牛登科 - 北京师范大学 - 生命科学学院

个人简介

2008年7月至今，北京师范大学生命科学学院，教授 2003年8月至2008年6月，北京师范大学生命科学学院，副教授 2001年11月至2003年8月，北京师范大学生命科学学院生态研究所，博士后研究 2000年9月至2001年8月，法国图卢兹第三大学CESAC实验室，博士后 1999年7月至2001年11月，中国科学院水生生物研究所，博士后研究 1996年9月至1999年7月，武汉大学生命科学学院植物学专业，博士 1993年9月至1996年7月，兰州大学生物学系细胞生物学专业，硕士 1989年9月至1993年7月，河北大学生物学系微生物及生化专业，学士讲授课程 “生命科学概论”全校本科生公共选修课 “基因组学”生命科学学院研究生课程主持科研项目国家自然科学基金面上项目，从受体的角度研究细胞器基因向细胞核基因组转移的机制，60万元，2017年1月至2020年12月，项目批准号：31671321 北京师范大学自主科研基金项目，真核生物编码蛋白质基因内部结构进化，35万元，2014年9月至2017年8月，项目编号：2014KJJCB18 国家自然科学基金面上项目，基因组大小与内含子进化的比较研究，80万元，2014年1月至2017年12月，项目批准号：31371283 国家自然科学基金面上项目，近缘物种间和物种内内含子数目变异的进化机制，35万元，2011年1月至2013年12月，项目批准号：31071112 教育部“新世纪优秀人才支持计划”，50万元，2008年1月至2010年12月国家自然科学基金面上项目，多细胞生物起源及其与癌发生的比较研究，18万元，2003年1月至2005年12月，项目批准号：30270695

研究领域

微生物基因组进化，包括探究影响原核生物的CRISPR-Cas等防御系统进化的生理、生态和遗传因素。氧气、干旱等生境条件对基因组进化的影响，包括自由基对遗传物质的损伤、GC含量、密码子偏好、基因组大小等。内含子和基因组大小进化，包括内含子存在的代价和带来的好处、进化历史上基因丢失和获得内含子的机理，基因组大小的主要贡献组分（内含子和基因间隔序列、转座子、假基因等）存在的利弊，或是既无利也无弊；基因组大小是否与细胞大小、生长发育速度、代谢速率、个体大小等表型特征存在相关性，如果存在，背后的生物学机理是什么？即基因组大小怎样影响这些表型。

