江瑞

2026

EpiZoo: a DNA sequence-aware foundation model for cross-species single-cell epigenomics

bioRxiv

DOI

2026

Hi-Cformer enables multiscale chromatin contact map modeling for single-cell Hi-C data analysis

Science Advances

DOI

2026

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

bioRxiv

DOI

2026

RegFM: an interpretable context-aware foundation model for human transcriptional regulation

bioRxiv

DOI

2026

HitAnno: Atlas-level cell type annotation based on scATAC-seq data via a hierarchical language model

bioRxiv

DOI

2026

A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis

Nature Communications

DOI

2025

EpiAgent: foundation model for single-cell epigenomics

Nature Methods

DOI

2025

CREATE: cell-type-specific cis-regulatory element identification via discrete embedding

Nature Communications

DOI

2025

Deciphering single-cell epigenomic language with a foundation model

Nature Methods

DOI

2025

Harnessing LLMs to decode genetic perturbations

Nature Computational Science

DOI

2025

hECA v2.0: an AI-ready ensemble cell atlas of single-cell RNA and ATAC sequencing data

Scientific Data

DOI

2025

Cross-modality representation and multi-sample integration of spatially resolved omics data

bioRxiv

DOI

2025

Human-scATAC-Corpus: a comprehensive database of scATAC-seq data

bioRxiv

DOI

2025

CASHeart: A database of single cells chromatin accessibility for the human heart

Quant. Biol.

DOI

2024

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

Genome Biology

DOI

2024

Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations

Genome Biology

DOI

2024

OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions

Bioinformatics Advances

DOI

2024

Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2024

Discrete latent embedding of single-cell chromatin accessibility sequencing data for uncovering cell heterogeneity

Nature Computational Science

DOI

2024

collectNET: a web server for integrated inference of cell–cell communication network

bioRxiv

DOI

2024

INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation

bioRxiv

DOI

2024

scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism

Bioinform.

DOI

2024

Detection of spatial chromatin accessibility patterns with inter-cellular correlations

bioRxiv

DOI

2023

SINFONIA: Scalable Identification of Spatially Variable Genes for Deciphering Spatial Domains

Cells

DOI

2023

scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data

Genome Biology

DOI

2023

Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics

Genome Research

DOI

2023

NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks

Proceedings of the National Academy of Sciences

DOI

2023

Cofea: correlation-based feature selection for single-cell chromatin accessibility data

Briefings in Bioinformatics

DOI

2023

simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data

Bioinformatics

DOI

2023

scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

Journal of genetics and genomics/Journal of Genetics and Genomics

DOI

2023

scIBD

Zenodo (CERN European Organization for Nuclear Research)

DOI

2022

DeepCAGE: Incorporating Transcription Factors in Genome-Wide Prediction of Chromatin Accessibility

Genomics Proteomics & Bioinformatics

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

基于生物网络的关系推断原理、方法与应用

《中国科学:信息科学》

2022

ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data

Bioinform.

DOI

2022

Deep generative modeling and clustering of single cell Hi-C data

Briefings in Bioinformatics

DOI

2022

scGraph: a graph neural network-based approach to automatically identify cell types

Bioinformatics

DOI

2022

HiChIPdb: a comprehensive database of HiChIP regulatory interactions

Nucleic Acids Research

DOI

2022

Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling

iScience

DOI

2022

Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding

Nature Machine Intelligence

DOI

2022

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

Journal of genetics and genomics/Journal of Genetics and Genomics

DOI

2021

DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers

Genomics,Proteomics & Bioinformatics

2021

RA3 is a reference-guided approach for epigenetic characterization of single cells

Nature Communications

DOI

2021

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions

Nucleic Acids Res.

DOI

2021

hECA: The cell-centric assembly of a cell atlas

bioRxiv

DOI

2021

Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model

bioRxiv

DOI

2021

Density estimation using deep generative neural networks

Proceedings of the National Academy of Sciences of the United States of America

DOI

2021

Toward a unified information framework for cell atlas assembly

National Science Review

DOI

2021

Reusability report: Compressing regulatory networks to vectors for interpreting gene expression and genetic variants

Nature Machine Intelligence

DOI

2020

Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data

NAR Genomics and Bioinformatics

DOI

2020

EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes

BMC Bioinformatics

DOI

2020

Roundtrip: A Deep Generative Neural Density Estimator

arXiv.org

2020

A method for scoring the cell type-specific impacts of noncoding variants in personal genomes

Proceedings of the National Academy of Sciences of the United States of America

DOI

2020

Simultaneous deep generative modeling and clustering of single cell genomic data

Nature Machine Intelligence

DOI

2020

SilencerDB: a comprehensive database of silencers

Nucleic Acids Res.

