Li Chen, PhD

Faculty

Li Chen, PhD

Assistant Professor of Biostatistics

Address

HITS 5025
HEMO
IN
Indianapolis, IN

Bio

I am a tenure-track Assistant Professor of Medicine and a member in Center for Computational Biology and Bioinformatics at Indiana University School of Medicine (IUSM). Before joining IUSM, I spent two years as an Assistant Professor in Harrison School of Pharmacy at Auburn University. I received a BS from China majoring in Bioinformatics in 2009; a MS in Biostatistics and another MS in Computer Science from the Johns Hopkins University in 2011 respectively. After that, I obtained my PhD in Computer Science and Informatics at Emory University in 2017. I also interned in CareerBuilder Data Science and Amazon Machine Learning in Summer 2014 and 2015 respectively.

Titles & Appointments

Assistant Professor of Biostatistics
Assistant Professor of Medicine

Education

2017 PhD Emory University

2011 MSE Johns Hopkins University

2011 MHS Johns Hopkins University

2009 BS Harbin Medical University
Research
I am interested in data science research with its application in large-scale omics data. I am leading a small interdisciplinary data science group working on bioinformatics & biostatistics projects. My current research focuses on developing statistical and informatics methods for analyzing of large-scale omics data. Projects include but not limited to
- Epigenomics: Develop statistical methods and database for analyzing epigenomic data
  - Differential binding. [Link to ChIPComp]
  - Database and web server. [Link to hmChIP]
- Genetics: Develop computational methods for annotating and analyzing functional variants (GWAS SNPs, cis-eQTL SNVs) by utilizing large-scale multi-omics profiles
- Metagenomics: Develop statistical methods for analyzing microbiome data
- Single-cell genomics: Develop statistical methods for clustering single-cell data
  - Clustering droplet-based single-cell transcriptomic data from population studies. [Link to BAMMSC]
- Transcriptomics: Develop statistical methods for analyzing non-coding RNAs
  - Genomic feature annotation and differential expression analysis of circular RNAs. [Link to circMeta]
Publications

powmic: an R package for power assessment in microbiome case-control studies.
Chen L; Bioinformatics (Oxford, England) 2020 Mar 18

Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules.
Yang G; Ma A; Qin ZS; Chen L; Bioinformatics (Oxford, England) 2020 Jan 3

Generic levothyroxine initiation and substitution among Medicare and Medicaid populations: a new user cohort study.
Huo N; Chen L; Ullah Mishuk A; Li C; Hansen RA; Harris I; Kiptanui Z; Wang Z; Dutcher SK; Qian J; Endocrine 2020 Jan 28

circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs.
Chen L; Wang F; Bruggeman EC; Li C; Yao B; Bioinformatics (Oxford, England) 2020 Jan 15

Ethnicity-specific and overlapping alterations of brain hydroxymethylome in Alzheimer's disease.
Qin L; Xu Q; Li Z; Chen L; Li Y; Yang N; Liu Z; Guo J; Shen L; Allen EG; Chen C; Ma C; Wu H; Zhu X; Jin P; Tang B; Human molecular genetics 2020 Jan 1

Destin: toolkit for single-cell analysis of chromatin accessibility.
Urrutia E; Chen L; Zhou H; Jiang Y; Bioinformatics (Oxford, England) 2019 Oct 1

TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction.
Chen L; Wang Y; Yao B; Mitra A; Wang X; Qin X; Bioinformatics (Oxford, England) 2019 May 1

Impact of a multi-component immunization intervention on pneumococcal and herpes zoster vaccinations: A randomized controlled trial of community pharmacies in 2 states.
Hohmann LA; Hastings TJ; Ha DR; Garza KB; Huston SA; Chen L; Westrick SC; Research in social & administrative pharmacy : RSAP 2019 Feb 7

