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Yijun Ruan
University of Connecticut Health Center
GenomeGeneticsChIA-PETChromatinBiology
176Publications
64H-index
37.5kCitations
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Publications 160
Newest
#1Tarik J. Salameh (PSU: Pennsylvania State University)H-Index: 4
#2Xiaotao Wang (NU: Northwestern University)H-Index: 1
Last. Feng Yue (NU: Northwestern University)
view all 8 authors...
Accurately predicting chromatin loops from genome-wide interaction matrices such as Hi-C data is critical to deepening our understanding of proper gene regulation. Current approaches are mainly focused on searching for statistically enriched dots on a genome-wide map. However, given the availability of orthogonal data types such as ChIA-PET, HiChIP, Capture Hi-C, and high-throughput imaging, a supervised learning approach could facilitate the discovery of a comprehensive set of chromatin interac...
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#1Michal Wlasnowolski (University of Warsaw)H-Index: 2
#2Michal Sadowski (University of Warsaw)H-Index: 2
Last. Dariusz Plewczynski (University of Warsaw)H-Index: 25
view all 8 authors...
: Structural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET d...
1 CitationsSource
#1Byoungkoo LeeH-Index: 3
#2Jiahui WangH-Index: 1
view all 13 authors...
ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control a...
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#1Ping WangH-Index: 4
#1Ping WangH-Index: 16
Last. Xiaoan RuanH-Index: 21
view all 13 authors...
BACKGROUND: Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis remain largely unknown. RESULTS: Using an inducible system, we comprehensively analyze the 3D genome organization in myeloid cells and its reorganization after PML-RARα induction and perform additional analyses in patient-derived APL cells with native PML-RARα. We discover that ...
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#1Henry B Zhang (UCSD: University of California, San Diego)
#2Minji KimH-Index: 4
Last. Yijun Ruan (University of Connecticut Health Center)H-Index: 64
view all 4 authors...
MOTIVATION: Modern genomic research is driven by next-generation sequencing experiments such as ChIP-seq and ChIA-PET that generate coverage files for transcription factor binding, as well as DHS and ATAC-seq that yield coverage files for chromatin accessibility. Such files are in a bedGraph text format or a bigWig binary format. Obtaining summary statistics in a given region is a fundamental task in analyzing protein binding intensity or chromatin accessibility. However, the existing Python pac...
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#1Pawel Trzaskoma (Nencki Institute of Experimental Biology)H-Index: 4
#2Blazej Ruszczycki (Nencki Institute of Experimental Biology)H-Index: 8
Last. Małgorzata A. Śliwińska (Nencki Institute of Experimental Biology)H-Index: 2
view all 19 authors...
The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 × 5 × 30 nm in xyz dimens...
2 CitationsSource
#1Yoshiki Higashijima (UTokyo: University of Tokyo)H-Index: 7
#2Yusuke Matsui (Nagoya University)H-Index: 5
Last. Masayuki Yoshida (Tokyo Medical and Dental University)H-Index: 39
view all 25 authors...
Histone H3 lysine-9 di-methylation (H3K9me2) and lysine-27 tri-methylation (H3K27me3) are linked to repression of gene expression, but the functions of repressive histone methylation dynamics during inflammatory responses remain enigmatic. Here, we report that lysine demethylases 7A (KDM7A) and 6A (UTX) play crucial roles in tumor necrosis factor (TNF)-alpha signaling in endothelial cells (ECs), where they are regulated by a novel TNF-alpha-responsive microRNA, miR-3679-5p. TNF-alpha rapidly ind...
2 CitationsSource
#1Haitham AshoorH-Index: 8
Last. Sheng LiH-Index: 1
view all 8 authors...
Chromatin interaction studies can reveal how the genome is organized into spatially confined sub-compartments in the nucleus. However, accurately identifying sub-compartments from chromatin interaction data remains a challenge in computational biology. Here, we present Sub-Compartment Identifier (SCI), an algorithm that uses graph embedding followed by unsupervised learning to predict sub-compartments using Hi-C chromatin interaction data. We find that the network topological centrality and clus...
1 CitationsSource
#1Ruhul Amin (NIH: National Institutes of Health)H-Index: 8
#2Anjali Shukla (NIH: National Institutes of Health)H-Index: 9
Last. Maxwell P. Lee (NIH: National Institutes of Health)H-Index: 24
view all 15 authors...
Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. It remains unclear how these mechanical signals are transmitted to the cell nucleus to regulate gene expression in metastasis. In an attempt to characterize metastasis-associated polymorphisms in the non-coding regulatory regions of the genome, we identified nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellul...
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#1Pawel Trzaskoma (Nencki Institute of Experimental Biology)H-Index: 4
#2Blazej Ruszczycki (Nencki Institute of Experimental Biology)H-Index: 8
Last. Małgorzata A. Śliwińska (Nencki Institute of Experimental Biology)H-Index: 2
view all 19 authors...
The human genome is extensively folded into 3-dimensional organization, yet the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of a novel electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra- resolution (5x5x30 nm in xyz dimension...
Source
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