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  • Liu S, Chen L. Deciphering Single-Cell Gene Expression Variability and Its Role in Drug Response Human Molecular Genetics (accepted)

  • Lin L, Zhao J, Kubota N, Li Z, Lam YL, Nguyen LP, Yang L, Pokharel SP, Blue SM, Yee BA, Chen R, Yeo GW, Chen CW, Chen L, Zheng S. Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. Neuron. 2024;112(13):2157-2176 e2112.

  • Guo X, Chen L. From G1 to M: a Comparative Study of Methods for Identifying Cell Cycle Phases Briefings in Bioinformatics. 2024;25(2)

  • 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.