DOI

2020

IRIS: A method for predicting in vivo RNA secondary structures using PARIS data

Quantitative Biology

DOI

2020

Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia

Frontiers in Genetics

DOI

2020

Association of Rare PTGIS Variants With Susceptibility and Pulmonary Vascular Response in Patients With Idiopathic Pulmonary Arterial Hypertension

JAMA Cardiology

DOI

2019

VPAC: Variational projection for accurate clustering of single-cell transcriptomic data

BMC Bioinformatics

DOI

2019

DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data

Nature Communications

DOI

2019

Incorporating Gene Expression in Genome-wide Prediction of Chromatin Accessibility via Deep Learning

bioRxiv

DOI

2019

hicGAN infers super resolution Hi-C data with generative adversarial networks

Bioinform.

DOI

2019

EnDisease: a manually curated database for enhancer-disease associations

Database J. Biol. Databases Curation

DOI

2019

EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information

Quantitative Biology

DOI

2019

EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model

PeerJ

DOI

2019

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

Nucleic Acids Research

DOI

2019

OPENANNO: annotating genomic regions with chromatin accessibility

bioRxiv

DOI

2019

Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network

Bioinformatics

DOI

2018

Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning.

Methods

DOI

2018

DeepHistone: a deep learning approach to predicting histone modifications

BMC Genomics

DOI

2018

Prediction of enhancer-promoter interactions via natural language processing

BMC Genomics

DOI

2018

Constructing tissue-specific transcriptional regulatory networks via a Markov random field

BMC Genomics

DOI

2017

Predicting enhancers with deep convolutional neural networks

BMC Bioinformatics

DOI

2017

Integrating embeddings of multiple gene networks to prioritize complex disease-associated genes

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2017

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data

Nature Communications

DOI

2017

Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks

Journal of Molecular Cell Biology

DOI

2017

Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data

Scientific Reports

DOI

2017

Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data

Nucleic Acids Research

DOI

2017

Modeling gene regulation from paired expression and chromatin accessibility data

Proceedings of the National Academy of Sciences of the United States of America

DOI

2017

Gene co-opening network deciphers gene functional relationships.

Molecular Biosystems

DOI

2017

Exploring functional variant using a deep learning framework

CASE

DOI

2017

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding

Bioinform.

DOI

2017

Mimvec: a deep learning approach for analyzing the human phenome

BMC Systems Biology

DOI

2017

Chromatin accessibility prediction via a hybrid deep convolutional neural network

Bioinform.

DOI

2017

A sequence-based method to predict the impact of regulatory variants using random forest

BMC Systems Biology

DOI

2016

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients

Genomics, Proteomics & Bioinformatics

DOI

2016

Global inference of disease-causing single nucleotide variants from exome sequencing data

BMC Bioinformatics

DOI

2016

DeepEnhancer: Predicting enhancers by convolutional neural networks

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2016

Whole genome sequencing and its applications in medical genetics

Quantitative Biology

DOI

2016

dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions

Database J. Biol. Databases Curation

DOI

2016

Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

National Science Review

DOI

2015

Walking on multiple disease-gene networks to prioritize candidate genes.

Journal of Molecular Cell Biology

DOI

2015

Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data

Scientific Reports

DOI

2015

Pinpointing disease genes through phenomic and genomic data fusion

BMC Genomics

DOI

2014

生物信息学课程导引：生物信息学研究生暑期学校讲义 = Basics of bioinformatics：lecture notes of the graduates summer school on bioinformatics of China

《清华大学出版社》

2014

Integrating Multiple Genomic Data to Predict Disease-Causing Nonsynonymous Single Nucleotide Variants in Exome Sequencing Studies

PLoS Genetics

DOI

2014

Detecting Epistatic Interactions in Metagenome-Wide Association Studies by metaBOOST

BioMed Research International

DOI

2014

Inferring non-synonymous single-nucleotide polymorphisms-disease associations via integration of multiple similarity networks.

