Journal articles

Key: § indicates (co-)corresponding author; † indicates advisee; ^indicates (co-) first author

2019

Chen L§, Wang F, Bruggeman E, Li C, Yao B§ (2019) circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs Bioinformatics circMeta software

Sun Z^, Chen L^, Xin H, Jiang Y, Huang Q, Cillo A, Tabib T, Kolls J, Bruno T, Lafyatis B, Vignali D, Chen K, Ding Y, Hu M, Chen W (2019). A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies Nature Communications BAMMSC software

Urrutia E, Chen L, Zhou H, Jiang Y (2019). Destin: toolkit for single-cell analysis of chromatin accessibility Bioinformatics Destin software

Hohmann L, Hastings T, Ha D, Garza K, Huston S, Chen L, Westrick S (2019). Impact of a multi-component immunization intervention on pneumococcal and herpes zoster vaccinations: A randomized controlled trial of community pharmacies in 2 states. Research in Social and Administrative Pharmacy

2018

Cheng Y, Sun M, Chen L, Li Y, Lin L, Yao B, Li Z, Wang Z, Chen J, Miao Z, Xin N, Huang L, Allen E, Wu H, Xu X, Jin P (2018). Ten-eleven translocation proteins modulate the response to environmental stress in mice Cell Reports Data

Xiao J, Chen L§, Johnson S, Zhang X, Chen J§ (2018). A phylogeny-regularized sparse regression model for predictive modeling of microbial community data Frontiers in Microbiology SICS software

Chen L§, Wang Y, Yao B, Mitra A, Wang X, Qin X (2018) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics TIVAN software

Yao B, Li Y, Wang Z, Chen L, Poidevin M, Zhang C, Lin L, Wang F, Bao H, Jiao B, Lim J, Cheng Y, Huang L, Phillips BL, Xu T, Duan R, Moberg K, Wu H, Jin P (2018). Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons Molecular Cell Data

Xiao J, Chen L§, Johnson S, Zhang X, Chen J§ (2018). Predictive modeling of microbiome data using a phylogeny-regularized generalized linear mixed model Frontiers in Microbiology glmmTree software

Chen L, Reeve J, Zhang L, Huang S, Wang X, Chen J (2018). GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data PeerJ PubMed GMPR software

2017

Chen L§, Qin ZS§ (2017). Using DIVAN to assess disease trait-associated single nucleotide variants in genome-wide scale BMC Research Notes doi:10.1186/s13104-017-2851-y PubMed DIVAN software

Yao B, Cheng Y, Wang Z, Li Y, Chen L, Huang L, Zhang W, Wu H, Tang B, Jin P (2017). DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress Nature Communication doi:10.1038/s41467-017-01195-y PubMed Data

Li X, Yao B, Chen L, Cheng Y, Kang Y, Lin L, Li Y, Pan F, Dai Q, Wu H, Shu Q, Qin ZS, He C, Xu M, Jin P (2017). Ten-eleven translocation 2 interacts with Forkhead box O3 and regulates adult neurogenesis Nature Communication doi: 10.1038/ncomms15903 PubMed Data

Sun X, Pittard WS, Xu T, Chen L, Zwick ME, Jiang X, Wang F, Qin ZS (2017). OmicSeq: A web-based search engine for exploring omics datasets Nucleic Acids Research doi:10.1093/nar/gkx258 PubMed OmicSeq software

Pan F, Wingo TS, Zhao Z, Gao R, Makishima H, Qu G, Lin L, Yu M, Ortega JR, Wang J, Nazha A, Chen L, Yao B, Liu C, Chen S, Weeks O, Ni H, Phillips BL, Huang S, Wang J, He C, Li GM, Radivoyevitch T, Aifantis I, Maciejewski JP, Yang FC, Jin P, Xu M (2017). Tet2 loss leads to hypermutagenicity in hematopoietic stem/progenitor cells Nature Communication doi:10.1038/ncomms15102 PubMed Data

