Plant genome annotation and evolutionary analysis of closely related plant genomes.
Genome-wide reconstruction and analysis of protein-protein interaction networks.
Phylogenomic analysis of completely sequenced microbial genomes, in particular for the bacterial genomes.
Book Chapters:
Lin K, Liu JH, Miller L, and Wong L.
Genome-wide cDNA Oligo Probe Design and its Application in Schizosaccharomyces Pombe.
The Practical Bioinformatician, edited by Limsoon Wong. Chapter 15, pp347--358. World Scientific, New Jersey, May 2004.
Kolatkar P and Lin K.
Construction of Biological Databases: A Case Study on the Protein Phosphatase Database (PPDB).
The Practical Bioinformatician, edited by Limsoon Wong. Chapter 18, pp401--416. World Scientific, New Jersey, May 2004.
Kolatkar P and Lin K.
PPiDB - A Protein-Protein Interactions Database.
CONFORMATIONAL PROTEOMICS of Macromolecular Architecture edited by R Holland Cheng & Lena Hammar (Karolinska Institutet, Sweden). Chapter 19, pp391--402. World Scientific, Singapore, June 2004.
Published Papers:
Bowen Zhang, Linlin Xu, Nan Li, Pengcheng Yan, Xinhua Jiang, Keith E Woeste Lin Kui, Susanne S Renner, Dayong Zhang, Weining Bai(2019).
Phylogenomics reveals an ancient hybrid origin of the Persian walnut.
Molecular biology and evolution, 2019, 4
[Online Text]
Yu-Ting Lai, Carol K. L. Yeung, Kevin E. Omland, Er-Li Pang, Yu Hao, Ben-Yang Liao, Hui-Fen Cao, Bo-Wen Zhang, Chia-Fen Yeh, Chih-Ming Hung, Hsin-Yi Hung, Ming-Yu Yang, Wei Liang, Yu-Cheng Hsu, Cheng-Te Yao, Lu Dongd, Lin Kui, Shou-Hsien L(2019).
Standing genetic variation as the predominant source for adaptation of a songbird.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019, 116(6) :2152-2157.
[Online Text]
Xiao-Lin Chu, Bo-Wen Zhang, Quan-Guo Zhang, Bi-Ru Zhu, Lin Kui, Da-Yong Zhang(2018).
Temperature responses of mutation rate and mutational spectrum in an Escherichia coli strain and the correlation with metabolic rate.
BMC EVOLUTIONARY BIOLOGY, 2018, 18 :126.
[Online Text]
Song Hongtao, Lin Kui, Hu Jinglu, Pang Erli(2018).
An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome.
Frontiers in Plant Science, 2018, 9 :325.
[Online Text]
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]
Dong, D., Lei, M., Hua, P., Pan, Y. H., Mu, S., & Zheng, G., et al. (2016).
The genomes of two bat species with long constant frequency echolocation calls.
Molecular Biology & Evolution, 34(1), 20.
[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, 291(3), 1127.
[Online Text]
APAPang, 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]
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]
Liu, T., Lin, K.(2015).
The distribution pattern of genetic variation in the transcript isoforms of the alternatively spliced protein-coding genes in the human genome. Mol Biosystems. 11(5):1378–1388.
[Online Text]
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]
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]
Luo, Y.Q., Battistuzzi, F., Lin, K. (2013)
Evolutionary Dynamics of Overlapped Genes in Salmonella.
PLOS ONE, doi:10.1371/journal.pone.0081016
[Online PDF]
Dong, W.P., Xu, C., Cheng, T., Lin, K. and Zhou, S.L. (2013)
Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales.
Genome Biology and Evolution, doi:10.1093/gbe/evt063.
[Online PDF]
Wu, X.M., Pang, E.L., Lin, K. and Pei, Z.M. (2013)
Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method.
PLOS ONE, doi:10.1371/journal.pone.0066745.
[Online PDF]
He, F.L., Zhang, D.Y., Lin, K. (2012)
Coexistence of nearly neutral species.
JOURNAL OF PLANT ECOLOGY, doi:10.1093/jpe/rtr040.
[Online PDF]
Zhang, D.Y., Zhang, B.Y., Lin, K.,..., O.A. (2012)
Demographic trade-offs determine species abundance and diversity.
JOURNAL OF PLANT ECOLOGY, doi: 10.1093/jpe/rtr039.
[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: facilitating stability of the yeast protein-protein interaction network.
Mol. BioSyst., doi:10.1039/C1MB05364G.
[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]
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]
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., ...
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]
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]
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]
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]
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]
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]
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]
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]
Ng, S.K., Zhang, Z., Tan, S.H. and Lin, K. (2003)
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes.
Nucleic Acids Research, 31(1):251-254.
[Online PDF]
Lin, K., Kuang, Y.Y., Joseph, J.S. and Kolatkar, P.R. (2002)
Conserved codon usage composition of ribosomal protein-coding genes in Escherichia coli, Mycobaterium tuberculosis and
Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics.
Nucleic Acids Research, 30(11):2599-2607.
[Online PDF]
Epstein, R.J., Lin, K. and Tan, T.W. (2000)
A functional significance for codon third bases.
Gene, 245(2):291-298.
[Online PDF]
Kangueane, P., Sakharkar, M.K., Lim, K.S., Han H., Lin K., Chee, R.E. and Kolatkar, P.R. (2000)
Knowledge based grouping of modeled HLA peptide complexes.
Human Immunology, 61:460-466.
[Online PDF]
Lin, K., Ting, A., Wang, J.R. and Wong, L. (1998)
Hunting TPR domain using Kleisli.
Proceedings of 9th Workshop on Genome Informatics, Tokyo, Japan, 173-182.
[Online PDF]
Zhang, D.Y. and Lin, K. (1997)
The effects of competitive asymmetry on the rate of competitive displacement: how robust is Hubbell’s community drift model?
Journal of Theoretical Biology, 188:361-367.
[Online PDF]