Deng-Ke Niu £¨pronounced as ¡°Dengker New¡±£©                           Homepage in Chinese

Other Name: Deng K. Niu

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Present address: College of Life Sciences, Beijing Normal University, Beijing, 100875, P. R. China

E-mail: dkniu@bnu.edu.cn, dengkeniu@hotmail.com

Tel: 86-10-58802064

Fax: 86-10-58807721

Researcher ID: http://www.researcherid.com/rid/B-6007-2008

Google Scholar citations: http://scholar.google.com/citations?user=p4HM9ywAAAAJ&hl=en

ORCID: http://orcid.org/0000-0003-4503-2658

 

Researches

I am interested in all mysteries of modern biology, especially evolutionary biology. Limited by time and knowledge, my students and I now study

1) the origin and evolution of introns;

2) the evolution of genome size;

3) the evolution of organelle genome and the transfer of their sequence to nucleus genomes.

 

"Discovery consists of seeing what everybody has seen and thinking what nobody has thought (by Albert von Szent-Gyorgyi)."

 

Here is one sentence to describe my work: ¡°Predict differences or correlations from biological knowledge, and then test their existence by bioinformatic methods¡±. Sometime, I will write theoretical or hypothetical papers if the ideas cannot be tested in my laboratory.

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Teaching

Basic Life Sciences for undergraduate students, Genomics for graduate students

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Graduate students and former graduate students supervised:

2003£ºWen-Ru Hou

2004£ºShu-Wei Li, Hai-Fang Wang, Liang Feng, Shan-Shan Chang

2005£ºXiao Liu, Ning Li

2006£ºYi-Fei Huang, Jie Lv, Bing-Jun Zhang, Lei-Ying Zhang

2007£ºNing Li (PhD candidate), Wen-Ping Guo, Jin-Hua Liu

2008£ºLei-Ying Zhang (PhD candidate), Jian-Li Cao, Yu-Fei Yang, Hong-Sheng Du

2009£ºMing Li, Li Jiang

2010£ºYu-Fei Yang (PhD candidate), Tao Zhu, Xue-Nan Li

2011£ºLi Jiang (PhD candidate), Shuai Tang, Ming-Yue Ma

2012£ºTao Zhu (PhD candidate), Heng-Yuan Liu, Wen-Hui Duan

2013£ºMing-Yue Ma (PhD candidate), Hao-Yuan Yu, Ting Zhou

2014£ºXi-Xi Li (PhD candidate)

2015£ºHong-Bin Chen (PhD candidate), Sidra Aslam (PhD candidate), Xin-Ran Lan

2016£ºZhi-Hua Ni (PhD candidate),  Jun-Peng Zhao

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Visiting Scholars

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2014-2015: Hong Xia, from School of Biomedical Engineering, Capital Medical University

2015-2016: Zhi-Hua Ni, from College of Life Sciences, Hebei Normal University

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Service

Member of the Editorial Board of Genomics, Proteomics & Bioinformatics (2012-).

Reviewing manuscripts for the following journals: Microbiology and Molecular Biology Reviews, Trends in Genetics, PLoS Genetics, Nucleic Acids Research, Molecular Biology and Evolution, Plant Journal, Bioinformatics, BMC Evolutionary Biology, BMC Genomics, Journal of Molecular Evolution, Molecular Genetics and Genomics, Genetica, Scientific Reports, PLoS ONE, Marine Genomics, Frontiers in Plant Science, Frontiers in Genetics, Hereditas, Current Genomics, Journal of Integrative Plant Biology, Cellular & Molecular Biology Letters, Genomics, Proteomics & Bioinformatics, Chinese Science Bulletin, Progress in Biochemistry and Biophysics, Acta Microbiologica Sinica, etc. Here is a summary of the number of manuscripts I have reviewed.

Reviewing grant application forms for several institutions: National Science Foundation of China, National Science Foundation (USA), Austrian Science Fund (FWF, Stand-alone Project)¡¢Ministry of Science, Culture and Sport (Bi-national Israeli-French research program).

Reviewing PhD and master theses for some Chinese universities.

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"The ultimate goal of scholarly scientific publishing (is) to advance our understanding of the natural world." (Alberts B et al. Reviewing peer review. Science 321: 15, 2008)

Publications (PDF files of these papers are available upon email request)  

Evolution and possible benefits of introns:

  1. Ma MY, Lan XR, Niu DK (2016). Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ 4: e2272  https://doi.org/10.7717/peerj.2272.

  2. Ma MY, Che XR, Porceddu A and Niu DK (2015). Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium. BMC Evolutionary Biology 15: 286 http://dx.doi.org/10.1186/s12862-015-0567-y.

  3. Ma MY, Zhu T, Li XN, Lan XR, Liu HY, Yang YF and Niu DK (2015). Imprecise intron losses are less frequent than precise intron losses but are not rare in plants. Biology Direct 10: 24. http://dx.doi.org/10.1186/s13062-015-0056-7.

  4. Jiang L, Li XN and Niu DK (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. http://dx.doi.org/10.4161/fly.29489.

  5. Yang YF, Zhu T and Niu DK (2013). Association of intron loss with high mutation rate in Arabidopsis: Implications for genome size evolution. Genome Biology and Evolution 5: 723-733. doi:10.1093/gbe/evt043. This article is recommended by F1000 Victor Norris and John Herrick 2013 Access the recommendation on F1000Prime.

