Hong-Dong Li

发表

Functional Gene Networks and Their Applications

Yuanfang Guan, Hong-Dong Li, Y. Guan, 2020 .

Brain-specific functional relationship networks inform autism spectrum disorder gene prediction

Yuanfang Guan, Margit Burmeister, Dennis P. Wall, 2018, Translational Psychiatry.

ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets.

G. Omenn, Hong-Dong Li, QUAN LIU, 2020, Journal of bioinformatics and computational biology.

The emerging era of genomic data integration for analyzing splice isoform function.

Y. Guan, G. Omenn, Hong-Dong Li, 2014, Trends in genetics : TIG.

Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.

Yang Zhang, Y. Guan, G. Omenn, 2015, Journal of proteome research.

Sc-GPE: A Graph Partitioning-Based Cluster Ensemble Method for Single-Cell

Hong-Dong Li, Jianxin Wang, Xiaoshu Zhu, 2020, Frontiers in Genetics.

Analysis of Single-Cell RNA-seq Data by Clustering Approaches

Hong-Dong Li, Fang-Xiang Wu, Xiaoshu Zhu, 2019, Current Bioinformatics.

RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest

Hong-Dong Li, Yunpei Xu, Yuan Zhao, 2021, Frontiers in Genetics.

Intron Retention as a Mode for RNA-Seq Data Analysis

Hong-Dong Li, Zhao-Yu Fang, Cui-Xiang Lin, 2020, Frontiers in Genetics.

Modeling the functional relationship network at the splice isoform level through heterogeneous data integration

Yang Zhang, Y. Guan, G. Omenn, 2014, bioRxiv.

Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.

Yang Zhang, Y. Guan, G. Omenn, 2017, Methods in molecular biology.

A Network of Splice Isoforms for the Mouse

Yang Zhang, Y. Guan, G. Omenn, 2016, Scientific Reports.

Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence

Y. Guan, G. Omenn, Hong-Dong Li, 2014, Proteomics.

An interpretable boosting model to predict side effects of analgesics for osteoarthritis

Yi Pan, Min Li, Jianxin Wang, 2018, BMC Systems Biology.

Modeling the functional relationship network at the isoform level through heterogeneous data integration

Yang Zhang, Y. Guan, G. Omenn, 2014 .

Trim33 is required for appropriate development of pre-cardiogenic mesoderm.

Hong-Dong Li, V. Kaartinen, Y. Mishina, 2019, Developmental biology.

Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning.

Yuanfang Guan, Gilbert S Omenn, Bharat Panwar, 2016, Journal of proteome research.

Yi Pan, Feng Luo, Jianxin Wang, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Single-Cell Clustering Based on Shared Nearest Neighbor and Graph Partitioning

Hong-Dong Li, Yunpei Xu, Xiaoshu Zhu, 2020, Interdisciplinary Sciences: Computational Life Sciences.

A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data

Xiaoshu Zhu, Fang-Xiang Wu, Jianxin Wang, 2019, Genes.

REBET: a method to determine the number of cell clusters based on batch effect removal

Qingsong Xu, Hong-Dong Li, Yunpei Xu, 2021, Briefings Bioinform..

Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease

Cory C. Funk, N. Price, G. Omenn, 2021, Alzheimer's & dementia : the journal of the Alzheimer's Association.

ClusterMine: a Knowledge-integrated Clustering Approach based on Expression Profiles of Gene Sets

Xiaoshu Zhu, Quan Liu, Jianxin Wang, 2018, bioRxiv.

Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics

Fang-Xiang Wu, Xiaoqing Peng, Jianxin Wang, 2020, Briefings Bioinform..

IsoCell: An Approach to Enhance Single Cell Clustering by Integrating Isoform-Level Expression Through Orthogonal Projection

Y. Liu, Hong-Dong Li, Yunpei Xu, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A Comparison of Topologically Associating Domain Callers Based on Hi-C Data

Hong-Dong Li, Yaohang Li, Jianxin Wang, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

iREAD: a tool for intron retention detection from RNA-seq data

Nathan D. Price, Cory C. Funk, Hong-Dong Li, 2017, BMC Genomics.

Identification of Disease-Associated Genes Based on Differential Intron Retention

Hong-Dong Li, Zhenpeng Wu, Jiantao Zheng, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data

Y. Guan, Hong-Dong Li, Jianxin Wang, 2021, Nucleic Acids Res..

Genome-wide prediction and integrative functional characterization of Alzheimer’s disease-associated genes

Hong-Dong Li, B. Hu, Fang-Xiang Wu, 2021, bioRxiv.

BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets

Yuanfang Guan, Margit Burmeister, Hong-Dong Li, 2018, Bioinform..

Genetic variants in PLG, LPA, and SIGLEC 14 as well as smoking contribute to plasma plasminogen levels.

Jun Z. Li, Y. Guan, Hong-Dong Li, 2014, Blood.

A splicing factor switch controls hematopoietic lineage specification of pluripotent stem cells

Hong-Dong Li, E. Bresnick, Jinhua Liu, 2020, EMBO reports.

Identification of Stage‐Specific Genes Associated With Lupus Nephritis and Response to Remission Induction in (NZB × NZW)F1 and NZM2410 Mice

Yuanfang Guan, Matthias Kretzler, Ridvan Eksi, 2014, Arthritis & rheumatology.

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads

Jianxin Wang, Xingyu Liao, Wenjing Zhang, 2019, Genes.

IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation

Jianxin Wang, Fang-Xiang Wu, Zhimin Zhang, 2020, Bioinform..

A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data

Hong-Dong Li, Fang-Xiang Wu, Guihua Duan, 2019, Genes.

Single-Cell Clustering Based on Shared Nearest Neighbor and Graph Partitioning

Jianxin Wang, Jie Zhang, Xiaoshu Zhu, 2020, Interdisciplinary Sciences: Computational Life Sciences.