李洪东

2025

Improving Cancer Gene Prediction by Enhancing Common Information Between the PPI Network and Gene Functional Association

Proceedings of the AAAI Conference on Artificial Intelligence

DOI

2025

Inspired by pathogenic mechanisms: A novel gradual multi-modal fusion framework for mild cognitive impairment diagnosis

Neural Networks

DOI

2025

ChromNet: A Multi‐Task Learning Framework for Cross‐Cell Type Prediction of 3D Chromatin Interactions Using Epigenetic Signals

Advanced Science

DOI

2025

Multiomics analysis uncovers subtype-specific mechanisms and biomarkers in idiopathic inflammatory myopathies

Annals of the Rheumatic Diseases

DOI

2025

diPaRIS: Dynamic and Interpretable Protein‐RNA Interactions Prediction With U‐Shaped Network and Novel Structure Encoding

Advanced Science

DOI

2024

A Survey on the Feedback Mechanism of LLM-based AI Agents

DOI

2024

LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes

Briefings in Bioinformatics

DOI

2024

MVFormer: Predicting the pathogenicity of missense variants using gated transformers

ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)

DOI

2024

Multi-Task Learning for Alzheimer's Disease Diagnosis and Mini-Mental State Examination Score Prediction

Big Data Mining and Analytics

DOI

2024

Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks

Bioinformatics

DOI

2024

Faster Stochastic Variance Reduction Methods for Compositional MiniMax Optimization

Proceedings of the AAAI Conference on Artificial Intelligence

DOI

2024

Alternative splicing and intron retention: Their profiles and roles in cutaneous fibrosis of systemic sclerosis

Journal of Autoimmunity

DOI

2024

scCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data

Nature Communications

DOI

2024

Characterised intron retention profiles in muscle tissue of idiopathic inflammatory myopathy subtypes

Annals of the Rheumatic Diseases

DOI

2024

Training Methods of Innovative Talents in Medical Imaging Informatics Under the Background of New Engineering

Communications in computer and information science

DOI

2024

Enhancing Database Principles Teaching with ChatGPT-Like Language Models

Communications in computer and information science

DOI

2023

Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease Diagnosis

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2023

FEED: a feature selection method based on gene expression decomposition for single cell clustering

Briefings in Bioinformatics

DOI

2023

IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions

Bioinformatics

DOI

2023

CellBRF: a feature selection method for single-cell clustering using cell balance and random forest

Bioinformatics

DOI

2023

Computational approaches for detecting disease-associated alternative splicing events

Briefings in Bioinformatics

DOI

2023

DeepRetention: A Deep Learning Approach for Intron Retention Detection

Big Data Mining and Analytics

DOI

2023

Artificial intelligence approaches for molecular representation in drug response prediction

Current Opinion in Structural Biology

DOI

2022

An Alzheimer’s disease gene prediction method based on ensemble of genome-wide association study summary statistics

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2022

KL-RF: Predicting disease-gene associations with model fusion

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2022

A Gene Set-Integrated Approach for Predicting Disease-Associated Genes

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2022

GTFtools: a software package for analyzing various features of gene models

Bioinformatics

DOI

2022

A comparison of computational approaches for intron retention detection

Big Data Mining and Analytics

DOI

2022

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

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2022

AlzCode: a platform for multiview analysis of genes related to Alzheimer’s disease

Bioinformatics

DOI

2021

“人工智能+X”背景下生物信息学方向科技创新人才培养体系探索与实践

《工业和信息化教育》

2021

GraphIsoFun: a graph neural network based approach for splice isoform function prediction

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2021

Improving the Prediction of Disease-associated Genes by Integrating Annotated Gene Sets

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2021

An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer’s disease

Briefings in Bioinformatics

DOI

2021

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

Briefings in Bioinformatics

DOI

2021

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

Nucleic Acids Research

DOI

2021

Reform and Practice of Open Teaching Mode Based on Innovation Ability Training

International Conference on Computer Science & Education (ICCSE)

DOI

2021

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

Frontiers in Genetics

DOI

2021

Integrative and sparse singular value decomposition method for biclustering analysis in multi-sources dataset

Chemometrics and Intelligent Laboratory Systems

DOI

2021

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

Alzheimer s & Dementia

DOI

2020

Joint Learning of Primary and Secondary Labels based on Multi-scale Representation for Alzheimer’s Disease Diagnosis

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2020

Identification of Disease-Associated Genes Based on Differential Intron Retention

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2020

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

Journal of Bioinformatics and Computational Biology

DOI

2020

IsoDetect: Detection of Splice Isoforms from Third Generation Long Reads Based on Short Feature Sequences

Current Bioinformatics

DOI

2020

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

EMBO Reports

DOI

2020

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

Frontiers in Genetics

DOI

2020

Intron Retention as a Mode for RNA-Seq Data Analysis

Frontiers in Genetics

DOI

2020

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

Interdisciplinary Sciences Computational Life Sciences

DOI

2019

A Global Similarity Learning for Clustering of Single-Cell RNA-Seq Data

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2019

A Gene Rank Based Approach for Single Cell Similarity Assessment and Clustering

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2019

Collaboration patterns and network in chemometrics

Chemometrics and Intelligent Laboratory Systems

DOI

2019

Trim33 is required for appropriate development of pre-cardiogenic mesoderm

Developmental Biology

DOI

2019

An overview of variable selection methods in multivariate analysis of near-infrared spectra

