

23. Yue, G., Lai, P.S., Yin, K., Sun, F.F., Nagele, R.G., Liu, X. Linask, K.K., Wang, C., Lin, K.T. and Wong, P. Y. (2001) Colon epithelial cell death in 2,4,6-trinitrobenzenesulfonic acid-induced colitis is associated with increased inducible nitric-oxide synthase expression and peroxynitrite production. J. Pharmacol. Exp. Ther. 297:915-925.

24. Linask, K.K., Ludwig, C., Han, M., Liu, X., Radice. G.L. and Knudson, K.A. (1998) N-Cadherin/Catenin-Mediated Morphoregulation of Somite Formation. Developmental Biology 202: 85-102

综述

1. Zhao, D., Chen, S., Liu, X.* (2019) Lateral neural borders as precursors of peripheral nervous systems: A comparative view across bilaterians. Development, Growth & Differentiation 61(1): 58-72.

学术报告和教授课程

础） 组织学术会议

第19界线虫大会神经科学会场，洛杉矶，美国，2013年6月，共同主持

叠） 受邀讲座

“A Conserved Regulatory Network Underlying the Development of Lateral Neural Borders in bilateria”

第1界亚洲进化大会，2018年4月18日

“A Conserved Regulatory Network for A Lateral Neural Plate Border Lineage from Worm to Vertebrate”

亚利桑那大学神经科学系，2017年2月15日

颁） 会议选用报告

“A Conserved Regulatory Network for A Lateral Neural Plate Border Lineage From Worm To Vertebrate”

第21界线虫大会生态和进化会场，洛杉矶，美国，2017年6月

顿） 教授课程

清华大学研究生课程

基因组学与功能基因组学，16课时

模式动物，8课时

生物信息学与系统生物学，9课时

系统生物学，14课时

基因组和表观遗传组，2课时

91糖心vlog传媒本科生课程

生命科学导论，32课时

科学服务

l 论文评审：《Development》、《Journal of Genetics and Genomics》、《Nature Communications》、《Quantitative Biology》、《Trends in Neurosceinces》

l 项目评审：基金委青年、面上和地区项目，C1 funding, University of Leuven, Belgium

荣誉和奖项

2018 北京市“高层次人才”计划

2011 第一批“青年千人”计划

2007 Larry L. Hillblom Foundation Posdoctoral Fellowship

2005 Phi Beta Kappa

国家级科研项目