A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies.
Sun Z; Chen L; Xin H; Jiang Y; Huang Q; Cillo AR; Tabib T; Kolls JK; Bruno TC; Lafyatis R; Vignali DAA; Chen K; Ding Y; Hu M; Chen W; Nature communications 2019 Apr 9

Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model.
Xiao J; Chen L; Johnson S; Yu Y; Zhang X; Chen J; Frontiers in microbiology 2018 Jun 27

A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data.
Xiao J; Chen L; Yu Y; Zhang X; Chen J; Frontiers in microbiology 2018 Dec 19

Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice.
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 EG; Wu H; Xu X; Jin P; Cell reports 2018 Dec 11

Active N<sup>6</sup>-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons.
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 KH; Wu H; Jin P; Molecular cell 2018 Aug 2

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data.
Chen L; Reeve J; Zhang L; Huang S; Wang X; Chen J; PeerJ 2018 Apr 2

Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale.
Chen L; Qin ZS; BMC research notes 2017 Oct 30

DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress.
Yao B; Cheng Y; Wang Z; Li Y; Chen L; Huang L; Zhang W; Chen D; Wu H; Tang B; Jin P; Nature communications 2017 Oct 24

Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis.
Li X; Yao B; Chen L; Kang Y; Li Y; Cheng Y; Li L; Lin L; Wang Z; Wang M; Pan F; Dai Q; Zhang W; Wu H; Shu Q; Qin Z; He C; Xu M; Jin P; Nature communications 2017 Jun 29

Omicseq: a web-based search engine for exploring omics datasets.
Sun X; Pittard WS; Xu T; Chen L; Zwick ME; Jiang X; Wang F; Qin ZS; Nucleic acids research 2017 Jul 3

Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells.
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; Nature communications 2017 Apr 25

5-Hydroxymethylcytosine-mediated alteration of transposon activity associated with the exposure to adverse in utero environments in human.
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; Human molecular genetics 2016 Mar 22

DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles.
Chen L; Jin P; Qin ZS; Genome biology 2016 Dec 6

Molecular signatures associated with ZIKV exposure in human cortical neural progenitors.
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; Nucleic acids research 2016 Aug 31

Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress.
Papale LA; Li S; Madrid A; Zhang Q; Chen L; Chopra P; Jin P; Keles S; Alisch RS; Neurobiology of disease 2016 Aug 26

Small Molecules Efficiently Reprogram Human Astroglial Cells into Functional Neurons.
Zhang L; Yin JC; Yeh H; Ma NX; Lee G; Chen XA; Wang Y; Lin L; Chen L; Jin P; Wu GY; Chen G; Cell stem cell 2015 Oct 17

Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress.
Li S; Papale LA; Zhang Q; Madrid A; Chen L; Chopra P; Keles S; Jin P; Alisch RS; Neurobiology of disease 2015 Nov 18

Combined Loss of Tet1 and Tet2 Promotes B Cell, but Not Myeloid Malignancies, in Mice.
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; Cell reports 2015 Nov 12

Altering 5-hydroxymethylcytosine modification impacts ischemic brain injury.
Miao Z; He Y; Xin N; Sun M; Chen L; Lin L; Li J; Kong J; Jin P; Xu X; Human molecular genetics 2015 Jul 30

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.
Wu H; Xu T; Feng H; Chen L; Li B; Yao B; Qin Z; Jin P; Conneely KN; Nucleic acids research 2015 Jul 15

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.
Chen L; Wang C; Qin ZS; Wu H; Bioinformatics (Oxford, England) 2015 Feb 13

traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.
Chen L; Qin ZS; Bioinformatics (Oxford, England) 2015 Dec 18

glmgraph: an R package for variable selection and predictive modeling of structured genomic data.
Chen L; Liu H; Kocher JP; Li H; Chen J; Bioinformatics (Oxford, England) 2015 Aug 26

Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma.
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; Cancer informatics 2014 Sep 21

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.
Chen L; Wu G; Ji H; Bioinformatics (Oxford, England) 2011 Mar 30

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