近期论文

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Hu EZ, Lan XR, Liu ZL, Gao J, Niu DK. A positive correlation between GC content and growth temperature in prokaryotes. BMC Genomics 2022; 23, 110. Lan XR, Liu ZL, Niu DK. Precipitous increase of bacterial CRISPR-Cas abundance at around 45°C. Frontiers in Microbiology 2022; 13: 773114. Ma MY, Xia J, Shu KX, Niu DK. Intron losses and gains in the nematodes. Biol Direct 2022; 17: 13. Li X, Fang C, Zhao JP, Zhou XY, Ni Z, Niu DK (2020). Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer. BMC Genomics 21: 452 [全文].https://doi.org/10.1186/s12864-020-06865-8. Ni Z, Zhou XY, Aslam S, Niu DK (2019). Characterization of human dosage-sensitive transcription factor genes. Frontiers in Genetetics 10: 1208. [全文]. https://doi.org/10.3389/fgene.2019.01208. Aslam S, Lan XR, Zhang BW, Chen ZL, Wang L, Niu DK (January 2019). Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have. BMC Evolutionary Biology 19: 35 [全文].https://doi.org/10.1186/s12862-019-1365-8. Chen H, Wang Q, Yin Y, Li S, Niu DK, Wang H (April 2018). Genotypic variations between wild-type and small colony variant of Staphylococcus aureus in prosthetic valve infectious endocarditis: a comparative genomic and transcriptomic analysis. International Journal of Antimicrobial Agents 51: 655-658 [全文].https://doi.org/10.1016/j.ijantimicag.2017.12.006. Ma MY, Lan XR, Niu DK (July 2016). Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ 4: e2272 [全文].https://doi.org/10.7717/peerj.2272. Ma MY, Che XR, Porceddu A and Niu DK (December 2015). Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium. BMC Evolutionary Biology 15: 286 [全文] http://dx.doi.org/10.1186/s12862-015-0567-y. Ma MY, Zhu T, Li XN, Lan XR, Liu HY, Yang YF and Niu DK (May 2015). Imprecise intron losses are less frequent than precise intron losses but are not rare in plants. Biology Direct 10: 24. [全文] http://dx.doi.org/10.1186/s13062-015-0056-7. Jiang L, Li XN and Niu DK (June 2014). Higher frequency of intron loss from the promoter proximally paused genes of Drosophila melanogaster: Evidence consistent with delays in intron splicing as a selective force. Fly 8: 120-125 [全文] http://dx.doi.org/10.4161/fly.29489. Yang YF, Zhu T and Niu DK (April 2013). Association of intron loss with high mutation rate in Arabidopsis: Implications for genome size evolution. Genome Biology and Evolution 5: 723-733 [全文] doi: 10.1093/gbe/evt043.(研究论文) 本文得到F1000专家Victor Norris和John Herrick推荐为“Very Good”，. Zhu T and Niu DK (April 2013). Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces. PLOS ONE 8: e61683.[全文] doi:10.1371/journal.pone.0061683. (研究论文) Zhu T and Niu DK (March 2013). Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss. BMC Biology 11: 23. [全文]doi:10.1186/1741-7007-11-23 (研究论文) Niu DK and Jiang L (January 2013). Can ENCODE tell us how much junk DNA we carry in our genome? Biochemical and Biophysical Research Communications 430: 1340-1343.[全文](观点评论) Niu DK and Yang YF (May 2011). Why eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity. Biology Direct 6: 24 doi:10.1186/1745-6150-6-24. [全文](观点假说) Hou WR, Li M and Niu DK (October 2011). Counting citations in texts rather than reference lists to improve the accuracy of assessing scientific contribution. BioEssays 33: 724-727. [全文](研究论文)此文被BioEssays专门Highlight了一下：Making a deeper impact: How to measure your actual scientific footprint? 国际同行的后续研究，"By asking authors to identify the key references in their own work, we created a data set in which citations were labeled according to their academic influence. Using automatic feature selection with supervised machine learning, we found a model for predicting academic influence that achieves good performance on this data set using only four features. The best features, among those we evaluated, were those based on the number of times a reference is mentioned in the body of a citing paper....One of our main results is that counting the number of times a paper is cited (countsInPaper_whole) is one of the best predictors of how influential a reference is. This confirms an earlier result by Hou et?al. (2011, p. 726) who stated,... " Zhang LY, Yang YF and Niu DK (December 2010). Evaluation of models of the mechanisms underlying intron loss and gain in Aspergillus fungi. Journal of Molecular Evolution 71:364-373. [全文](研究论文) Niu DK and Cao JL (August 2010). Nucleosome deposition and DNA methylation may participate in the recognition of premature termination codon in nonsense-mediated mRNA decay. FEBS Letters 584: 3509-3512.