Reforgene Medicine
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Publications

Selected publications (in the original language, cited in standard academic format).

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Gene editing & stem cell research

  1. Yu J, Lu W, Ge T, Huang R, Chen B, Ye M, Bai Y, Shi G, Songyang Z, Ma W, Huang J. Interaction Between Sympk and Oct4 Promotes Mouse Embryonic Stem Cell Proliferation. Stem Cells. 2019;37(6):743-753. doi: 10.1002/stem.2992
  2. Liang P, Xie X, Zhi S, Sun H, Zhang X, Chen Y, Chen Y, Xiong Y, Ma W, Liu D, Huang J, Songyang Z. Genome-wide profiling of adenine base editor specificity by EndoV-seq. Nature Communications. 2019;10(1):67. doi: 10.1038/s41467-018-07988-z
  3. Liang P, Sun H, Zhang X, Xie X, Zhang J, Bai Y, Ouyang X, Zhi S, Xiong Y, Ma W, Liu D, Huang J, Songyang Z. Effective and precise adenine base editing in mouse zygotes. Protein & Cell. 2018;9(9):808-813. doi: 10.1007/s13238-018-0566-z
  4. Zhang Z, Wan T, Chen Y, Chen Y, Sun H, Cao T, Songyang Z, Tang G, Wu C, Ping Y, Xu F, Huang J. Cationic Polymer‐Mediated CRISPR/Cas9 Plasmid Delivery for Genome Editing. Macromolecular Rapid Communications. 2018;40(5):1800068. doi: 10.1002/marc.201800068
  5. Zhan S, Cao S, Du H, Sun Y, Li L, Ding C, Zheng H, Huang J. Parental genetic material and oxygen concentration affect hatch dynamics of mouse embryo in vitro. Reproductive Biology and Endocrinology. 2018;16(1):39. doi: 10.1186/s12958-018-0356-8
  6. Zhang Z, Sun H, Chen Y, Cao T, Songyang Z, Huang J, Huang Y. Analysis of hpf1 expression and function in early embryonic development of zebrafish. Development Genes and Evolution. 2018;228(2):141-147. doi: 10.1007/s00427-018-0608-9

RNA & oncology research

  1. Xiao Z, Han L, Lee H, Zhuang L, Zhang Y, Baddour J, Nagrath D, Wood CG, Gu J, Wu X, Liang H, Gan B. Energy stress-induced lncRNA FILNC1 represses c-Myc-mediated energy metabolism and inhibits renal tumor development. Nature Communications. 2017;8(1):783. doi: 10.1038/s41467-017-00902-z
  2. Dai F, Lee H, Zhang Y, Zhuang L, Yao H, Xi Y, Xiao Z, You MJ, Li W, Su X, Gan B. BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response. Proceedings of the National Academy of Sciences. 2017;114(12):3192-3197. doi: 10.1073/pnas.1619588114
  3. Liu X, Xiao Z, Han L, Zhang J, Lee S, Wang W, Lee H, Zhuang L, Chen J, Lin H, Wang J, Liang H, Gan B. LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nature Cell Biology. 2016;18(4):431-442. doi: 10.1038/ncb3328
  4. Xiao Z, Liu X, Zhuang L, Gan B. NBR2: A former junk gene emerges as a key player in tumor suppression. Molecular & Cellular Oncology. 2016;3(4):e1187322. doi: 10.1080/23723556.2016.1187322
  5. Kim M. Long non-coding RNAs in cancer. Non-coding RNA Research. 2019;4(2):45. doi: 10.1016/j.ncrna.2019.02.003
  6. Lee H, Dai F, Zhuang L, Xiao Z, Kim J, Zhang Y, Ma L, You MJ, Wang Z, Gan B. BAF180 regulates cellular senescence and hematopoietic stem cell homeostasis through p21. Oncotarget. 2016;7(15):19134-19146. doi: 10.18632/oncotarget.8102
  7. Liu X, Xiao Z, Gan B. An lncRNA switch for AMPK activation. Cell Cycle. 2016;15(15):1948-1949. doi: 10.1080/15384101.2016.1184515
  8. Wang W, Xiao Z, Li X, Aziz KE, Gan B, Johnson RL, Chen J. AMPK modulates Hippo pathway activity to regulate energy homeostasis. Nature Cell Biology. 2015;17(4):490-499. doi: 10.1038/ncb3113
  9. Diao L, Xiao Z, Leng X, Li B, Li J, Luo Y, Li S, Yu C, Zhou H, Qu L. Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes in Ascomycota. RNA. 2014;20(9):1376-1385. doi: 10.1261/rna.042309.113
  10. Xiao Z, Diao L, Yang J, Xu H, Huang M, Deng Y, Zhou H, Qu L. Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Research. 2012;41(1):e5-e5. doi: 10.1093/nar/gks821
  11. Zhou A, Diao L, Xu H, Xiao Z, Li J, Zhou H, Qu L. β-Catenin/LEF1 transactivates the microRNA-371-373 cluster that modulates the Wnt/β-catenin-signaling pathway. Oncogene. 2011;31(24):2968-2978. doi: 10.1038/onc.2011.461
  12. Xu H, He J, Xiao Z, Zhang Q, Chen Y, Zhou H, Qu L. Liver-Enriched Transcription Factors Regulate MicroRNA-122 That Targets CUTL1 During Liver Development. Hepatology. 2010;52(4):1431-1442. doi: 10.1002/hep.23818
  13. Liu N, Xiao Z, Yu C, Shao P, Liang Y, Guan D, Yang J, Chen C, Qu L, Zhou H. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics. 2009;10(1):515. doi: 10.1186/1471-2164-10-515
  14. Shao P, Zhou H, Xiao Z, He J, Huang M, Chen Y, Qu L. Identification of novel chicken microRNAs and analysis of their genomic organization. Gene. 2008;418(1-2):34-40. doi: 10.1016/j.gene.2008.04.004
  15. He H, Zhou H, Xiao Z, Zeng X, Chen J, Zheng T, Qu L. Identification of three novel noncoding RNAs from Drosophila melanogaster. Chinese Science Bulletin. 2006;51(22):2737-2742. doi: 10.1007/s11434-006-2202-1

