Deng-Ke Niu £¨pronounced as ¡°Dengker New¡±£© Homepage in Chinese
Other Name: Deng K. Niu
Researcher ID: http://www.researcherid.com/rid/B-6007-2008
Google Scholar citations: http://scholar.google.com/citations?user=p4HM9ywAAAAJ&hl=en
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.
Basic Life Sciences for undergraduate students, Genomics for graduate students
Graduate students and former graduate students supervised:
2005£ºXiao Liu, Ning Li
2009£ºMing Li, Li Jiang
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
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
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.
"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)
(PDF files of these papers are available upon email request)
Evolution and possible benefits of introns:
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.
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.
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.
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.
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 .
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.
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]
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.
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]
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]
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?
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]
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]
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]
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]
Song L, Niu DK, Lei L, Ou D,
Gevrey M, Liu Y, Hou G and
Lek S (2004). Predictive model of algal blooms in
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¡±.
And several papers in Chinese with English abstracts.
2003---now. Faculty member in
2001---2003. Postdoc in
2000---2001. Postdoc in CESAC, CNRS-University Paul
1999---2001. Postdoc in
Ph.D. in Botany
(Specialization in Evolutionary Biology),
M.Sc in Cell
Biology (Specialization in Plant Somatic Cell Genetics),
Microbiology and Biochemistry,