- Guo X, Chen L. From G1 to M: a Comparative Study of Methods for Identifying Cell Cycle Phases Brief Bioinform bbad517
- Yin Q, Chen L. CellTICS: an explainable neural network for cell-type identification and interpretation based on single-cell RNA-seq data. Brief Bioinform 2023 Nov 22;25(1):bbad449.
- Li Z, Chen L. Predicting functional consequences of SNPs on mRNA translation via machine learning. Nucleic Acids Research. 2023 Jul 10:gkad576.
- Sun B, Chen L. Interpretable deep learning for improving cancer patient survival based on personal transcriptomes. Scientific Reports. 2023;13:11344
- Sun B, Chen L. Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues. Genome Biology. 2023;24(1):164.
- Jiang W, Chen L. Tissue Specificity of Gene Expression Evolves Across Mammal Species. J Comput Biol. 2022;29(8):880-91
- Vuong JK, Ergin V, Chen L, Zheng S. Multilayered regulations of alternative splicing, NMD, and protein stability control temporal induction and tissue-specific expression of TRIM46 during axon formation. Nat Commun. 2022;13(1):2081.
- Zhao J, Li Z, Puri R, Liu K, Nunez I, Chen L, Zheng S. Molecular profiling of individual FDA-approved clinical drugs identifies modulators of nonsense-mediated mRNA decay. Mol Ther Nucleic Acids. 2022;27:304-18.
- Jiang W, Chen L*, Zheng S*. Global Reprogramming of Apoptosis-Related Genes during Brain Development. Cells. 2021;10(11).
- Jiang W, Chen L. Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing. Computational and Structural Biotechnology Journal. 2021;19:183-195.
- Chen L*, Zheng S*. Understand variability of COVID-19 through population and tissue variations in expression of SARS-CoV-2 host genes. Informatics in Medicine Unlocked 2020; 21 (100443).
- Lin L, Zhang M, Stoilov P, Chen L, Zheng S. Developmental attenuation of neuronal apoptosis by neural specific splicing of Bak1 microexon. Neuron. 2020 Jul 16;S0896-6273(20)30490-6.
- Sun B, Chen L. Quantile regression for challenging cases of eQTL mapping. Briefings in Bioinformatics 2019; Nov 3. pii: bbz097
- Zhang M, Ergin V, Lin L, Stork C, Chen L*, Zheng S*. Axonogenesis is coordinated by alternative splicing programming and splicing regulator PTBP2. Neuron 2019;101(4):690-706.
- Xu M, Chen L. An empirical likelihood ratio test robust to individual heterogeneity for differential expression analysis of RNA-seq. Briefings in Bioinformatics. 2018;19(1):109-17.
- Cippa PE#, Sun B#, Liu J, Chen L, Naesens M, McMahon AP. Transcriptional trajectories of human kidney injury progression. JCI Insight. 2018;3(22).
- Chen L*, Zheng S*. BCseq: accurate single cell RNA-seq quantification with bias correction. Nucleic Acids Research. 2018;46(14):e82.
- Vuong JK, Lin CH, Zhang M, Chen L, Black DL, Zheng S. PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing. Cell Reports. 2016;17(10):2766-75.
- Lee H, Chen L. Inference of kinship using spatial distributions of SNPs for genome-wide association studies. BMC Genomics. 2016;17:372.
- Zhang J, Kuo CC, Chen L. WemIQ: an accurate and robust isoform quantification method for RNA-seq data. Bioinformatics. 2015;31(6):878-85.
- Guan L, Yang Q, Gu M, Chen L, Zhang X. Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation. Quantitative Biology. 2014;2(2):71-9.
- Zheng S, Damoiseaux R, Chen L, Black DL. A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing. Genome Research. 2013;23(6):998-1007.
- Lee CY, Chen L. Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. Bioinformatics. 2013;29(14):1713-7.
- Chen L. Characterization and comparison of human nuclear and cytosolic editomes. Proc Natl Acad Sci U S A. 2013;110(29):E2741-7.
