Journal articles

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

2025

Pham AT, Virk S, Oliveira AC, Alves MD, Fu C, Zhang Y, Alvarez-Castanon J, Lee BB, Lee KL, Mashina R, Ray KE, Donabedian P, Ebrahimi E, Patel H, Patel R, Lewis D, Huo Z, Karmouty-Quintana H, Chen L, Jin L, Bryant AJ (2025) Opposing role for myeloid and smooth muscle cell STING in pulmonary hypertension JCI Insight

Clarke HA^, Ma X^^†, Shedlock CJ^, Medina T, Hawkinson TR, Wu L, Ribas RA, Keohane S, Ravi S, Bizon JL, Burke SN, Abisambra JF, Merritt ME, Prentice BM, Vander Kooi CW, Gentry MS^§, Chen L^§, Sun RC^§ (2025) Spatial mapping of the brain metabolome lipidome and glycome Nature Communications

Zhang Y^†, Ding H, Huo Z^§, Chen L^§ (2025) A novel Bayesian hierarchical model for detecting differential circadian pattern in transcriptomic applications Briefings in Bioinformatics

Ma, X.^, Shedlock, C. J., Medina, T., Ribas, R. A., Clarke, H. A., Hawkin- son, T. R., Dande, P. K., Golamari, H.K.R, Wu, L., Ziani B.E., Burke, S. N., Merritt, M. E., Kooi, C. W. V., Gentry, M. S., Yadav, N. N., Chen L^§, & Sun R.C.^§ (2025). AI-driven framework to map the brain metabolome in three dimensions. Nature Metabolism

Clarke HA, Hawkinson TR, Shedlock CJ, Medina T, Ribas RA, Wu L, Liu Z, Ma X, Xia Y, Huang Y, He X, Chang JE, Young LEA, Juras JA, Buoncristiani MD, James AN, Rushin A, Merritt ME, Mestas A, Lamb JF, Manauis EC, Austin GL, Chen L, Singh PK, Bian J, Vander Kooi CW, Evers BM, Brainson CF, Allison DB, Gentry MS, Sun RC (2025) Glycogen drives tumour initiation and progression in lung adenocarcinoma Nature Metabolism

Brothwell JA, Wei YH, Wang J, Guo T, Zhang C, Fortney KR, Duplantier R, Chen L, Batteiger TA, Kaplan MH, Spinola SM, Cao S. A high-resolution view of the immune and stromal cell response to Haemophilus ducreyi infection in human volunteers. mBio

2024

Wang F, Li Y, Shen H, Martinez-Feduchi P, Ji X, Teng P, Krishnakumar S, Hu J, Chen L, Feng Y, Yao B (2024) Identification of pathological pathways centered on circRNA dysregulation in association with irreversible progression of Alzheimer’s disease Genome Medicine

Hou T, Shen X, Zhang S, Liang M, Chen L, Lu Q (2024) AIGen: An Artificial Intelligence Software for Complex Genetic Data Analysis Briefings in Bioinformatics

Zhao F^†, Li Y, Chen L^§, Yao B^§ (2024) Identification of brain region-specific landscape and functions of clustered circRNAs in Alzheimer’s disease using circMeta2 Communications Biology

Jin W^†, Xia Y^†, Nizomov J^†, Liu Y, Li Z, Lu,Q, Chen L^§ (2024) MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants Bioinformatics

Yuan Z, Pei G, Shan Z, Xiao F, Cai G, Chen L, Lu Q (2024) Multi-modal Functional Deep Learning for Multi-omics Data Briefings in Bioinformatics

Ma X^†, Thela S^†, Zhao F^†, Yao B, Wen Z, Jin P, Zhao, J, Chen L^§ (2024) Deep5hmC: Predicting genome-wide 5-Hydroxymethylcytosine landscape via a multimodal deep learning model Bioinformatics

Zhao F^†, Ma X^†, Yao B, Lu Q, Chen L^§ (2024) scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data Plos Computational Biology

2023

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 Bioinformatics

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

2022

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

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

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

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

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

2021

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

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

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

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

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

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

2020

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

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

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

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

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

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

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

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

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

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

2019

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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