Laboratory of Computational Molecular Biology

Publications

• 2015-2014

  • Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z.,…,Zhang, Y.C., Lin, K.,…, Huang, S. (2014). Genomic analyses provide insights into the history of tomato breeding. Nature Genetics, 46(11), 1220–1226. doi:10.1038/ng.3117 [Online PDF]
  • Jiang, L., Li, X.N. and Niu, D.K., (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 [Online PDF]
  • Lin, K., Limpens, E., Zhang, Z.H, Ivanov, S., Saunders, DGO., Mu, D.S., Pang, E.L., Cao, H.F., Cha, H.H., Lin, T., Zhou, Q., Shang, Y., Li, Y., Sharma, T., Velzen, R.V., Ruijter, N., Aanen, D.K., Win, J., Kamoun, S., Bisseling, T., Geurts, R., Huang, S.W. (2014) Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus. PLoS Genet 10(1): e1004078. doi:10.1371/journal.pgen.1004078 [Online PDF]

• 2013-2012

  • 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, doi: 10.1093/gbe/evt043. [Online PDF]
  • 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. [Online PDF]
  • 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, doi:10.1186/1741-7007-11-23. [Online PDF]
  • Niu DK and Jiang L (2013). Can ENCODE tell us how much junk DNA we carry in our genome? Biochemical and Biophysical Research Communications, doi:10.1016/j.bbrc.2012.12.074. [Online PDF]
  • Guo, S.G., Zhang, J.G., Sun, H.H.,..., Tan, T., Pang E.L., Lin K.,..., Fei, Z.J. and Xu, Y. (2012) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics, doi:10.1038/ng.2470. [Online PDF]
  • Zhang, Y. and Lin, K. (2012) A phylogenomic analysis of Escherichia coli / Shigella group: implications of genomic features associated with pathogenicity and ecological adaptation. BMC Evolutionary Biology, doi:10.1186/1471-2148-12-174. [Online PDF]
  • Pang, E.L., Tan, T. and Lin, K. (2012) Promiscuous domains: faci litating stability of the yeast protein-protein interaction network. Mol. BioSyst., doi:10.1039/C1MB05364G. [Online PDF]

• 2011-2010

  • Niu, D.K. and Yang, Y.F. (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. [Online PDF]
  • Li, Z., Zhang, Z.H., Yan, P.C., Huang, S.W., Fei, Z.j., and Lin, K. (2011) RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, doi: 10.1186/1471-2164-12-540 [Online PDF]
  • Hou, W.R., Li, M. and Niu, D.K. (2011). Counting citations in texts rather than reference lists to improve the accuracy of assessing scientific contribution. BioEssays 33: 724-727. [Online PDF]
  • Pang, E.L. and Lin, K. (2010) Yeast protein–protein interaction binding sites: prediction from the motif–motif, motif–domain and domain–domain levels. Molecular BioSystems, doi: 10.1039/C0MB00038H. [Online PDF]
  • Niu DK and Cao JL (2010). Nucleosome deposition and DNA methylation may participate in the recognition of premature termination codon in non-sense-mediated mRNA decay. FEBS Letters, 584: 3509-3512. [Online PDF]
  • 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, doi:10.1007/s00239-010-9391-6. [Online PDF]

• 2009-2008

  • Fu, C., Li, J. and Wang, E. (2009) Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression. Molecular BioSystems, 5: 1809-1816. [Online PDF]
  • Huang, S.W., Li, R.Q., Zhang, Z.H., Li, L., Gu, X.F., Fan, W., Lucas, W.J., Wang, X.W., Xie, B.Y., Ni, P.X., Ren, Y.Y., Zhu, H.M., Li, J., Lin, K., Jin, W.W., Fei, Z.J., Li, G.C., Stabu, J., Kilian, A., Vossen, E.A., Wu, Y., Guo, J., He, J., Jia, Z.Q., Ren, Y., Tian, G., Lu, Y., Ruan, J., Qian, W.B., Wang, M.W., Huang, Q.F., Li, B., Xuan, Z.L., Cao, J.J., Asan, Wu, Z.G., Zhang, J.B., Cai, Q.L., Bai, Y.Q., Zhao, B.W., Han, Y.H., Li, Y., Li, X.F., Wang, S.H., Shi, Q.X., Liu, S.Q., Cho, W.K., Kim, J.Y., Xu, Y., Uszynska, K.H., Miao, H., Cheng, Z.C., Zhang, S.P., Wu, J., Yang, Y.H., Kang, H.X., Li, M., Liang, H.Q., Ren, X.L., Shi, Z.B., Wen, M., Jian, M., Yang, H.L., Zhang, G.J., Yang, Z.T., Chen, R., Liu, S.F., Li, J.W., Ma, L.J., Liu, H., Zhou, Y., Zhao, J., Fang, X.D., Li, G.Q., Fang, L., Li, Y.R., Liu, D.Y., Zheng, H.K., Zhang, Y., Qin, N., Li, Z., Yang, G.H., Yang, S., Bolund, L., Kristiansen, K., Zheng, H.C., Li, S.C., Zhang, X.Q., Yang, H.M., Wang, J., Sun, R.F., Zhang, B.X., Jiang, S.Z., Wang, J., Du, Y.C. and Li, S.G. (2009) The genome of the cucumber, Cucumis sativus L. Nature Genetics, 41:1275-1281. [Online PDF]
  • Wu, X.M., Guo, J., Zhang, D.Y. and Lin, K. (2009) The properties of hub proteins in a yeast-aggregated cell cycle network and its phase sub-networks. Proteomics, 9:4812-4824. [Online PDF]
  • Fu, C. and Lin, K. (2009) Computational Analysis of miRNA and Target mRNA Interactions: Combined Effects of The Quantity and Quality of Their Binding Sites. Progress in Biochemistry and Biophysics, 36(5):608-615. [Online PDF]
  • Li, N., Lv, J. and Niu, D.K. (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. [Online PDF]
  • Lin, K., Zhang, D.Y. and He, F. (2009) Demographic trade-offs in a neutral model explains death rate-abundance rank relationship. Ecology, 90(1):31-38. [Online PDF]
  • Niu, D.K. (2008) Exon definition as a potential negative force against intron losses in evolution. Biology Direct, 3:46. [Online PDF]
  • Lv, J., Li, N. and Niu, D.K. (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. [Online PDF]
  • Huang, Y.F. and Niu, D.K. (2008) Evidence against the energetic cost hypothesis for the short introns in highly expressed genes. BMC Evolutionary Biology, 8:154. [Online PDF]
  • Zhou, H.J. and Lin, K. (2008) Excess of microRNAs in large and very 5' biased introns. Biochemical and Biophysical Research Communications, 368:709-715. [Online PDF]
  • Guo, J., Wu, X.M., Zhang, D.Y. and Lin, K. (2008) Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset. Nucleic Acids Research, 36(6):2002-2011. [Online PDF]

