古槿

2026

A hybrid neighborhood enhanced contrastive learning and self-knowledge distillation method for scRNA-seq data clustering analysis

Bioinform.

DOI

2026

Identifying prognosis-associated spatial patterns by integrating bulk RNA-seq and spatial transcriptomic data.

IEEE transactions on computational biology and bioinformatics

DOI

2026

scCT: Mapping Single-Cell Data to Human Reference Atlases to Identify Deviated Cell States

International Symposium on Bioinformatics Research and Applications

DOI

2026

SpatialZoomer: multi-scale feature analysis of spatial transcriptomics

Nature Biomedical Engineering

DOI

2026

Remodeling the pancreatic tumor microenvironment by chemotherapy: New opportunities for combination therapy

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer

DOI

2026

A single-cell feature selection method based on subspace and minimum redundancy, applicable to multi-omics

Pattern Recognition

DOI

2025

[Review] Assisted diagnosis of neuropsychiatric disorders based on functional connectivity: A survey on application and performance evaluation of graph neural network

Expert Systems With Applications，Vol. 265

DOI

2025

Predicting drug‐perturbed transcriptional responses using multi‐conditional diffusion transformer

Quant. Biol.

DOI

2025

uniLIVER: a human liver cell atlas for data-driven cellular state mapping

Journal of genetics and genomics/Journal of Genetics and Genomics

DOI

2025

scTrace+: Enhancing cell fate inference by integrating the lineage-tracing and multi-faceted transcriptomic similarity information.

Cell Systems

DOI

2025

ViTrace detects viral signatures in tumor transcriptomes using a hybrid language model

Communications Biology

DOI

2025

GeST: Towards Building A Generative Pretrained Transformer for Learning Cellular Spatial Context

bioRxiv

DOI

2025

Decipher the single-cell level responses to chemotherapy in pancreatic ductal adenocarcinoma by a cross-time context graph model.

Cancer Letters

DOI

2025

Multi-omic analysis of gallbladder cancer identifies distinct tumor microenvironments associated with disease progression

Nature Genetics

DOI

2025

HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells

Genomics, Proteomics & Bioinformatics

DOI

2025

Computational modeling of single-cell dynamics data

Briefings Bioinform.

DOI

2025

BCMA: An integrative and versatile database for multi-scale and multi-omics molecular atlas of breast cancer

Computational and Structural Biotechnology Journal

DOI

2025

scLT-kit: a versatile toolkit for automated processing and analysis of single-cell lineage tracing data

Frontiers of Computer Science

DOI

2025

A Multi‐Scale Residual Network Based on Kolmogorov–Arnold Networks Combined With Raman Spectroscopy for Rapid Diagnosis of Membranous Glomerulonephritis

Journal of Raman Spectroscopy

DOI

2025

A single-cell RNA sequencing data imputation method based on non-negative matrix factorization and multi-kernel similarity network fusion

Engineering Applications of Artificial Intelligence

DOI

2025

High-order graph convolutional networks for circular Ribonucleic Acid and disease association prediction incorporating multiple biological relationships

Engineering Applications of Artificial Intelligence

DOI

2024

CancerSRT: a spatially resolved transcriptomics database for human cancers.

Journal of genetics and genomics = Yi chuan xue bao

DOI

2024

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes

Genome Biology

DOI

2024

Deep whole-genome analysis of 494 hepatocellular carcinomas

Nature

DOI

2024

HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

Genomics, Proteomics & Bioinformatics

DOI

2024

STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning

Communications Biology

DOI

2024

Disentangled global and local features of multi-source data variational autoencoder: An interpretable model for diagnosing IgAN via multi-source Raman spectral fusion techniques

Artificial Intelligence in Medicine

DOI

2023

Building digital life systems for future biology and medicine

Quantitative Biology

DOI

2023

scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution

bioRxiv

DOI

2023

Single-cell and spatially resolved transcriptomics for liver biology.

Hepatology

DOI

2023

Decoding functional cell–cell communication events by multi-view graph learning on spatial transcriptomics

Briefings in Bioinformatics

DOI

2023

Integrated transcriptome study of the tumor microenvironment for treatment response prediction in male predominant hypopharyngeal carcinoma

Nature Communications

DOI

2022

数基生命系统——用控制和系统的观点对生命的数字化建模

《厦门大学学报(自然科学版)》

2022

TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics

Genomics,Proteomics & Bioinformatics

2022

Highly Regional Genes: graph-based gene selection for single cell RNA-seq data.

Journal of genetics and genomics = Yi chuan xue bao

DOI

2022

Yanda Li: A never‐stopping pioneer, investigator and founder

Quantitative Biology

DOI

2022

Elucidating minimal residual disease of paediatric B-cell acute lymphoblastic leukaemia by single-cell analysis

Nature Cell Biology

DOI

2022

JEBIN: analyzing gene co-expressions across multiple datasets by joint network embedding

Briefings Bioinform.

