37 Publications (Page 1 of 2)
2024
Deep5hmC: Predicting genome-wide 5-Hydroxymethylcytosine landscape via a multimodal deep learning model
Ma, Xin⋅Ma, Xin⋅Thela, Sai Ritesh⋅Thela, Sai Ritesh⋅Zhao, Fengdi⋅Zhao, Fengdi⋅Yao, Bing⋅Yao, Bing⋅Wen, Zhexing⋅Wen, Zhexing⋅Jin, Peng⋅Jin, Peng⋅Zhao, Jinying⋅Zhao, Jinying⋅Chen, Li and Chen, Li
Bioinformatics (Oxford, England), Aug 28, 2024. | Journal Article
 
MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants
Jin, Weijia⋅Jin, Weijia⋅Jin, Weijia⋅Xia, Yi⋅Xia, Yi⋅Xia, Yi⋅Nizomov, Javlon⋅Nizomov, Javlon⋅Nizomov, Javlon⋅Liu, Yunlong⋅Liu, Yunlong⋅Liu, Yunlong⋅Li, Zhigang⋅Li, Zhigang⋅Li, Zhigang⋅Lu, Qing⋅Lu, Qing⋅Lu, Qing⋅Chen, Li⋅Chen, Li and Chen, Li
Bioinformatics (Oxford, England), Sep 26, 2024. | Journal Article
 
scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data
Zhao, Fengdi⋅Zhao, Fengdi⋅Ma, Xin⋅Ma, Xin⋅Yao, Bing⋅Yao, Bing⋅Lu, Qing⋅Lu, Qing⋅Chen, Li and Chen, Li
PLoS computational biology, vol. 20, (no. 8), pp. e1011854, Aug 2024. | Journal Article
2023
TIVAN-indel: A computational framework for annotating and predicting noncoding regulatory small insertions and deletions.
Agarwal, Aman⋅Zhao, Fengdi⋅Jiang, Yuchao and Chen, Li
Bioinformatics (Oxford, England), January 27, 2023. | Journal Article
2022
Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation
Li, Yangping⋅Li, Yangping⋅Wang, Feng⋅Wang, Feng⋅Teng, Peng⋅Teng, Peng⋅Ku, Li⋅Ku, Li⋅Chen, Li⋅Chen, Li⋅Feng, Yue⋅Feng, Yue⋅Yao, Bing and Yao, Bing
Genome Biology, vol. 23, pp. 1-27, 2022. | Journal Article
 
DeepPerVar: a multimodal deep learning framework for functional interpretation of genetic variants in personal genome.
Wang, Ye and Chen, Li
Bioinformatics (Oxford, England), October 22, 2022. | Journal Article
 
DeepPHiC: Predicting promoter-centered chromatin interactions using a novel deep learning approach.
Agarwal, Aman and Chen, Li
Bioinformatics (Oxford, England), December 10, 2022. | Journal Article
 
Early Wnt signaling activation promotes inner ear differentiation via cell caudalization in mouse stem cell-derived organoids.
Tang, Pei-Ciao⋅Chen, Li⋅Singh, Sunita⋅Groves, Andrew K⋅Koehler, Karl R⋅Liu, Xue Zhong and Nelson, Rick F
Stem cells (Dayton, Ohio), September 25, 2022. | Journal Article
 
Exploiting deep transfer learning for the prediction of functional noncoding variants using genomic sequence.
Chen, Li and Wang, Ye
Bioinformatics (Oxford, England), April 7, 2022. | Journal Article
 
Using Machine Learning Approaches to Predict Short-Term Risk of Cardiotoxicity Among Patients with Colorectal Cancer After Starting Fluoropyrimidine-Based Chemotherapy
Li, Chao and Chen, Li
Cardiovascular Toxicology, vol. 22, (no. 2), pp. 130-140, Feb 2022. | Journal Article
2021
Patient factors associated with oral generic olanzapine initiation and substitution among Medicaid beneficiaries: a new user cohort study.
Mishuk, Ahmed Ullah⋅Chen, Li⋅Li, Chao⋅Huo, Nan⋅Hansen, Richard A⋅Harris, Ilene⋅Kiptanui, Zippora and Qian, Jingjing
Current medical research and opinion, vol. 37, (no. 4), pp. 655-664, April 2021. | Journal Article
 
Risk Factors of Fluoropyrimidine Induced Cardiotoxicity Among Cancer Patients: A Systematic Review and Meta-analysis.
Li, Chao⋅Ngorsuraches, Surachat⋅Chou, Chiahung⋅Chen, Li and Qian, Jingjing
Critical reviews in oncology/hematology, pp. 103346, April 27, 2021. | Journal Article
 