- Chen L. Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing. Statistics in Biosciences. 2013;5(1):138-55.
- Zhang J, Kuo CC, Chen L. VERSE: A Varying Effect Regression for Splicing Elements Discovery. Journal of Computational Biology. 2012;19(6):855-65.
- Tong T, Chen L, Zhao H. Improved mean estimation and its application to diagonal discriminant analysis. Bioinformatics. 2012;28(4):531-7.
- Zhang J, Kuo CC, Chen L. GC content around splice sites affects splicing through pre-mRNA secondary structures. BMC Genomics. 2011;12:90.
- Masly JP, Dalton JE, Srivastava S, Chen L, Arbeitman MN. The genetic basis of rapidly evolving male genital morphology in Drosophila.Genetics. 2011;189(1):357-74.
- Srivastava S, Chen L. A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Research. 2010;38(17):e170.
- Srivastava S, Chen L. Model selection methods for genome wide association studies.Communications in Information and Systems. 2010;10:39-52.
- Chen L. A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms. Nucleic Acids Research. 2010;38(4):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):855-9.
- Zheng S, Chen L. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Research. 2009;37(10):e75.
- Srivastava S, Chen L. 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:S21.
- Liu J, Chen L, Zhao H, Moore DF, Lin Y, Shi WJ. On calculating the probability of a set of orthologous sequences. Journal of Advances and Applications in Bioinformatics and Chemistry. 2009;2:37-48.
- Chen L, Zheng S. Studying alternative splicing regulatory networks through partial correlation analysis. Genome Biology. 2009;10(1):R3.
- Chen L. Statistical and computational studies on alternative splicing. Handbook of Computational Statistics: Statistical Bioinformatic2009.
- Chen L, Zheng S. Identify alternative splicing events based on position-specific evolutionary conservation. PLoS One. 2008;3(7):e2806.
- Chen L*, Tong T, Zhao H*. Considering dependence among genes and markers for false discovery control in eQTL mapping. Bioinformatics. 2008;24(18):2015-22.
- Liu Y, Sun N, Liu J, Chen L, McIntosh M, Zheng L, Zhao H. Identifying stage-specific genes by combining information from two different types of oligonucleotide arrays. In: McConnell P, Lin S, Hurban P, editors. Methods of Microarray Data Analysis V: Springer; 2007. p. 59-74.
- Wang S, Huang S, Liu N, Chen L, Oh C, Zhao H. Whole-genome linkage analysis in mapping alcoholism genes using single-nucleotide polymorphisms and microsatellites. BMC Genetics. 2005;6 Suppl 1:S28.
- Oh C, Wang S, Liu N, Chen L, Zhao H. 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:S116.
- Liu N, Chen L, Wang S, Oh C, Zhao H. Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genetics. 2005;6 Suppl 1:S26.
- Huang S, Wang S, Liu N, Chen L, Oh C, Zhao H. Whole-genome association analysis to identify markers associated with recombination rates using single-nucleotide polymorphisms and microsatellites. BMC Genetics. 2005;6 Suppl 1:S51.
- Chen L, Zhao HY. Integrating mRNA decay information into co-regulation study. Journal of Computer Science and Technology. 2005;20(4):434-8.
- Chen L, Zhao H. Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains. BMC Genomics. 2005;6(1):44.
- Chen L, Zhao H. Negative correlation between compositional symmetries and local recombination rates. Bioinformatics. 2005;21(21):3951-8.
- Chen L, Liu N, Wang S, Oh C, Carriero NJ, Zhao H. Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites. BMC Genetics. 2005;6 Suppl 1:S130.
- Lai Y, Wu B, Chen L, Zhao H. A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics. 2004;20(17):3146-55.
- Sun LV, Chen L, Greil F, Negre N, Li TR, Cavalli G, Zhao H, Van Steensel B, White KP. Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc Natl Acad Sci U S A. 2003;100(16):9428-33.