DOI

2021

基于细胞—计算机交互的细胞控制方法

《自动化学报》

DOI

2021

基于生物网络的关系推断原理、方法与应用

Scientia Sinica Informationis

DOI

2021

Comprehensive analysis of spatial architecture in primary liver cancer

bioRxiv

DOI

2021

Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models

Clinical Cancer Research

DOI

2021

Discovery of a Carbamoyl Phosphate Synthetase 1–Deficient HCC Subtype With Therapeutic Potential Through Integrative Genomic and Experimental Analysis

Hepatology

DOI

2021

Single-Cell Decoding of Minimal Residual Disease in Pediatric B Cell Acute Lymphoblastic Leukemia

Blood

DOI

2021

DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations

medRxiv

DOI

2021

ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

Briefings in Bioinformatics

DOI

2020

New gene association measures by joint network embedding of multiple gene expression datasets

bioRxiv

DOI

2020

Artificial-cell-type aware cell-type classification in CITE-seq

bioRxiv

DOI

2020

Targeted sequencing reveals the mutational landscape responsible for sorafenib therapy in advanced hepatocellular carcinoma

Theranostics

DOI

2020

scCancer: a package for automated processing of single-cell RNA-seq data in cancer

Briefings in Bioinformatics

DOI

2019

Integrative molecular analysis of metastatic hepatocellular carcinoma

BMC Medical Genomics

DOI

2018

VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder

Genomics, Proteomics & Bioinformatics

DOI

2018

Integrative molecular analysis of hepatocellular carcinoma by HCCDB

Cancer Biology & Medicine

2018

HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas

Genomics, Proteomics & Bioinformatics

DOI

2018

ClustEx2: Gene Module Identification using Density-Based Network Hierarchical Clustering

ACM Cloud and Autonomic Computing Conference

DOI

2017

Network embedding-based representation learning for single cell RNA-seq data

Nucleic Acids Research

DOI

2017

Recurrently deregulated lncRNAs in hepatocellular carcinoma

Nature Communications

DOI

2016

Integrative clustering methods of multi-omics data for molecule-based cancer classifications

Quantitative Biology

DOI

2016

Genome-wide DNA methylation analysis identifies candidate epigenetic markers and drivers of hepatocellular carcinoma

Briefings Bioinform.

DOI

2016

Evaluating the molecule-based prediction of clinical drug responses in cancer

Bioinform.

DOI

2015

Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification

BMC Genomics

DOI

2015

SCT Promoter Methylation is a Highly Discriminative Biomarker for Lung and Many Other Cancers

bioRxiv

DOI

2014

Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method

BMC Bioinformatics

DOI

2014

OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs

Bioinform.

DOI

2014

Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer.

Molecular Biosystems

DOI

2013

FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer

PLoS ONE

DOI

2013

Inferring pathway crosstalk networks using gene set co-expression signatures.

Molecular Biosystems

DOI

2013

Inferring the Perturbed microRNA Regulatory Networks in Cancer Using Hierarchical Gene Co-Expression Signatures

PLoS ONE

DOI

2012

Towards integrative annotation of the cell-type specific gene functional and signaling map in vascular endothelial cells.

Molecular Biosystems

DOI

2011

Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells

Bioinformatics

DOI

2010

A Multiple-Instance Scoring Method to Predict Tissue-Specific Cis-Regulatory Motifs and Regions

DOI

2010

Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis

BMC Systems Biology

DOI

2009

Integrative Computational Identifications of the Signaling Pathway Network Related to TNF-alpha Stimulus in Vascular Endothelial Cells

2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing

DOI

2008

Computational Identification of 99 Insect MicroRNAs Using Comparative Genomics

DOI

2008

Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species

Bioinform.

DOI

2008

Brief review: frontiers in the computational studies of gene regulations

Frontiers of Electrical and Electronic Engineering in China

DOI

2007

Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila

BMC Bioinformatics

DOI

2006

Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences

Mammalian Genome

DOI

2005

MicroRNA identification based on sequence and structure alignment

Bioinformatics

DOI

2019

精准肿瘤医学:从基因组到单细胞

《2019年中国肿瘤标志物学术大会暨第十三届肿瘤标志物青年科学家论坛论文集》

DOI

2017

肝癌基因表达图谱构建与分析

《中国生物工程学会第二届青年科技论坛暨首届青年工作委员会学术年会摘要集》

2016

Recurrently deregulated lncRNAs associated with HCC tumorigenesis and metastasis revealed by genomic,epigenomic,and transcriptomic profiling in paired primary tumor and PVTT samples

《第九届全国核糖核酸学术讨论会》

2010

A new gene network clustering algorithm based on minimum spanning tree

《第四届全国生物信息学与系统生物学学术大会》

2025

Inference of heterogeneous effects in single-cell genetic perturbation screens

Research Square

DOI

2022

Total-mRNA-Aware Analysis for Droplet-Based Single Cell Sequencing

Research Square

DOI