Ten-eleven translocation protein 1 modulates medulloblastoma progression.
Kim, Hyerim⋅Kim, Hyerim⋅Kang, Yunhee⋅Kang, Yunhee⋅Li, Yujing⋅Li, Yujing⋅Chen, Li⋅Chen, Li⋅Lin, Li⋅Lin, Li⋅Johnson, Nicholas D⋅Johnson, Nicholas D⋅Zhu, Dan⋅Zhu, Dan⋅Robinson, M Hope⋅Robinson, M Hope⋅McSwain, Leon⋅McSwain, Leon⋅Barwick, Benjamin G⋅Barwick, Benjamin G⋅Yuan, Xianrui⋅Yuan, Xianrui⋅Liao, Xinbin⋅Liao, Xinbin⋅Zhao, Jie⋅Zhao, Jie⋅Zhang, Zhiping⋅Zhang, Zhiping⋅Shu, Qiang⋅Shu, Qiang⋅Chen, Jianjun⋅Chen, Jianjun⋅Allen, Emily G⋅Allen, Emily G⋅Kenney, Anna M⋅Kenney, Anna M⋅Castellino, Robert C⋅Castellino, Robert C⋅Van Meir, Erwin G⋅Van Meir, Erwin G⋅Conneely, Karen N⋅Conneely, Karen N⋅Vertino, Paula M⋅Vertino, Paula M⋅Jin, Peng⋅Jin, Peng⋅Li, Jian and Li, Jian
Genome biology, vol. 22, (no. 1), pp. 125, April 29, 2021. | Journal Article
 
Using Machine Learning Approaches to Predict Short-Term Risk of Cardiotoxicity Among Patients with Colorectal Cancer After Starting Fluoropyrimidine-Based Chemotherapy.
Li, Chao⋅Chen, Li⋅Chou, Chiahung⋅Ngorsuraches, Surachat and Qian, Jingjing
Cardiovascular toxicology, November 18, 2021. | Journal Article
 
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.
Y, Wang⋅Wang, Ye⋅Wang, Ye⋅Jiang, Yuchao⋅Jiang, Yuchao⋅Y, Jiang⋅Yao, Bing⋅B, Yao⋅Yao, Bing⋅Huang, Kun⋅K, Huang⋅Huang, Kun⋅Liu, Yunlong⋅Y, Liu⋅Liu, Yunlong⋅Wang, Yue⋅Wang, Yue⋅Y, Wang⋅Qin, Xiao⋅Qin, Xiao⋅X, Qin⋅Saykin, Andrew J⋅AJ, Saykin⋅Saykin, Andrew J⋅Chen, Li⋅L, Chen and Chen, Li
Briefings in bioinformatics, vol. 22, (no. 6), November 5, 2021. | Journal Article
2020
A novel deep learning method for predictive modeling of microbiome data.
Wang, Ye⋅Wang, Ye⋅Bhattacharya, Tathagata⋅Bhattacharya, Tathagata⋅Jiang, Yuchao⋅Jiang, Yuchao⋅Qin, Xiao⋅Qin, Xiao⋅Wang, Yue⋅Wang, Yue⋅Liu, Yunlong⋅Liu, Yunlong⋅Saykin, Andrew J⋅Saykin, Andrew J⋅Chen, Li and Chen, Li
Briefings in bioinformatics, May 14, 2020. | Journal Article
 
Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules.
Yang, Guodong⋅Ma, Aiqun⋅Qin, Zhaohui S and Chen, Li
Bioinformatics (Oxford, England), January 3, 2020. | Journal Article
 
Generic escitalopram initiation and substitution among Medicare beneficiaries: A new user cohort study.
Li, Chao⋅Li, Chao⋅Li, Chao⋅Li, Chao⋅Chen, Li⋅Chen, Li⋅Chen, Li⋅Chen, Li⋅Huo, Nan⋅Huo, Nan⋅Huo, Nan⋅Huo, Nan⋅Mishuk, Ahmed U⋅Mishuk, Ahmed Ullah⋅Mishuk, Ahmed Ullah⋅Mishuk, Ahmed Ullah⋅Hansen, Richard A⋅Hansen, Richard A⋅Hansen, Richard A⋅Hansen, Richard A⋅Harris, Ilene⋅Harris, Ilene⋅Harris, Ilene⋅Harris, Ilene⋅Kiptanui, Zippora⋅Kiptanui, Zippora⋅Kiptanui, Zippora⋅Kiptanui, Zippora⋅Wang, Zhong⋅Wang, Zhong⋅Wang, Zhong⋅Wang, Zhong⋅Qian, Jingjing⋅Qian, Jingjing⋅Qian, Jingjing and Qian, Jingjing
PloS one, vol. 15, (no. 4), pp. e0232226, 2020. | Journal Article
 
