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Publications

  1. 1. Ying Liu, Zhihui Niu, Rile Wu, Dezhi Yang, Jun Chen, Guoqing Liu*, Jun Zhao*. Transcriptomic analysis reveals pathways underlying the multi-antibiotic resistance of Klebsiella pneumonia. IET System Biology, 2024, doi: 10.1049/syb2.12112
  2. 2. Guoqing Liu#*, Yan Yang#, Xuejia Kang#, Hao Xu, Jing AI, Min Cao, Guojun Liu*. A pan-cancer analysis of lipid metabolic alterations in primary and metastatic cancers. Sci Rep, 2023, 13: 13810, doi: 10.1038/s41598-023-40858-3
  3. 3. Qiguo Zhang and Guoqing Liu*. SNP-based computational analysis reveals recombination-associated genome evolution in humans. Current Bioinformatics, 2023, 18:192-204, doi: 10.2174/1574893618666221226142329
  4. 4. Guoqing Liu*, Zhi Zhang, Biyu Dong, Jia Liu. DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells. Int J Mol Sci, 2022, 23(22):14488, doi: 10.3390/ijms232214488
  5. 5. Guoqing Liu*, Yu Sun, Lumeng Jia, Ruifeng Li, Yongchun Zuo*. Chromatin accessibility shapes meiotic recombination in mouse primordial germ cells through assisting double-strand breaks and loop formation. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms, 2022, 1865(5):194844, doi: 10.1016/j.bbagrm.2022.194844
  6. 6. Zhao H, Guo M, Zhang F, Shao X, Liu G, Xing Y, Zhao X, Luo L, Cai L. Nucleosome Assembly and Disassembly in vitro Are Governed by Chemical Kinetic Principles. Front Cell Dev Biol, 2021, 9:762571, doi: 10.3389/fcell.2021.762571
  7. 7. Guoqing Liu*, Shuangjian Song, Qiguo Zhang, Biyu Dong, Yu Sun, Guojun Liu, Xiujuan Zhao. Epigenetic marks and variation of sequence-based information along genomic regions are predictive of recombination hot/cold spots in Saccharomyces cerevisiae. Frontiers in Genetics, 2021, 12:705038, doi: 10.3389/fgene.2021.705038
  8. 8. Guoqing Liu*, Hongyu Zhao, Hu Meng, Yongqiang Xing, Lu Cai. A deformation energy model reveals sequence-dependent property of nucleosome positioning. Chromosoma, 2021, 130:27-40, doi: 10.1007/s00412-020-00750-9
  9. 9. Chen Z, Liu G, Liu G, Bolkov MA, Shinwari K, Tuzankina IA, Chereshnev VA, Wang Z. Defining muscle-invasive bladder cancer immunotypes by introducing tumor mutation burden, CD8+ T cells, and molecular subtypes. Hereditas, 2021, 158(1):1
  10. 10. Guoqing Liu*, Guo-Jun Liu, Xiangjun Cui, Ying Xu*. Transcriptomic data analyses reveal a reprogramed lipid metabolism in HCV-derived hepatocellular cancer. Frontiers in Cell and Developmental Biology, 2020, 8: 581863, doi: 10.3389/fcell.2020.581863
  11. 11. Guoqing Liu*, Hongyu Zhao, Hu Meng, Yongqiang Xing, Hui Yang, Hao Lin*. Deform-nu: a DNA deformation energy-based predictor for nucleosome positioning. Front Cell Dev Biol, 2020, 8:596341, doi: 10.3389/fcell.2020.596341
  12. 12. Xing Y, Yang W, Liu G, Cui X, Meng H, Zhao H, Zhao X, Li J, Liu Z, Zhang MQ, Cai L. Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development. Front Bioeng Biotechnol, 2020, 8:35, doi: 10.3389/fbioe.2020.00035
  13. 13. Chen Z, Liu G, Hossain A, Danilova IG, Bolkov MA, Liu G, Tuzankina IA, Tan W. A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival. Hereditas, 2019, 156:24, doi: 10.1186/s41065-019-0100-1
  14. 14. Guoqing Liu*, Guo-Jun Liu, Jiu-Xin Tan, Hao Lin*. DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions. Genomics, 2019, 111:1167-1175, doi: 10.1016/j.ygeno.2018.07.013
  15. 15. Guojun Liu, Zihao Chen, Irina G. Danilova, Mikhail A. Bolkov, Irina A. Tuzankina, Guoqing Liu*. Identification of miR-200c and miR141-mediated lncRNA-mRNA crosstalks in muscle-invasive bladder cancer subtypes. Front Genet, 2018, 9:422, doi: 10.3389/fgene.2018.00422
  16. 16. Hongyu Zhao, Fenghui Zhang, Mingxing Guo, Yongqiang Xing, Guoqing Liu, Xiujuan Zhao, Lu Cai*. The affinity of DNA sequences containing R5Y5 motif and TA repeats with 10.5-bp periodicity to histone octamer in vitro. J Biomol Struct Dyn, 2018, 37(8):1935-1943, doi: 10.1080/07391102.2018.1495578
  17. 17. Guoqing Liu*, Yongqiang Xing, Hongyu Zhao, Lu Cai, Jianying Wang. The implication of DNA bending energy for nucleosome positioning and sliding. Scientific Reports, 2018, 8(1):8853, doi: 10.1038/s41598-018-27188-5