Genomics research

  1. Yin X, Du Y, Zhang H, Wang Z, Wang J, Fu X, Cui Y, Chen C, Liang J, Xuan Z, Zhang X. Identification of a de novo fetal variant in osteogenesis imperfecta by targeted sequencing-based noninvasive prenatal testing. Journal of Human Genetics. 2018;63(11):1129-1137. doi: 10.1038/s10038-018-0489-9
  2. Wei H, Wang M, Ou J, Jiang W, Tian F, Sheng Y, Li H, Xu H, Zhang R, Guan A, Wang C, Jiang H, Ren Y, He J, Liu J, Huang W, Liao N, Cai X, Ming J, Ling R, Xu Y, Hu C, Zhang J, Guo B, Ouyang L, Shuai P, Liu Z, Zhong L, Jing R, Zeng Z, Zhang M, Zhang T, Xuan Z, Tan X, Liang J, Pan Q, Chen L, Zhang F, Fan L, Zhang Y. Multicenter cross‑sectional screening of the BRCA gene for Chinese high hereditary risk breast cancer populations. Oncology Letters. 2018. doi: 10.3892/ol.2018.8538
  3. Li J, Jing R, Wei H, Wang M, Xiaowei Q, Liu H, Jian L, Ou J, Jiang W, Tian F, Sheng Y, Li H, Xu H, Zhang R, Guan A, Liu K, Jiang H, Ren Y, He J, Huang W, Liao N, Cai X, Ming J, Ling R, Xu Y, Hu C, Zhang J, Guo B, Ouyang L, Shuai P, Liu Z, Zhong L, Zeng Z, Zhang T, Xuan Z, Tan X, Liang J, Pan Q, Chen L, Zhang F, Fan L, Zhang Y, Yang X, BoLi J, Chen C, Jiang J. Germline mutations in 40 cancer susceptibility genes among Chinese patients with high hereditary risk breast cancer. International Journal of Cancer. 2018;144(2):281-289. doi: 10.1002/ijc.31601
  4. Xie Y, Luo X, Li Y, Chen L, Ma W, Huang J, Cui J, Zhao Y, Xue Y, Zuo Z, Ren J. DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning. Genomics, Proteomics & Bioinformatics. 2018;16(4):294-306. doi: 10.1016/j.gpb.2018.04.007
  5. Qi H, Xuan Z, Du Y, Cai L, Zhang H, Wen X, Kong X, Yang K, Mi Y, Fu X, Cao S, Wang J, Chen C, Liang J. High resolution global chromosomal aberrations from spontaneous miscarriages revealed by low coverage whole genome sequencing. European Journal of Obstetrics & Gynecology and Reproductive Biology. 2018;224:21-28. doi: 10.1016/j.ejogrb.2018.03.008
  6. Zhao P, Liang J, Deng Z, Wang M, Qin J, Chen C, Hu X. Association of Gene Mutations with Response to Arsenic-Containing Compound Qinghuang Powder (复方青黄散) in Patients with Myelodysplastic Syndromes. Chinese Journal of Integrative Medicine. 2018;25(6):409-415. doi: 10.1007/s11655-018-2977-3
  7. Borensztein M, Syx L, Ancelin K, Diabangouaya P, Picard C, Liu T, Liang J, Vassilev I, Galupa R, Servant N, Barillot E, Surani A, Chen C, Heard E. Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. Nature Structural & Molecular Biology. 2017;24(3):226-233. doi: 10.1038/nsmb.3365
