Author details

Full Name

Yijun Ruan

Affiliation

ORCID

Career Start Year

1994

Papers

147

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37419111	Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.	Mol Cell	2023
36973268	Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.	Nat Commun	2023
37474564	Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions.		2023
36639381	ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs.		2023
37198186	Author Correction: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.	Nat Commun	2023
37066361	Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions.		2023
34727520	An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity.	Neuron	2022
35860407	Multi-scale phase separation by explosive percolation with single-chromatin loop resolution.	Computational and Structural Biotechnology Journal	2022
35402101	Identification and charactering of APX genes provide new insights in abiotic stresses response in .	PeerJ	2022
35595799	Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy.	Scientific Reports	2022
36911294	3D-Epigenomic Regulation of Gene Transcription in Hepatocellular Carcinoma.	Adv Genet (Hoboken)	2022
37117750	Multidimensional single-cell analysis of human peripheral blood reveals characteristic features of the immune system landscape in aging and frailty.		2022
36539456	Publisher Correction: Superâ¿¿resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy.		2022
34903738	Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response.	Nat Commun	2021
33542221	LncRNA LTSCCAT promotes tongue squamous cell carcinoma metastasis via targeting the miR-103a-2-5p/SMYD3/TWIST1 axis.	Cell Death and Disease	2021
34162542	RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription.	Science advances	2021
33836152	Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.	Cancer Cell	2021
34351700	In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing.	Current Protocols	2021
32832596	ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.	Science advances	2020
32128389	LATS kinase-mediated CTCF phosphorylation and selective loss of genomic binding.	Science advances	2020
32127534	Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data.	Nat Commun	2020
32125007	Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells.	EMBO J	2020
31896606	Corrigendum: Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues.	Cold Spring Harbor Protocols	2020
32358536	Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.	Nature Communications	2020
31629084	Methods for comparative ChIA-PET and Hi-C data analysis.	Methods	2020
32000125	lncRNA CISAL Inhibits BRCA1 Transcription by Forming a Tertiary Structure at Its Promoter.	iScience	2020
32393309	Chromatin topology reorganization and transcription repression by PML-RARÎ± in acute promyeloid leukemia.	Genome Biol	2020
32044918	pyBedGraph: a python package for fast operations on 1D genomic signal tracks.		2020
32442297	3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.	Nucleic Acids Research	2020
31481103	Correction to: Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.		2019
31571508	The 5th International 3D Genomics Workshop 2018: conference report.	Epigenomics	2019
31767038	MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms.		2019
30606742	An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.	Genome Res	2019
30650367	Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic Î² Cell Identity and Function.	Cell Rep	2019
30798120	Downregulation of RGMA by HIF-1A/miR-210-3p axis promotes cell proliferation in oral squamous cell carcinoma.		2019
31362752	Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.		2019
30778195	Multiplex chromatin interactions with single-molecule precision.	Nature	2019
29700467	Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture.	Nature Genetics	2018
30017478	The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations.	Cancer Cell	2018
30241609	The Energetics and Physiological Impact of Cohesin Extrusion.	Cell	2018
29895565	Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues.	Cold Spring Harbor Protocols	2018
29895563	Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues.	Cold Spring Harbor Protocols	2018
29706548	The Energetics and Physiological Impact of Cohesin Extrusion.	Cell	2018
28116354	ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis.	Science advances	2017
28826674	Evolutionarily Conserved Principles Predict 3D Chromatin Organization.	Molecular Cell	2017
28358394	Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions.		2017
28394353	Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction.	Nature Genetics	2017
29078395	STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the gene locus.	Proceedings of the National Academy of Sciences of the United States of America	2017
27789526	An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.	Genome Research	2016
27336171	QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.	PLoS Comput Biol	2016