Before 2017

Papale LA, Li S, Madrid A, Zhang Q, Chen L, Chopra P, Jin P, Keles S, Alisch RS (2016). Gender-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress Neurobiology of Disease 96:54-66 PubMed

Chen L, Jin P, Qin ZS (2016). DIVAN: Accurate identification of non-coding disease-specific risk variants based on multi-omics profiles Genome Biology 17:252 PubMed DIVAN software

Zhang F, Hammack C, Ogden SC, Cheng Y, Lee EM, Wen Z, Qian X, Nguyen HN, Li Y, Yao B, Xu M, Xu T, Chen L, Wang Z, Feng H, Huang WK, Yoon KJ, Shan C, Huang L, Qin Z, Christian KM, Shi PY, Xu M, Xia M, Zheng W, Wu H, Song H, Tang H, Ming GL, Jin P (2016). Molecular Signatures Associated with ZIKV Exposure in Human Cortical Neural Progenitors and Astrocytes Nucleic Acids Research 44(18):8610-8620 PubMed Data

Sun M, Song MM, Wei B, Gao Q, Li L, Yao B, Chen L, Lin L, Dai Q, Zhou X, Tao J, Chen J, He C, Jin P, Xu Z (2016). 5-Hydroxymethylcytosine-mediated alteration of transposon activity associated with the exposure to adverse in utero environments in human Human Molecular Genetics 25(11): 2208-2219 PubMed Data

Li S, Papale LA, Zhang Q, Madrid A, Chen L, Chopra P, Keles S, Jin P, Alisch RS (2016). Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress Neurobiology of Disease 86:99-108 PubMed Data

Chen L, Qin ZS (2016). traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals Bioinformatics 32(8):1214-1216 PubMed traseR software

Chen L, Liu H, Kocher JP, Li H, Chen J (2015). glmgraph: an R package for variable selection and predictive modeling of structured genomic data Bioinformatics 31(12):1889-96 PubMed glmgraph software

Zhang L, Yin JC, Yeh H, Ma NX, Lee G, Chen XA, Wang Y, Lin L, Chen L, Jin P, Wu GY, Chen G (2015). Small molecules efficiently reprogram human astroglial cells into functional neurons Cell Stem Cell 7(6):735-747 PubMed

Zhao Z^, Chen L^, Dawlaty MM^, Pan F, Weeks O, Zhou Y, Cao Z, Shi H, Wang J, Lin L, Chen S, Yuan W, Qin Z, Ni H, Nimer SD, Yang FC, Jaenisch R, Jin P, Xu M (2015). Combined loss of Tet1 and Tet2 promotes B-cell, but not myeloid malignancies in mice. Cell Reports 13(8):1692-1704 PubMed Data

Miao Z, He Y, Xin N, Sun M, Chen L, Lin L, Li J, Kong J, Jin P, Xu X (2015). Altering 5-hydroxymethylcytosine modification impacts ischemic brain injury Human Molecular Genetics 24(20):5855-5866 PubMed Data

Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin Z, Jin P, Conneely KN (2015). Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates Nucleic Acids Research 43(21):e141 PubMed DSS software

Chen L, Wang C, Qin ZS, Wu H (2015). A novel statistical method for quantitative comparison of multiple ChIP-seq datasets Bioinformatics 31(12):1889-96 PubMed ChIPComp software

Yang R, Chen L, Newman S, Gandhi K, Doho G, Moreno CS, Vertino PM, Bernal-Mizarchi L, Lonial S, Boise LH, Rossi M, Kowalski J, Qin ZS (2014). Integrated Analysis of Whole-Genome Paired-End and Mate-Pair Sequencing Data for Identifying Genomic Structural Variations in Multiple Myeloma Cancer Informatics 13(Suppl2):49-53 PubMed

Chen L, Wu G, Ji H (2011). hmChIP: a web server for exploring publicly available human and mouse ChIP-chip and ChIP-seq data Bioinformatics 27(10):1447-1448 PubMed hmChIP software