  18. 18. Guoqing Liu*, Qin Ma, Ying Xu*. Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome. Mathematical Biosciences, 2018, 301:50-58, doi: 10.1016/j.mbs.2018.04.004
  19. 19. Hui Yang, Wang-Ren Qiu, Guoqing Liu, Feng-Biao Guo, Wei Chen, Kuo-Chen Chou, Hao Lin. iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC. International Journal of Biological Sciences, 2018, 14:883-891, doi: 10.7150/ijbs.24616
  20. 20. Guoqing Liu*, Xiangjun Cui, Hong Li, Lu Cai. Evolutionary direction of processed pseudogenes. Science China Life Sciences, 2016, 59(8):839–849, doi: 10.1007/s11427-016-5034-5
  21. 21. Guoqing Liu*, Yongqiang Xing, Hongyu Zhao, Jianying Wang, Yu Shang and Lu Cai*. A deformation energy-based model for predicting nucleosome dyads and occupancy. Scientific Reports, 2016, 6:24133, doi: 10.1038/srep24133
  22. 22. Yongqiang Xing, Xiujuan Zhao, Tao Yu, Dong Liang, Jun Li, Guanyun Wei, Guoqing Liu, Xiangjun Cui, Hongyu Zhao, Lu Cai*. MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs. Plos One, 2016, 11(5):e0155443, doi: 10.1371/journal.pone.0155443
  23. 23. Guoqing Liu*, Fen Feng, Xiujuan Zhao, Lu Cai*. Nucleosome organization around pseudogenes in the human genome. BioMed Research International, 2015:821596, doi: 10.1155/2015/821596
  24. 24. Hongyu Zhao, Yongqiang Xing, Guoqing Liu, Ping Chen, Xiujuan Zhao, Guohong Li, Lu Cai*. GAA triplet-repeats cause nucleosome depletion in the human genome. Genomics, 2015, 106(2):88-95, doi: 10.1016/j.ygeno.2015.06.003
  25. 25. Guoqing Liu*, Yongqiang Xing, Lu Cai*. Using weighted features to predict recombination hotspots in Saccharomyces cerevisiae. Journal of Theoretical Biology, 2015, 382:15–22, doi: 10.1016/j.jtbi.2015.06.036
  26. 26. Bingjie Zhang, Guoqing Liu*. Predicting recombination hotspots in yeast based on DNA sequence and chromatin structure. Curr Bioinformatics, 2014, 9(1):28-33
  27. 27. Guoqing Liu, Jia Liu, Bingjie Zhang. Compositional bias is a major determinant of the distribution pattern and abundance of palindromes in Drosophila melanogaster. J Mol Evol, 2012, 72:130-140, doi: 10.1007/s00239-011-9478-8
  28. 28. Jian-Ying Wang, Jingyan Wang, Guoqing Liu*. Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning. Chromosome Research, 2012, 20(7):889-902, doi: 10.1007/s10577-012-9314-z
  29. 29. Guoqing Liu*, Jia Liu, Xiangjun Cui, Lu Cai. Sequence-dependent prediction of recombination hotspots in Saccharomyces cerevisiae. J Theor Biol, 2012, 293:49-54, doi: 10.1016/j.jtbi.2011.10.008
  30. 30. Guoqing Liu*, Hong Li, Lu Cai. Processed pseudogenes are located preferentially in regions of low recombination rates in the human genome. J Evol Biol, 2010, 23(5):1107-1115, doi: 10.1111/j.1420-9101.2010.01975.x
  31. 31. Guoqing Liu, Hong Li*. The correlation between recombination rate and dinucleotide bias in Drosophila melanogaster. Journal of Molecular Evolution, 2008, 67(4):358-367, doi: 10.1007/s00239-008-9156-7
  32. 32. 刘国庆，白音宝力高，邢永强. 假基因研究进展. 生物化学与生物物理进展, 2010，37(11):1165-1174
  33. 33. 刘国庆，罗辽复. 人类基因组信息量的扩增速率受重组的影响. 生物化学与生物物理进展, 2012, 39：368-377
  34. 34. Yongqiang Xing, Guoqing Liu, Xiujuan Zhao, Hongyu Zhao, Lu Cai*. Genome-wide characterization and prediction of Arabidopsis thaliana replication origins. BioSystems, 2014, 124:1–6, doi: 10.1016/j.biosystems.2014.09.009
  35. 35. Hong Li, Guoqing Liu, Xuhua Xia. Correlations between recombination rate and intron distributions along chromosomes of C. elegans. Progress in Natural Science, 2009, 19(4):517-522
  36. 36. Jia Liu, Guo-Qing Liu, Xiao-Hong Du. The effect of impurities in a three-qubit Ising spin Model. International Journal of Theoretical Physics, 2012, 51(4):1509-1517
  37. 37. Xing Yong-qiang, Liu Guo-qing, Zhao Xiu-juan, Cai Lu*. An analysis and prediction of nucleosome positioning based on information content. Chromosome Res, 2013, 21(1):63-74, doi: 10.1007/s10577-012-9339-3
  38. 38. Xiang-Jun Cui, Hong Li, Guo-Qing Liu. Combinatorial patterns of histone modifications in Saccharomyces cerevisiae. Yeast, 2011, 28:683-691
  39. 39. Tonglaga Bao, Hong Li, Xiaoqing Zhao, Guoqing Liu. Predicting nucleosome binding motif set and analyzing their distributions flanking functional sites of human genes. Chromosome Research, 2012, 20:685-698, doi: 10.1007/s10577-012-9302-3

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