IET Systems Biology

DOI

2014

Prioritizing protein complexes implicated in human diseases by network optimization

BMC Systems Biology

DOI

2014

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data

Bioinformatics

DOI

2014

An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus

Molecular Psychiatry

DOI

2013

Walking on a Tissue-Specific Disease-Protein-Complex Heterogeneous Network for the Discovery of Disease-Related Protein Complexes

BioMed Research International

DOI

2013

Computational Systems Biology

TheScientificWorldJournal

DOI

2013

Basics of Bioinformatics

Springer Berlin Heidelberg

DOI

2013

Prediction of Deleterious Nonsynonymous Single-Nucleotide Polymorphism for Human Diseases

TheScientificWorldJournal

DOI

2013

Integrating human omics data to prioritize candidate genes

BMC Medical Genomics

DOI

2013

Basic Statistics for Bioinformatics

DOI

2013

PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data

Bioinformatics

DOI

2013

Identifying potential cancer driver genes by genomic data integration

Scientific Reports

DOI

2013

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data

Nucleic Acids Research

DOI

2012

Integrating multiple gene semantic similarity profiles to infer disease genes

Proceedings of the 31st Chinese Control Conference

2012

Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data

Int. J. Comput. Biol. Drug Des.

DOI

2012

Constructing human phenome-interactome networks for the prioritization of candidate genes

DOI

2011

Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach

BMC Bioinformatics

DOI

2011

Integrating sequence conservation features and a domain-domain interaction network to detect disease-associated nsSNPs

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

DOI

2011

Constructing a gene semantic similarity network for the inference of disease genes

BMC Systems Biology

DOI

2011

Prioritisation of candidate Single Amino Acid Polymorphisms using one-class learning machines

Int. J. Comput. Biol. Drug Des.

DOI

2011

Prioritization of Candidate Nonsynonymous Single Nucleotide Polymorphisms via Sequence Conservation Features

DOI

2011

Extraction of Sequence Conservation Features for the Prioritization of Candidate Single Amino Acid Polymorphisms

DOI

2011

Prediction of Disease-associated Single Amino Acid Polymorphisms Based on Physiochemical Features

International Journal of Bioscience Biochemistry and Bioinformatics

DOI

2011

Evaluation of next-generation sequencing software in mapping and assembly

Journal of Human Genetics

DOI

2011

Uncover disease genes by maximizing information flow in the phenome–interactome network

Bioinformatics

DOI

2011

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

Bioinformatics

DOI

2011

DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases

BMC Systems Biology

DOI

2010

Comparative study of ensemble learning approaches in the identification of disease mutations

International Conference on BioMedical Engineering and Informatics

DOI

2010

Comparative study of network-based prioritization of protein domains associated with human complex diseases

DOI

2010

A Max-Flow-Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data

IEEE Transactions on Computational Biology and Bioinformatics

DOI

2010

Prioritisation of associations between protein domains and complex diseases using domain–domain interaction networks

IET Systems Biology

DOI

2009

A random forest approach to the detection of epistatic interactions in case-control studies

BMC Bioinformatics

DOI

2009

Align human interactome with phenome to identify causative genes and networks underlying disease families

Bioinform.

DOI

2009

Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy

PLoS Genetics

DOI

2009

Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units

DOI

2009

Bayesian Models and Gibbs Sampling Strategies for Local Graph Alignment and Motif Identification in Stochastic Biological Networks

Communications in Information and Systems

DOI

2008

Network-based global inference of human disease genes

Molecular Systems Biology

DOI

2008

Logic motif of combinatorial control in transcriptional networks

DOI

2008

A MAX-FLOW BASED APPROACH TO THE IDENTIFICATION OF PROTEIN COMPLEXES USING PROTEIN INTERACTION AND MICROARRAY DATA

DOI

2007

Sequence-Based Prioritization of Nonsynonymous Single-Nucleotide Polymorphisms for the Study of Disease Mutations

The American Journal of Human Genetics

DOI

2010

Identification of disease domains underlying human genetic diseases:A Bayesian regression approach

《第四届全国生物信息学与系统生物学学术大会论文集》

2010

Optimizing subnetwork markers for the classification of breast cancer metastases

《第四届全国生物信息学与系统生物学学术大会》

2026

scMTG reconstructs single-cell temporal dynamics with Markov transition generators

bioRxiv (Cold Spring Harbor Laboratory)

DOI

2023

uniHEART: An Ensemble Atlas of Cardiac Cells Provides Multifaceted Portraits of the Human Heart

Research Square

DOI

2018

SIP: An Interchangeable Pipeline for scRNA-seq Data Processing

bioRxiv (Cold Spring Harbor Laboratory)

DOI

2018

PTGIS is a Novel Susceptibility Gene for Pulmonary Arterial Hypertension

SSRN Electronic Journal

DOI

2014

ProbAlign: a re-alignment method for long sequencing reads

bioRxiv (Cold Spring Harbor Laboratory)

DOI