Author details

Full Name

Rui Jiang

Affiliation

ORCID

Career Start Year

2000

Papers

111

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37502861	EpiGePT: a Pretrained Transformer model for epigenomics.	bioRxiv	2024
37494428	simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data.		2023
36240936	Hotspots of riverine greenhouse gas (CH, CO, NO) emissions from Qinghai Lake Basin on the northeast Tibetan Plateau.	Science of the Total Environment	2023
36215037	HiChIPdb: a comprehensive database of HiChIP regulatory interactions.	Nucleic Acids Res	2023
36831270	SINFONIA: Scalable Identification of Spatially Variable Genes for Deciphering Spatial Domains.		2023
37023129	NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks.	Proc Natl Acad Sci U S A	2023
36575566	Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames.		2023
36610708	ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data.		2023
36458445	Deep generative modeling and clustering of single cell Hi-C data.	Brief Bioinform	2023
35144027	Highly Regional Genes: graph-based gene selection for single-cell RNA-seq data.	Journal of Genetics and Genomics	2022
36182762	REDDA: Integrating multiple biological relations to heterogeneous graph neural network for drug-disease association prediction.	Computers in Biology and Medicine	2022
35394015	scGraph: a graph neural network-based approach to automatically identify cell types.	Bioinformatics	2022
35428192	DualGCN: a dual graph convolutional network model to predict cancer drug response.	BMC Bioinformatics	2022
35992073	Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling.	iScience	2022
35602947	hECA: The cell-centric assembly of a cell atlas.	iScience	2022
35350228	Toward a unified information framework for cell atlas assembly.	National Science Review	2022
35293310	DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility.	Genomics Proteomics Bioinformatics	2022
33045745	SilencerDB: a comprehensive database of silencers.	Nucleic Acids Research	2021
34179690	Simultaneous deep generative modeling and clustering of single cell genomic data.	Nat Mach Intell	2021
33751971	Responses of cyanobacterial aggregate microbial communities to algal blooms.	Water Res	2021
33581335	DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers.		2021
33846355	RA3 is a reference-guided approach for epigenetic characterization of single cells.	Nature Communications	2021
33999180	OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.	Nucleic Acids Res	2021
33833061	Density estimation using deep generative neural networks.	Proc Natl Acad Sci U S A	2021
31318408	Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network.		2020
32439386	A deep metric learning approach for histopathological image retrieval.	Methods	2020
33575579	Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data.	NAR Genomics and Bioinformatics	2020
33381841	DeepCDR: a hybrid graph convolutional network for predicting cancer drug response.	Bioinformatics	2020
32817564	A method for scoring the cell type-specific impacts of noncoding variants in personal genomes.	Proc Natl Acad Sci U S A	2020
33193662	Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia.	Frontiers in Genetics	2020
32938367	EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes.	BMC Bioinformatics	2020
30788500	EnDisease: a manually curated database for enhancer-disease associations.	Database : the journal of biological databases and curation	2019
31601804	DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data.	Nat Commun	2019
31565573	EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model.	PeerJ	2019
30541001	Association of Circulating Adipsin, Visfatin, and Adiponectin with Nonalcoholic Fatty Liver Disease in Adults: A Case-Control Study.	Annals of Nutrition and Metabolism	2019
30928408	Nicotinamide riboside protects against liver fibrosis induced by CCl via regulating the acetylation of Smads signaling pathway.	Life Sciences	2019
31510693	hicGAN infers super resolution Hi-C data with generative adversarial networks.	Bioinformatics	2019
30869141	DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.	Nucleic Acids Res	2019
30967126	DeepHistone: a deep learning approach to predicting histone modifications.	BMC Genomics	2019
31074382	VPAC: Variational projection for accurate clustering of single-cell transcriptomic data.	BMC Bioinformatics	2019
29679894	Nicotinamide riboside attenuates alcohol induced liver injuries via activation of SirT1/PGC-1Î±/mitochondrial biosynthesis pathway.	Redox Biology	2018
30598101	Constructing tissue-specific transcriptional regulatory networks via a Markov random field.	BMC Genomics	2018
30210803	GePMI: A statistical model for personal intestinal microbiome identification.	NPJ Biofilms Microbiomes	2018
29874547	Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning.	Methods	2018
30416739	Erratum: Author Correction: GePMI: a statistical model for personal intestinal microbiome identification.	NPJ Biofilms Microbiomes	2018
29898429	Cyanidin-3-O-Î²-glucoside regulates the activation and the secretion of adipokines from brown adipose tissue and alleviates diet induced fatty liver.		2018
29764360	Prediction of enhancer-promoter interactions via natural language processing.	BMC Genomics	2018
29712439	Blood-based novel biomarkers for nonalcoholic steatohepatitis.	Biomarkers in Medicine	2018
29069282	Chromatin accessibility prediction via a hybrid deep convolutional neural network.	Bioinformatics	2018
29151965	Combined Inhibitions of Glycolysis and AKT/autophagy Can Overcome Resistance to EGFR-targeted Therapy of Lung Cancer.	Journal of Cancer	2017