Publications
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
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
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
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
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