Li Chen

Li Chen,

Associate Professor

Department: PHHP-COM BIOSTATISTICS
Business Phone: (352) 294-5909
Business Email: li.chen1@ufl.edu

About Li Chen

Dr. Li Chen is a tenured associate professor in the Department of Biostatistics at University of Florida. He joined the department under the UF artificial intelligence initiative. Dr. Chen focuses on developing deep learning and statistical methods and software for analyzing large-scale multi-omics data, including but not limited to genetics, single-cell genomics and metagenomics. He is interested in applying the methods developed to study aging and cancer, disseminating software developed for public health researchers to use, and integrating multi-omics data with imaging and EHR data.

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Accomplishments

Maximizing Investigators’ Research Award
2021 · NIGMS
Showalter Research Trust Fund Award
2020 · Indiana CTSI
American Association of Colleges of Pharmacy New Investigator Award
2019 · American Association of Colleges of Pharmacy

Teaching Profile

Courses Taught
2023-2024
PHC6937 Special Topics in Public Health
2023-2025
HSC4970 Public Health and Health Professions Senior Honors Thesis
2023-2025
PHC7979 Advanced Research

Publications

2023
DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach.
Bioinformatics (Oxford, England). 39(1) [DOI] 10.1093/bioinformatics/btac801. [PMID] 36495179.
2023
Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data.
Frontiers in genetics. 14 [DOI] 10.3389/fgene.2023.1089936. [PMID] 36873935.
2023
Early Wnt Signaling Activation Promotes Inner Ear Differentiation via Cell Caudalization in Mouse Stem Cell-Derived Organoids.
Stem cells (Dayton, Ohio). 41(1):26-38 [DOI] 10.1093/stmcls/sxac071. [PMID] 36153788.
2023
TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions.
Bioinformatics (Oxford, England). 39(2) [DOI] 10.1093/bioinformatics/btad060. [PMID] 36707993.
2022
Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation.
Genome biology. 23(1) [DOI] 10.1186/s13059-022-02621-1. [PMID] 35130952.
2022
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome.
Bioinformatics (Oxford, England). 38(24):5340-5351 [DOI] 10.1093/bioinformatics/btac696. [PMID] 36271868.
2022
Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence.
Bioinformatics (Oxford, England). 38(12):3164-3172 [DOI] 10.1093/bioinformatics/btac214. [PMID] 35389435.
2022
Multi-task deep autoencoder to predict Alzheimer’s disease progression using temporal DNA methylation data in peripheral blood.
Computational and structural biotechnology journal. 20:5761-5774 [DOI] 10.1016/j.csbj.2022.10.016. [PMID] 36756173.
2022
Using Machine Learning Approaches to Predict Short-Term Risk of Cardiotoxicity Among Patients with Colorectal Cancer After Starting Fluoropyrimidine-Based Chemotherapy.
Cardiovascular toxicology. 22(2):130-140 [DOI] 10.1007/s12012-021-09708-4. [PMID] 34792740.
2021
5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer’s disease.
Cell reports. 35(4) [DOI] 10.1016/j.celrep.2021.109042. [PMID] 33910000.
2021
A novel deep learning method for predictive modeling of microbiome data.
Briefings in bioinformatics. 22(3) [DOI] 10.1093/bib/bbaa073. [PMID] 32406914.
2021
Editorial: Deciphering Non-Coding Regulatory Variants: Computational and Functional Validation.
Frontiers in bioengineering and biotechnology. 9 [DOI] 10.3389/fbioe.2021.769614. [PMID] 34805122.
2021
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines.
Briefings in bioinformatics. 22(3) [DOI] 10.1093/bib/bbaa135. [PMID] 32672832.
2021
Patient factors associated with oral generic olanzapine initiation and substitution among Medicaid beneficiaries: a new user cohort study.
Current medical research and opinion. 37(4):655-664 [DOI] 10.1080/03007995.2021.1882413. [PMID] 33507825.
2021
Risk Factors of Fluoropyrimidine Induced Cardiotoxicity among Cancer Patients: A Systematic Review and Meta-analysis.
Critical reviews in oncology/hematology. 162 [DOI] 10.1016/j.critrevonc.2021.103346. [PMID] 33930532.
2021
Ten-eleven translocation protein 1 modulates medulloblastoma progression.
Genome biology. 22(1) [DOI] 10.1186/s13059-021-02352-9. [PMID] 33926529.
2021
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.
Briefings in bioinformatics. 22(6) [DOI] 10.1093/bib/bbab189. [PMID] 34021560.
2020
Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules.
Bioinformatics (Oxford, England). 36(8):2352-2358 [DOI] 10.1093/bioinformatics/btz975. [PMID] 31899481.
2020
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs.
Bioinformatics (Oxford, England). 36(2):539-545 [DOI] 10.1093/bioinformatics/btz606. [PMID] 31373611.
2020
Ethnicity-specific and overlapping alterations of brain hydroxymethylome in Alzheimer’s disease.
Human molecular genetics. 29(1):149-158 [DOI] 10.1093/hmg/ddz273. [PMID] 31814020.
2020
Generic escitalopram initiation and substitution among Medicare beneficiaries: A new user cohort study.
PloS one. 15(4) [DOI] 10.1371/journal.pone.0232226. [PMID] 32353006.
2020
Generic levothyroxine initiation and substitution among Medicare and Medicaid populations: a new user cohort study.
Endocrine. 68(2):336-348 [DOI] 10.1007/s12020-020-02211-w. [PMID] 31993992.
2020
In vitro and ex vivo gene expression profiling reveals differential kinetic response of HSPs and UPR genes is associated with PI resistance in multiple myeloma.
