Laboratory of Computational Molecular Biology

Publications

• 2017-2016

  • Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin(2017). Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family BMC Bioinformatics, 2017 , 18 (1) :439 [Online Text]
  • Liu, X., Liu, Y., Peng, H., Ma, Y., Qing, Z., & Qi, T., et al.(2017). The genome of medicinal plant macleaya cordata, provides new insights into benzylisoquinoline alkaloids metabolism. Molecular Plant10(7), 975. [Online Text]
  • Pang, E., Hao, Y., Sun, Y., & Lin, K.(2016). Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. Bmc Evolutionary Biology16(1), 260. [Online Text]
  • Cao, H., Pang, E., & Lin, K.(2016). Hierarchical Map of Orthologous Genomic Regions Reconstructed from Two Closely Related Genomes: Cucumber Case Study. The Plant Genome, 9(3). [Online Text]
  • Pang, E., Wu, X., & Lin, K. (2016). Different evolutionary patterns of snps between domains and unassigned regions in human protein-coding sequences. Molecular Genetics & Genomics, 1-10. [Online Text]

• 2015-2014

  • Zhang Y C, Lin K.(2015). Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions[J]. Evolutionary Bioinformatics , 2015, 11(Suppl 2): 1. [Online Text]
  • Zhang Y C, Zhang Y, Zhu B R, et al. Genome sequences of two closely related strains of Escherichia coli K-12 GM4792[J]. Standards in Genomic Sciences , 2015, 10(1): 1-9. [Online Text]
  • Ma MY, Che XR, Porceddu A, Niu DK (December 2015). Evaluation of the mechanisms of intron loss and gain in the social amoebae Dictyostelium. BMC Evolutionary Biology . 115: 286. [Online Text]
  • Pang E, Cao H, Zhang B, Lin, K. Crop Genome Annotation: A Case Study for the Brassica rapa Genome[M]//The Brassica rapa Genome. Springer Berlin Heidelberg, 2015: 53-64. [Online Text]
  • Ma MY, Zhu T, Li XN, Lan XR, Liu HY, Yang YF, Niu DK (May 2015). Imprecise intron losses are less frequent than precise intron losses but are not rare in plants. Biology Direct. 10: 24. [Online Text]s
  • 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]