Journal articles

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


Guan PY, Lee JS, Wang L, Lin KZ, Mei W, Chen L, Jiang Y (2023) Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data Frontiers in Genetics

Agarwal A, Zhao F, Jiang Y, Chen L§ (2023) TIVAN-indel: A computational framework for annotating and predicting noncoding regulatory small insertions and deletions BioinformaticsTIVAN-indel Software

Agarwal A, Chen L§ (2023) DeepPHiC: Predicting promoter-centered chromatin interactions using a novel deep learning approach Bioinformatics DeepPHiC Software


Wang Y, Chen L§ (2022) DeepPerVar: a multimodal deep learning framework for functional interpretation of genetic variants in personal genome Bioinformatics DeepPerVar Software

Chen L§, Saykin AJ, Yao B, Zhao F (2022) Multi-task deep autoencoder to predict Alzheimer’s disease progression using temporal DNA methylation data in peripheral blood Computational and Structural Biotechnology Journal MTAE Software

Tang PC, Chen L, Singh S, Groves AK, Koehler KR, Liu XZ, Nelson RF (2022) Early Wnt signaling activation promotes inner ear differentiation via cell caudalization in mouse stem cell-derived organoids Stem Cells PubMed Data

Chen L§, Wang Y, Zhao F (2022) Exploiting deep transfer learning for the prediction of functional noncoding variants using genomic sequence Bioinformatics TLVar software PubMed

Li Y, Wang F, Teng P, Ku L, Chen L, Feng Y, Yao B (2022) Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation. Genome Biology PubMed Data


Li C, Chen L, Chou C, Ngorsuraches S, Qian J (2021) Using Machine Learning Approaches to Predict Short-Term Risk of Cardiotoxicity Among Patients with Colorectal Cancer after Starting Fluoropyrimidine-based Chemotherapy. Cardiovascular Toxicology

Chen L, Li MJ (2021) Editorial: Deciphering Noncoding Regulatory Variants Computational and Functional Validation. Frontiers in Bioengineering and Biotechnology

Kim H, Kang Y, Li Y, Chen L, Lin L, Johnson ND, Zhu D, Robinson MH, McSwain L, Barwick BG, Yuan X, Liao X, Zhao J, Zhang Z, Shu Q, Chen J, Allen EG, Kenney AM, Castellino RC, Van Meir EG, Conneely KN, Vertino PM, Jin P, Li J (2021) Ten-eleven translocation protein 1 modulates medulloblastoma progression. Genome Biology PubMed Data

Wang Y, Jiang Y, Yao B, Huang K, Liu Y, Wang Y, Qin X, Saykin AJ, Chen L§ (2021) WEVar: a novel statistical learning framework for predicting noncoding regulatory variants. Briefings in Bioinformatics MDeep software PubMed

Li C, Ngorsuraches S, Chou C, Chen L, Qian J (2021) Risk Factors of Fluoropyrimidine Induced Cardiotoxicity Among Cancer Patients: A Systematic Review and Meta-analysis. Critical Reviews in Oncology/Hematology

Kuehner JN, Chen J, Bruggeman EC, Wang F, Li Y, Xu C, McEachin ZT, Li Z, Chen L, Hales CM, Wen Z, Yang J, Yao B (2021) 5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer’s disease. Cell Reports PubMed Data

Mishuk AU, Chen L, Li C, Huo N, Hansen RA, Harris I, Kiptanui Z, Qian J (2021) Patient factors associated with oral generic olanzapine initiation and substitution among Medicaid beneficiaries: a new user cohort study. Current Medical Research and Opinion PubMed

Brothwell J, Griesenauer B, Chen L and Spinola SM (2021) Interactions of the Skin Pathogen Haemophilus ducreyi With the Human Host Frontiers in Immunology PubMed

Mishuk AU, Chen L, Gaillard P, Westrick S, Hansen RA, Qian J (2021) National Trends in Prescription Proton Pump Inhibitors (PPI) Use and Expenditure in the U.S. in 2002-2017 Journal of the American Pharmacists Association


Chen L, Li C, Huo N, Mishuk AU, Hansen RA, Harris I, Kiptanui Z, Qian J (2020) Oral Generic Tacrolimus Initiation and Substitution in The Medicaid Population: A New User Cohort Study Current Medical Research & Opinion PubMed

Mei W, Jiang Z, Chen Y, Chen L, Sancar A, Jiang Y (2020) Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines Briefings in Bioinformatics PubMed

Mitra AK, Kumar H, Ramakrishnan V, Chen L, Kumar S, Rajkumar SV, Van Ness B (2020) In vitro and ex vivo gene expression profiling reveals differential kinetic response of HSPs and UPR genes are associated with PI-resistance in multiple myeloma Blood Cancer Journal PubMed

Li C, Chen L, Huo N, Mishuk AU, Hansen RA, Harris I, Kiptanui Z, Wang Z, Qian J (2020) Generic escitalopram initiation and substitution among Medicare beneficiaries: A new user cohort study Plos One PubMed

Wang Y, Bhattacharya T, Jiang Y, Qin X, Wang Y, Liu Y, Saykin AJ, Chen L§ (2020) A novel deep learning method for predictive modeling of microbiome data Briefings in Bioinformatics MDeep software PubMed

Chen L§ (2020) powmic: an R package for power assessment in microbiome case-control studies Bioinformatics powmic software PubMed

Huo N, Chen L, Ullah Mishuk A, Li C, Hansen RA, Harris I, Kiptanui Z, Wang Z, Dutcher SK, Qian J (2020) Generic levothyroxine initiation and substitution among Medicare and Medicaid populations: a new user cohort study Endocrine PubMed

Yang G, Ma A, Qin ZS§, Chen L§ (2020) Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules Bioinformatics tfLDA software PubMed

Chen L§, Wang F, Bruggeman E, Li C, Yao B§ (2020) circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs Bioinformatics circMeta software PubMed

Qin L, Xu Q, Li Z, Chen L, Li Y, Yang N, Liu Z, Guo J, Shen L, Allen GE, Chen C, Ma C, Wu H, Zhu X, Jin P, Tang B (2020) Ethnicity-specific and overlapping alterations of brain hydroxymethylome in Alzheimer’s disease Human Molecular Genetics PubMed


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 PubMed

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

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 PubMed

Chen L§, Wang Y, Yao B, Mitra AK, Wang X, Qin X (2019) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction Bioinformatics TIVAN software PubMed


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 PubMed

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 PubMed

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 PubMed

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 PubMed

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


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