Blood cancer journal. 10(7) [DOI] 10.1038/s41408-020-00344-9. [PMID] 32724061.
2020
Interactions of the Skin Pathogen Haemophilus ducreyi With the Human Host.
Frontiers in immunology. 11 [DOI] 10.3389/fimmu.2020.615402. [PMID] 33613541.
2020
National trends in prescription proton pump inhibitor use and expenditure in the United States in 2002-2017.
Journal of the American Pharmacists Association : JAPhA. [DOI] 10.1016/j.japh.2020.09.015. [PMID] 34756356.
2020
Oral generic tacrolimus initiation and substitution in the Medicaid population: a new user cohort study.
Current medical research and opinion. 36(9):1533-1540 [DOI] 10.1080/03007995.2020.1793750. [PMID] 32644886.
2020
powmic: an R package for power assessment in microbiome case-control studies.
Bioinformatics (Oxford, England). 36(11):3563-3565 [DOI] 10.1093/bioinformatics/btaa197. [PMID] 32186690.
2019
A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies.
Nature communications. 10(1) [DOI] 10.1038/s41467-019-09639-3. [PMID] 30967541.
2019
Destin: toolkit for single-cell analysis of chromatin accessibility.
Bioinformatics (Oxford, England). 35(19):3818-3820 [DOI] 10.1093/bioinformatics/btz141. [PMID] 30821321.
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 & administrative pharmacy : RSAP. 15(12):1453-1463 [DOI] 10.1016/j.sapharm.2019.01.006. [PMID] 30777645.
2019
TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction.
Bioinformatics (Oxford, England). 35(9):1573-1575 [DOI] 10.1093/bioinformatics/bty872. [PMID] 30304335.
2018
A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data.
Frontiers in microbiology. 9 [DOI] 10.3389/fmicb.2018.03112. [PMID] 30619188.
2018
Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons.
Molecular cell. 71(5):848-857.e6 [DOI] 10.1016/j.molcel.2018.07.005. [PMID] 30078725.
2018
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data.
PeerJ. 6 [DOI] 10.7717/peerj.4600. [PMID] 29629248.
2018
Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model.
Frontiers in microbiology. 9 [DOI] 10.3389/fmicb.2018.01391. [PMID] 29997602.
2018
Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice.
Cell reports. 25(11):3194-3203.e4 [DOI] 10.1016/j.celrep.2018.11.061. [PMID] 30540950.
2017
DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress.
Nature communications. 8(1) [DOI] 10.1038/s41467-017-01195-y. [PMID] 29066820.
2017
Omicseq: a web-based search engine for exploring omics datasets.
Nucleic acids research. 45(W1):W445-W452 [DOI] 10.1093/nar/gkx258. [PMID] 28402462.
2017
Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis.
Nature communications. 8 [DOI] 10.1038/ncomms15903. [PMID] 28660881.
2017
Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells.
Nature communications. 8 [DOI] 10.1038/ncomms15102. [PMID] 28440315.
2017
Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale.
BMC research notes. 10(1) [DOI] 10.1186/s13104-017-2851-y. [PMID] 29084591.
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 [PMID] 27005421.
2016
DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles.
Genome biology. 17(1) [PMID] 27923386.
2016
Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress.
Neurobiology of disease. 86:99-108 [DOI] 10.1016/j.nbd.2015.11.010. [PMID] 26598390.
2016
Molecular signatures associated with ZIKV exposure in human cortical neural progenitors.
Nucleic acids research. 44(18):8610-8620 [PMID] 27580721.
2016
Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress.
Neurobiology of disease. 96:54-66 [DOI] 10.1016/j.nbd.2016.08.014. [PMID] 27576189.
2016
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.
Bioinformatics (Oxford, England). 32(8):1214-6 [DOI] 10.1093/bioinformatics/btv741. [PMID] 26685307.
2015
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.
Bioinformatics (Oxford, England). 31(12):1889-96 [DOI] 10.1093/bioinformatics/btv094. [PMID] 25682068.
2015
Altering 5-hydroxymethylcytosine modification impacts ischemic brain injury.
Human molecular genetics. 24(20):5855-66 [DOI] 10.1093/hmg/ddv307. [PMID] 26231219.
2015
Combined Loss of Tet1 and Tet2 Promotes B Cell, but Not Myeloid Malignancies, in Mice.
Cell reports. 13(8):1692-704 [DOI] 10.1016/j.celrep.2015.10.037. [PMID] 26586431.
2015
Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.
Nucleic acids research. 43(21) [DOI] 10.1093/nar/gkv715. [PMID] 26184873.
2015
glmgraph: an R package for variable selection and predictive modeling of structured genomic data.
Bioinformatics (Oxford, England). 31(24):3991-3 [DOI] 10.1093/bioinformatics/btv497. [PMID] 26315909.
2015
Small Molecules Efficiently Reprogram Human Astroglial Cells into Functional Neurons.
Cell stem cell. 17(6):735-747 [DOI] 10.1016/j.stem.2015.09.012. [PMID] 26481520.
2014
Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma.
Cancer informatics. 13(Suppl 2):49-53 [DOI] 10.4137/CIN.S13783. [PMID] 25288879.
2011
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.
Bioinformatics (Oxford, England). 27(10):1447-8 [DOI] 10.1093/bioinformatics/btr156. [PMID] 21450710.

Education

PhD/Computer Science and Informatics
2017 · Emory University
MS/Biostatistics
2011 · Johns Hopkins University
MS/Computer Science
2011 · Johns Hopkins University

Contact Details

Phones:
Business:
(352) 294-5909
Emails:
Business:
li.chen1@ufl.edu
Addresses:
Business Street:
CTRB 5th Floor
2004 Mowry Road
GAINESVILLE FL 32611