• 2007-2006

  • Luo, Y.Q., Fu, C., Zhang, D.Y. and Lin, K. (2007) BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes. BMC Bioinformatics, 8:266. [Online PDF]
  • Li, S.W., Feng, L. and Niu, D.K. (2007) Selection for the miniaturization of highly expressed genes. Biochemical and Biophysical Research Communications, 360:586-592. [Online PDF]
  • Wang, H.F., Hou, W.R. and Niu, D.K. (2007) Strand compositional asymmetries in vertebrate large genes. Molecular Biology Reports, 35:163-169. [Online PDF]
  • Niu, D.K. (2007) Protecting exons from deleterious R-loops: a potential advantage of having introns. Biology Direct, 2:11. [Online PDF]
  • Feng, L. and Niu, D.K. (2007) Relationship between mRNA stability and length: An old question with a new twist. Biochemical Genetics, 45:131-137. [Online PDF]
  • Wang, H.F., Feng, L. and Niu, D.K. (2007) Relationship between mRNA stability and intron presence. Biochemical and Biophysical Research Communications, 354:203-208. [Online PDF]
  • Wu, X.M., Zhu, L., Guo, J., Fu, C., Zhou, H.J., Dong, D., Li, Z.B., Zhang, D.Y. and Lin, K. (2006) SPIDer: Saccharomyces protein-protein interaction database. BMC Bioinformatics, 7:S16. [Online PDF]
  • Luo, Y.Q., Fu, C., Zhang, D.Y. and Lin, K. (2006) Overlapping genes as rare genomic markers: the γ-Proteobacteria phylogeny as a case study. Trends in Genetics, 22(11):593-596. [Online PDF]
  • Lin, K., Zhu, L. and Zhang, D.Y. (2006) An initial strategy for comparing proteins at the domain architecture level. Bioinformatics, 22(17):2081-2086. [Online PDF]
  • Wu, X.M., Zhu, L., Guo, J., Zhang,D.Y. and Lin, K. (2006) Prediction of yeast protein–protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Research, 34(7):2137-2150. [Online PDF]
  • He, Y.W., Xu, M., Lin, K., Ng, Y.J., Wen, C.M., Wang, L.H., Liu, Z.D., Zhang, H.B., Dong, Y.H., Dow, J.M. and Zhang, L.H. (2006) Genome scale analysis of diffusible signal factor regulon in Xanthomonas campestris pv. campestris: identification of novel cell-cell communication-dependent genes and functions. Molecular Microbiology, 59(2):610-22. [Online PDF]
  • Hou, W.R., Wang, H.F. and Niu, D.K. (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. [Online PDF]

• 2005 and before

  • Sun, Q.L., Zhou, H.J., Lin, K. (2005) The Evolutionary Relationship of the Domain Architectures in the RhoGEF-containing Proteins. Genomics, Proteomics & Bioinformatics, 3:94-106.
  • Lin, K. and Zhang, D.Y. (2005) The excess of 5' introns in eukaryotic genomes. Nucleic Acids Research, 33:6522-6527. [Online PDF]
  • Niu, D.K. (2005) Low-level illegitimate transcription of genes may be to silence the genes. Biochemical and Biophysical Research Communications, 337:413-414. [Online PDF]
  • Niu, D.K., Hou, W.R. and Li, S.W. (2005) mRNA-mediated intron losses: Evidence from extraordinarily large exons. Molecular Biology and Evolution, 22:1475-1481. [Online PDF]
  • Peng, X., Karuturi, R.K.M., Miller, L.D., Lin, K., Jia, Y.H., Kondu, P., Wang, L., Wong, L.S., Liu, E.T., Balasubramanian, M.K. and Liu, J.H. (2005) Identification of Cell Cycle-regulated Genes in Fission Yeast. Molecular Biology Cell, 16:1026-1042. [Online PDF]
  • Zhang, D.Y., Lin, K. and Hanski, I. (2004) Coexistence of cryptic species. Ecology Letters, 7:165-169. [Online PDF]
  • Song, L., Niu, D.K., 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.
  • Niu, D.K., Lin, K. and Zhang, D.Y. (2003) Strand compositional asymmetries of nuclear DNA in eukaryotes. Journal of Molecular Evolution, 57:325-334. [Online PDF]