  6. Zhu T and Niu DK (2013). Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces. PLoS ONE doi:10.1371/journal.pone.0061683.

  7. Zhu T and Niu DK (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. [Abstract/Free Full Text]

  8. Niu DK and Jiang L (2013). Can ENCODE tell us how much junk DNA we carry in our genome? Biochemical and Biophysical Research Communications 430: 1340-1343. doi:10.1016/j.bbrc.2012.12.074.

  9. Niu DK and Yang YF (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 [Abstract/Free Full Text]

  10. Zhang LY, Yang YF and Niu DK (2010). Evaluation of models of the mechanisms underlying intron loss and gain in Aspergillus fungi. Journal of Molecular Evolution 71: 364-373. [Abstract]

  11. Niu DK (2008). Exon definition as a potential negative force against intron losses in evolution. Biology Direct 3: 46 doi:10.1186/1745-6150-3-46. [Abstract/Free Full Text][ISI]

  12. Huang YF and Niu DK (2008). Evidence against the energetic cost hypothesis for the short introns in highly expressed genes. BMC Evolutionary Biology 8: 154. [Abstract/Free Full Text][ISI]

  13.  Li SW, Feng L and Niu DK (2007). Selection for the miniaturization of highly expressed genes. Biochemical and Biophysical Research Communications 360: 586-592. [Abstract][ISI]

  14. Niu DK (2007). Protecting exons from deleterious R-loops: a potential advantage of having introns. Biology Direct 2: 11. [Medline] [Abstract/Free Full Text][ISI]

  15. Wang HF, Feng L and Niu DK (2007). Relationship between mRNA stability and intron presence. Biochemical and Biophysical Research Communications 354: 203-208.[Medline][ISI]

  16. Niu DK, Hou WR and Li SW (2005). mRNA-mediated intron losses: Evidence from extraordinarily large exons. Molecular Biology and Evolution 22: 1475-1481. [Abstract/Free Full Text][ISI]

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Other subjects:

  1. Hou WR, Li M and Niu DK (2011). Counting citations in texts rather than reference lists to improve the accuracy of assessing scientific contribution. BioEssays 33: 724-727. [Abstract] This paper has been highlighted by BioEssays: Making a deeper impact: How to measure your actual scientific footprint?  

  2. Niu DK and Cao JL (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. [Abstract]

  3. Li N, Lv J and Niu DK (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. [Medline][ISI]

  4. Lv J, Li N and Niu DK (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. [Medline][ISI]

  5. Wang HF, Hou WR and Niu DK (2008). Strand compositional asymmetries in vertebrate large genes. Molecular Biology Reports  35: 163-169. [Medline][ISI]

  6. Feng L and Niu DK (2007). Relationship between mRNA stability and length: An old question with a new twist, Biochemical Genetics 45: 131-137.[Medline][ISI]

  7. Hou WR, Wang HF and Niu DK (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. [Medline][ISI]

  8. Niu DK (2005). Low-level illegitimate transcription of genes may be to silence the genes. Biochemical and Biophysical Research Communications 337: 413-414. [Medline][ISI]

  9. 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.

  10. Niu DK, Lin K and Zhang DY (2003). Strand compositional asymmetries of nuclear DNA in eukaryotes. Journal of Molecular Evolution 57: 325-334. [Medline][ISI]

  11. Niu, D. K., Chen, J.-K. and Liu, Y.¨CD. (2001). Margulis' theory on division of labour in cells revisited. Acta Biotheoretica 49: 23-28. [Medline][ISI]

  12. Niu, D. K. and Chen, J.-K. (1998/1999). Origin of cancerous cells from tumour. Acta Biotheoretica 46: 379-381. [Medline][ISI]

  13. Niu, D. K. and Chen, J.-K. (1997). Evolutionary advantages of cell specialization: Save and protect DNA. Journal of Theoretical Biology 187: 39-43. [Medline][ISI]

  14. Niu, D. K., Wang, M. G. and Wang, Y. F. (1997). Plant cellular osmotica. Acta Biotheoretica 45: 161-169.[Abstract][ISI]

  15. Niu, D. K. and Wang Y. F. (1995). Why animals have tumours. Acta Biotheoretica 43: 279-280. [Medline] [ISI]Now, the first author does not hold such idea. He is now searching for other possible answers for ¡°why animals have tumours¡±.

  16. And several papers in Chinese with English abstracts.

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Working Experience

¡¤       2003---now.  Faculty member in College of Life Sciences, Beijing Normal University, Beijing, China

¡¤       2001---2003. Postdoc in College of Life Sciences, Beijing Normal University, Beijing, China

¡¤       2000---2001. Postdoc in CESAC, CNRS-University Paul Sabatier, Toulouse III, France

¡¤       1999---2001. Postdoc in Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, China

 

Education

¡¤       Ph.D. in Botany (Specialization in Evolutionary Biology), Wuhan University, China

¡¤       M.Sc  in Cell Biology (Specialization in Plant Somatic Cell Genetics), Lanzhou University, China

¡¤       B.Sc  in Microbiology and Biochemistry, Heibei University, China

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