TrAC Trends in Analytical Chemistry

DOI

2019

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

Genes

DOI

2019

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

Genes

DOI

2018

生物信息学研究进展

《玉林师范学院学报》

2018

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

Bioinformatics

DOI

2018

BioRank: A Similarity Assessment Method for Single Cell Clustering

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2018

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

Current Bioinformatics

DOI

2018

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

BMC Systems Biology

DOI

2018

Chemometrics in instrumental analysis of complex systems—in honor and memory of Yi‐Zeng Liang

Journal of Chemometrics

DOI

2018

libPLS: An integrated library for partial least squares regression and linear discriminant analysis

Chemometrics and Intelligent Laboratory Systems

DOI

2018

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

Translational Psychiatry

DOI

2017

An interpretable model for predicting side effects of analgesics for osteoarthritis

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI

2017

A selective review and comparison for interval variable selection in spectroscopic modeling

Chemometrics and Intelligent Laboratory Systems

DOI

2017

In honor of Professor Yizeng Liang (May 1950–Oct. 2016): A scientist of passion and innovation

Chemometrics and Intelligent Laboratory Systems

DOI

2017

A phase diagram for gene selection and disease classification

Chemometrics and Intelligent Laboratory Systems

DOI

2016

A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling

Briefings Bioinform.

DOI

2015

MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse

Database J. Biol. Databases Curation

DOI

2014

Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation

Bioinform.

DOI

2013

A strategy that iteratively retains informative variables for selecting optimal variable subset in multivariate calibration

Analytica Chimica Acta

DOI

2013

Analysis of the raw serum peptidomic pattern in glioma patients

Clinica Chimica Acta

DOI

2013

An efficient method of wavelength interval selection based on random frog for multivariate spectral calibration

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy

DOI

2013

The continuity of sample complexity and its relationship to multivariate calibration: A general perspective on first-order calibration of spectral data in analytical chemistry

Chemometrics and Intelligent Laboratory Systems

DOI

2013

A perspective demonstration on the importance of variable selection in inverse calibration for complex analytical systems

The Analyst

DOI

2013

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data

PLoS Comput. Biol.

DOI

2012

A model population analysis method for variable selection based on mutual information

Chemometrics and Intelligent Laboratory Systems

DOI

2012

Human Plasma Metabolic Profiles of Coronary Heart Disease by Gas Chromatography-Mass Spectrometry with Monte Carlo Tree Approach

Analytical Letters

DOI

2012

Random frog: An efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification

Analytica Chimica Acta

DOI

2012

GC–MS Based Serum Metabolomic Analysis of Isoflurane-Induced Postoperative Cognitive Dysfunctional Rats: Biomarker Screening and Insight into Possible Pathogenesis

Chromatographia

DOI

2012

Variable complementary network: a novel approach for identifying biomarkers and their mutual associations

Metabolomics

DOI

2012

Model-population analysis and its applications in chemical and biological modeling

TrAC Trends in Analytical Chemistry

DOI

2011

Recipe for uncovering predictive genes using support vector machines based on model population analysis

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2011

Application of Competitive Adaptive Reweighted Sampling Method to Determine Effective Wavelengths for Prediction of Total Acid of Vinegar

Food Analytical Methods

DOI

2011

Elastic Net Grouping Variable Selection Combined with Partial Least Squares Regression (EN-PLSR) for the Analysis of Strongly Multi-collinear Spectroscopic Data

Applied Spectroscopy

DOI

2011

Noise incorporated subwindow permutation analysis for informative gene selection using support vector machines

The Analyst

DOI

2010

A metabolic profiling strategy for biomarker screening by GC-MS combined with multivariate resolution method and Monte Carlo PLS-DA

Analytical Methods

DOI

2010

Uncover the path from PCR to PLS via elastic component regression

Chemometrics and Intelligent Laboratory Systems

DOI

2010

Model population analysis for variable selection

Journal of Chemometrics

DOI

2010

Recipe for revealing informative metabolites based on model population analysis

Metabolomics

DOI

2010

GC–MS Combined with Chemometrics for Analysis of the Components of the Essential Oils of Sweet Potato Leaves

Chromatographia

DOI

2010

Plasma metabolic fingerprinting of childhood obesity by GC/MS in conjunction with multivariate statistical analysis

Journal of Pharmaceutical and Biomedical Analysis

DOI

2010

Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis

BMC Systems Biology

DOI

2009

Identification of free fatty acids profiling of type 2 diabetes mellitus and exploring possible biomarkers by GC–MS coupled with chemometrics

Metabolomics

DOI

2009

Essential Oil Composition of Osmanthus fragrans Varieties by GC-MS and Heuristic Evolving Latent Projections

Chromatographia

DOI

2009

Key wavelengths screening using competitive adaptive reweighted sampling method for multivariate calibration

Analytica Chimica Acta

DOI

2008

Support vector machines and its applications in chemistry

Chemometrics and Intelligent Laboratory Systems

DOI

2007

Comparative analysis of essential oil components in Pericarpium Citri Reticulatae Viride and Pericarpium Citri Reticulatae by GC–MS combined with chemometric resolution method

Journal of Pharmaceutical and Biomedical Analysis

DOI

2026

stEDGE enables edge-guided multiscale reconstruction of hierarchical spatial domains and transition interfaces in spatial transcriptomics

bioRxiv (Cold Spring Harbor Laboratory)

DOI

2025

Inference and visualization of multi-scale cell tree for decoding functional diversity with scMustree

bioRxiv (Cold Spring Harbor Laboratory)

DOI

2021

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

bioRxiv (Cold Spring Harbor Laboratory)

DOI

2020

Functional Gene Networks and Their Applications

Computational biology

DOI