- Chen, L.*, Characterization and comparison of human nuclear and cytosolic editomes. Proceedings of the National Academy of Sciences of the United States of America, 2013 (accepted)
- Lee,C., L. Chen*, Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. Bioinformatics, 2013 (in print)
- Zheng, S., R. Damoiseaux, L. Chen, D.L. Black, A broadly applicable high-throughput screening strategy identifies new regulators of Psd-95 alternative splicing. Genome Research, 2013 (in print).
- Zhang, J., C.C. Kuo, and L. Chen*, VERSE: A Varying Effect Regression for Splicing Elements Discovery. Journal of Computational Biology, 2012. 19(6): p. 855-65.
- Tong, T., L. Chen, and H. Zhao, Improved mean estimation and its application to diagonal discriminant analysis. Bioinformatics, 2012. 28(4): p. 531-7.
- Chen, L.*, Statistical and computational methods for high throughput sequencing data analysis of alternative splicing. Statistics in Biosciences, (Epub ahead of print) 2012.
- Zhang, J., C.C. Kuo, and L. Chen*, GC content around splice sites affects splicing through pre-mRNA secondary structures. BMC Genomics, 2011. 12: p. 90.
- Masly, J.P., J.E. Dalton, S. Srivastava, L. Chen, and M.N. Arbeitman, The genetic basis of rapidly evolving male genital morphology in Drosophila. Genetics, 2011. 189(1): p. 357-74.
- Srivastava, S. and L. Chen*, A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Research, 2010. 38(17): p. e170.
- Srivastava, S. and L. Chen*, Model selection methods for genome wide association studies. Communications in Information and Systems, 2010. 10: p. 39-52.
- Chen, L.*, A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms. Nucleic Acids Research, 2010. 38(4): p. 1086-97.
- Chen, L.*, A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells. Bioinformatics, 2010. 26(7): p. 855-9.
- Zheng, S. and L. Chen*, A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Research, 2009. 37(10): p. e75.
- Srivastava, S. and L. Chen*, Comparison between the stochastic search variable selection and the least absolute shrinkage and selection operator for genome-wide association studies of rheumatoid arthritis. BMC Proceedings, 2009. 3 Suppl 7: p. S21.
- Liu, J., L. Chen, H. Zhao, D.F. Moore, Y. Lin, and W.J. Shi, On calculating the probability of a set of orthologous sequences. Journal of Advances and Applications in Bioinformatics and Chemistry, 2009. 2: p. 37-48.
- Chen, L.* and S. Zheng, Studying alternative splicing regulatory networks through partial correlation analysis. Genome Biology, 2009. 10(1): p. R3.
- Chen, L.*, Statistical and computational studies on alternative splicing. in Handbook of Computational Statistics: Statistical Bioinformatic. 2009.
- Chen, L.* and S. Zheng, Identify alternative splicing events based on position-specific evolutionary conservation. PLoS One, 2008. 3(7): p. e2806.
- Chen, L.*, T. Tong, and H. Zhao*, Considering dependence among genes and markers for false discovery control in eQTL mapping. Bioinformatics, 2008. 24(18): p. 2015-22. (co-corresponding authors)
- Liu, Y., N. Sun, J. Liu, L. Chen, M. McIntosh, L. Zheng, and H. Zhao, Identifying stage-specific genes by combining information from two different types of oligonucleotide arrays. in Methods of Microarray Data Analysis V. 2007.
- Wang, S., S. Huang, N. Liu, L. Chen, C. Oh, and H. Zhao, Whole-genome linkage analysis in mapping alcoholism genes using single-nucleotide polymorphisms and microsatellites. BMC Genetics, 2005. 6 Suppl 1: p. S28.
- Oh, C., S. Wang, N. Liu, L. Chen, and H. Zhao, A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method. BMC Genetics, 2005. 6 Suppl 1: p. S116.
- Liu, N., L. Chen, S. Wang, C. Oh, and H. Zhao, Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genetics, 2005. 6 Suppl 1: p. S26.
- Huang, S., S. Wang, N. Liu, L. Chen, C. Oh, and H. Zhao, Whole-genome association analysis to identify markers associated with recombination rates using single-nucleotide polymorphisms and microsatellites. BMC Genetics, 2005. 6 Suppl 1: p. S51.
- Chen, L. and H.Y. Zhao, Integrating mRNA decay information into co-regulation study. Journal of Computer Science and Technology, 2005. 20(4): p. 434-438.
- Chen, L. and H. Zhao, Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains. BMC Genomics, 2005. 6(1): p. 44.
- Chen, L. and H. Zhao, Negative correlation between compositional symmetries and local recombination rates. Bioinformatics, 2005. 21(21): p. 3951-8.
- Chen, L., N. Liu, S. Wang, C. Oh, N.J. Carriero, and H. Zhao, Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites. BMC Genetics, 2005. 6 Suppl 1: p. S130.
- Lai, Y., B. Wu, L. Chen, and H. Zhao,A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics, 2004. 20(17): p. 3146-55.
- Sun, L.V., L. Chen, F. Greil, N. Negre, T.R. Li, G. Cavalli, H. Zhao, B. Van Steensel, and K.P. White, Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 2003. 100(16): p. 9428-33.