[全文](观点假说) Li N, Lv J and Niu DK (March 2009). Low contents of carbon and nitrogen in highly abundant proteins: Evidence of selection for the economy of atomic composition. Journal of Molecular Evolution 68: 248-255. [全文] (研究论文) Niu DK (November 2008). Exon definition as a potential negative force against intron losses in evolution. Biology Direct 3: 46 doi:10.1186/1745-6150-3-46. [全文] (观点假说) Lv J, Li N and Niu DK (October 2008). Association between the availability of environmental resources and the atomic composition of organismal proteomes: Evidence from Prochlorococcus strains living at different depths. Biochemical and Biophysical Research Communications 375: 241-246. [全文] (研究论文) Wang HF, Hou WR and Niu DK (June 2008). Strand compositional asymmetries in vertebrate large genes. Molecular Biology Reports 35: 163-169. [全文] (研究论文) Huang YF and Niu DK (May 2008). Evidence against the energetic cost hypothesis for the short introns in highly expressed genes. BMC Evolutionary Biology 8: 154. [全文] (研究论文) Li SW, Feng L and Niu DK (August 2007). Selection for the miniaturization of highly expressed genes. Biochemical and Biophysical Research Communications 360: 586-592. [全文] (研究论文) 我们在这篇文章上倾注了大量心血，对研究结果也很满意。但此文投稿过程颇为曲折，历经多种期刊、无数次修改，见识了形形色色的审稿意见，当然从中我们也学到了很多。 Niu DK (April 2007). Protecting exons from deleterious R-loops: a potential advantage of having introns. Biology Direct 2: 11. [全文] (观点假说) Feng L and Niu DK (February 2007). Relationship between mRNA stability and length: An old question with a new twist. Biochemical Genetics 45: 131-137. [全文] (研究论文) Wang HF, Feng L and Niu DK (March 2007). Relationship between mRNA stability and intron presence. Biochemical and Biophysical Research Communications 354: 203-208. [全文]. (研究论文) 很高兴，最近J. Biol. Chem.上发表的一篇实验论文证实了我们计算的结果，“The half-life of KC mRNA was markedly prolonged when the primary transcript was obtained from a genomic clone containing three introns as compared with the half-life observed with sequence-identical KC mRNA derived from an intron-free cDNA construct….“ Hou WR, Wang HF and Niu DK (June 2006). Replication-associated strand asymmetries in vertebrate genomes and implications for replicon size, DNA replication origin and termination. Biochemical and Biophysical Research Communications 344: 1258-1262. [全文] (研究论文) Niu DK (November 2005). Low-level illegitimate transcription of genes may be to silence the genes. Biochemical and Biophysical Research Communications 337: 413-414. [全文] (观点假说) Niu DK, Hou WR and Li SW (June 2005). mRNA-mediated intron losses: Evidence from extraordinarily large exons. Molecular Biology and Evolution 22: 1475-1481. [全文] (研究论文) Song L, Niu DK, Lei L, Ou D, Gevrey M, Liu Y, Hou G and Lek S (2004). Predictive model of algal blooms in Dianchi Lake using artificial neural networks. The Japanese Journal of Phycology 52: S41-S47. (研究论文) Niu DK, Lin K and Zhang DY (September 2003). Strand compositional asymmetries of nuclear DNA in eukaryotes. Journal of Molecular Evolution 57: 325-334. [全文] (研究论文) Niu DK, Chen JK and Liu YD (March 2001). Margulis' theory on division of labor in cells revisited. Acta Biotheoretica 49: 23-28. [全文] (研究论文) Niu DK and Chen JK (1998). Origin of cancerous cells from tumour. Acta Biotheoretica 46: 379-381. [全文] (观点假说) Niu DK and Chen JK ( July 1997). Evolutionary advantages of cell specialization: Save and protect DNA. Journal of Theoretical Biology 187: 39-43. [全文] (观点假说) Niu DK, Wang MG and Wang YF (June 1997). Plant cellular osmotica. Acta Biotheoretica 45: 161-169. [全文] (观点假说) Niu DK and Wang YF (September 1995). Why animals have tumours. Acta Biotheoretica 43: 279-280. [全文] (观点假说) 第一作者现在自己认为此文中关于肿瘤的假说正确的可能性微乎其微，请读者慎重引用。倪建福，周文麟，牛登科等. (1995). 长穗偃麦草DNA导入小麦后代变异系醇溶蛋白的研究。西北植物学报 15(5): 21-24。(研究论文) 王鸣刚，牛登科等. (1995). 小麦耐盐变异体的筛选。II. 小麦耐盐细胞系的筛选及生理生化特性的分析。西北植物学报 15(5): 15-20。(研究论文) 高清祥，王鸣刚，牛登科等. (1995). 离体筛选小麦变异系的研究。西北植物学报 15(8): 144-152。 (研究论文) 裴新梧，倪建福，仲乃琴，牛登科. (1995). 用改良缺体回交选育小麦──黑麦异代换系。甘肃农业科技 1995(5): 3-4。(研究论文)