Generic levothyroxine initiation and substitution among Medicare and Medicaid populations: a new user cohort study.
Huo, Nan⋅Huo, Nan⋅Chen, Li⋅Chen, Li⋅Ullah Mishuk, Ahmed⋅Ullah Mishuk, Ahmed⋅Li, Chao⋅Li, Chao⋅Hansen, Richard A⋅Hansen, Richard A⋅Harris, Ilene⋅Harris, Ilene⋅Kiptanui, Zippora⋅Kiptanui, Zippora⋅Wang, Zhong⋅Wang, Zhong⋅Dutcher, Sarah K⋅Dutcher, Sarah K⋅Qian, Jingjing and Qian, Jingjing
Endocrine, vol. 68, (no. 2), pp. 336-348, May 2020. | Journal Article
 
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines.
Mei, W⋅Mei, Wenwen⋅Jiang, Zhiwen⋅Jiang, Z⋅Chen, Y⋅Chen, Yang⋅Chen, L⋅Chen, Li⋅Sancar, Aziz⋅Sancar, A⋅Jiang, Y and Jiang, Yuchao
Briefings in bioinformatics, July 16, 2020. | Journal Article
 
Interactions of the Skin Pathogen Haemophilus ducreyi With the Human Host.
Brothwell, Julie A⋅Griesenauer, Brad⋅Chen, Li and Spinola, Stanley M
Frontiers in immunology, vol. 11, pp. 615402, 2020. | Journal Article
 
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
Mitra, Amit K⋅Mitra, Amit K⋅Mitra, Amit Kumar⋅Kumar, Harish⋅Kumar, Harish⋅Kumar, Harish⋅Ramakrishnan, Vijay⋅Chen, Li⋅Chen, Li⋅Chen, Li⋅Baughn, Linda⋅Baughn, Linda⋅Baughn, Linda⋅Kumar, Shaji⋅Kumar, Shaji⋅Kumar, Shaji⋅Vincent, Rajkumar S⋅Vincent, Rajkumar S⋅Rajkumar, S Vincent⋅Van Ness, Brian G⋅ and
Blood Cancer Journal, vol. 10, (no. 7), Jul 2020. | Journal Article
 
Oral generic tacrolimus initiation and substitution in the Medicaid population: a new user cohort study.
Chen, Li⋅Li, Chao⋅Huo, Nan⋅Mishuk, Ahmed Ullah⋅Hansen, Richard A⋅Harris, Ilene⋅Kiptanui, Zippora and Qian, Jingjing
Current medical research and opinion, pp. 1, July 9, 2020. | Journal Article
 
powmic: an R package for power assessment in microbiome case-control studies.
Chen, Li
Bioinformatics (Oxford, England), March 18, 2020. | Journal Article
2019
A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies
Sun, Zhe⋅Sun, Zhe⋅Sun, Zhe⋅Sun, Zhe⋅Sun, Zhe⋅Sun, Zhe⋅Chen, Li⋅Chen, Li⋅Chen, Li⋅Chen, Li⋅Chen, Li⋅Chen, Li⋅Xin, Hongyi⋅Xin, Hongyi⋅Xin, Hongyi⋅Xin, Hongyi⋅Xin, Hongyi⋅Jiang, Yale⋅Jiang, Yale⋅Jiang, Yale⋅Jiang, Yale⋅Jiang, Yale⋅Jiang, Yale⋅Huang, Qianhui⋅Huang, Qianhui⋅Huang, Qianhui⋅Huang, Qianhui⋅Huang, Qianhui⋅Cillo, Anthony R⋅Cillo, Anthony R⋅Cillo, Anthony R⋅Cillo, Anthony R⋅Cillo, Anthony R⋅Cillo, Anthony R⋅Tabib, Tracy⋅Tabib, Tracy⋅Tabib, Tracy⋅Tabib, Tracy⋅Tabib, Tracy⋅Kolls, Jay K⋅Kolls, Jay K⋅Kolls, Jay K⋅Kolls, Jay K⋅Kolls, Jay K⋅Kolls, Jay K⋅Bruno, Tullia C⋅Bruno, Tullia C⋅Bruno, Tullia C⋅Bruno, Tullia C⋅Bruno, Tullia C⋅Bruno, Tullia C⋅Lafyatis, Robert⋅Lafyatis, Robert⋅Lafyatis, Robert⋅Lafyatis, Robert⋅Lafyatis, Robert⋅Lafyatis, Robert⋅⋅Vignali, Dario A A⋅Vignali, Dario A A⋅Vignali, Dario A A⋅Vignali, Dario A A⋅Vignali, Dario A A⋅Chen, Kong⋅Chen, Kong⋅Chen, Kong⋅Chen, Kong⋅Chen, Kong⋅Chen, Kong⋅Ding, Ying⋅Ding, Ying⋅Ding, Ying⋅Ding, Ying⋅Ding, Ying⋅Ding, Ying⋅Hu, Ming⋅Hu, Ming⋅Hu, Ming⋅Hu, Ming⋅Hu, Ming⋅Hu, Ming⋅Chen, Wei⋅Chen, Wei⋅Chen, Wei⋅Chen, Wei⋅Chen, Wei and Chen, Wei
Nature communications, vol. 10, (no. 1), pp. 1649, 2019-04-09. | Journal Article