Li Chen,
Associate Professor
About Li Chen
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.
Related Links:
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
2023-2024
HSC4970 Public Health and Health Professions Senior Honors Thesis
2023-2024
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