  8. Wang B, Liu Y, Hou G, Wang L, Lv N, Xu Y, Xu Y, Wang X, Xuan Z, Jing Y, Li H, Jin X, Deng A, Wang L, Gao X, Dou L, Liang J, Chen C, Li Y, Yu L. Mutational spectrum and risk stratification of intermediate-risk acute myeloid leukemia patients based on next-generation sequencing. Oncotarget. 2016;7(22):32065-32078. doi: 10.18632/oncotarget.7028
  9. Zhang H, Zhao Y, Song J, Zhu Q, Yang H, Zheng M, Xuan Z, Wei Y, Chen Y, Yuan P, Yu Y, Li D, Liang J, Fan L, Chen C, Qiao J. Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation. Scientific Reports. 2015;5(1):16106. doi: 10.1038/srep16106
  10. Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biology. 2014;15(2):R36. doi: 10.1186/gb-2014-15-2-r36
  11. Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. Nature Genetics. 2014 Mar;46(3):234-44.
  12. Yang F, Gu B, Zhang L, Xuan J, Luo H, Zhou P, Zhu Q, Yan S, Chen S, Cao Z, Xu J, Xing Q, Luo X. HLA-B*13:01 Is Associated with Salazosulfapyridine-Induced Drug Rash with Eosinophilia and Systemic Symptoms in Chinese Han Population. Pharmacogenomics. 2014;15(11):1461-1469. doi: 10.2217/pgs.14.69
  13. Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole-Genome Sequencing Uncovers the Genetic Basis of Chronic Mountain Sickness in Andean Highlanders. The American Journal of Human Genetics. 2013;93(3):452-462. doi: 10.1016/j.ajhg.2013.07.011
  14. Kelly MA, Rees SD, Hydrie MZI, Shera AS, Bellary S, O’Hare JP, Kumar S, Taheri S, Basit A, Barnett AH, , . Circadian Gene Variants and Susceptibility to Type 2 Diabetes: A Pilot Study. PLoS ONE. 2012;7(4):e32670. doi: 10.1371/journal.pone.0032670
  15. Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. Nature Genetics. 2011 Aug 28;43(10):984-9.
  16. Liu N, Enkemann SA, Liang P, Hersmus R, Zanazzi C, Huang J, Wu C, Chen Z, Looijenga LHJ, Keefe DL, Liu L. Genome-wide Gene Expression Profiling Reveals Aberrant MAPK and Wnt Signaling Pathways Associated with Early Parthenogenesis. Journal of Molecular Cell Biology. 2010;2(6):333-344. doi: 10.1093/jmcb/mjq029
  17. Gu B, Wang L, Zhang A, Ma G, Zhao X, Li H, Feng G, He L, Xing Q. Association between a polymorphism of the HTR3A gene and therapeutic response to risperidone treatment in drug-naive Chinese schizophrenia patients. Pharmacogenetics and Genomics. 2008;18(8):721-727. doi: 10.1097/fpc.0b013e32830500e2