Match!
Yijun Ruan
University of Connecticut Health Center
160Publications
63H-index
35.2kCitations
Publications 148
Newest
#1Michal Sadowski (University of Warsaw)H-Index: 2
#2Agnieszka Kraft (University of Warsaw)H-Index: 1
Last.Dariusz Plewczynski (University of Warsaw)H-Index: 24
view all 7 authors...
The number of reported examples of chromatin architecture alterations involved in the regulation of gene transcription and in disease is increasing. However, no genome-wide testing has been performed to assess the abundance of these events and their importance relative to other factors affecting genome regulation. This is particularly interesting given that a vast majority of genetic variations identified in association studies are located outside coding sequences. This study attempts to address...
2 CitationsSource
The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges. Thus, we developed MIA-Sig, an algorithmic solution based on signal processing and information theory. We demonstrate its ability to de-noise the multiplex data, assess the statistical significance of chromatin complexes, and id...
Source
#1Michal Sadowski (University of Warsaw)H-Index: 2
#2Agnieszka Kraft (University of Warsaw)H-Index: 1
Last.Dariusz Plewczynski (University of Warsaw)H-Index: 24
view all 7 authors...
Following publication of the original article [1], it was noticed that the incorrect Fig. 2 and Fig. 3. were processed during production. It was also noticed that Fig. 4a was processed with a superfluous “1e7” symbol in the upper right corner.
Source
#1Dan CapursoH-Index: 1
#2Zhonghui TangH-Index: 13
Last.Yijun Ruan (University of Connecticut Health Center)H-Index: 63
view all 3 authors...
Abstract The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review metho...
1 CitationsSource
#1Henry B Zhang (UCSD: University of California, San Diego)
#2Minji KimH-Index: 2
Last.Yijun RuanH-Index: 63
view all 4 authors...
Motivation: Modern genomic research relies heavily on 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 Pytho...
Source
#1Minji KimH-Index: 2
#2Meizhen ZhengH-Index: 5
Last.Yijun Ruan (University of Connecticut Health Center)H-Index: 63
view all 7 authors...
Abstract The single-molecule multiplex chromatin interaction data generated by emerging non-ligation-based 3D genome mapping technologies provide novel insights into high dimensional chromatin organization, yet introduce new computational challenges. We developed MIA-Sig (https://github.com/TheJacksonLaboratory/mia-sig.git), an algorithmic framework to de-noise the data, assess the statistical significance of chromatin complexes, and identify topological domains and inter-domain contacts. On chr...
Source
#2Daniel CapursoH-Index: 2
Last.Yijun RuanH-Index: 63
view all 6 authors...
ChIA-Drop is a new experimental method for mapping multiplex chromatin interactions with single-molecule precision by barcoding chromatin complexes inside microfluidics droplets, followed by pooled DNA sequencing. The chromatin DNA reads with the same droplet-specific barcodes are inferred to be derived from the same chromatin interaction complex. Here, we describe an integrated computational pipeline, named ChIA-DropBox, that is specifically designed for reconstructing chromatin reads in each d...
1 CitationsSource
#1Sarah J. Benjamin (University of Connecticut Health Center)H-Index: 2
#2Kelly L. Hawley (University of Connecticut Health Center)H-Index: 6
Last.Juan Carlos Salazar Uribe (University of Connecticut Health Center)H-Index: 35
view all 11 authors...
Abstract Lyme disease is a tick-borne illness caused by the spirochete Borrelia burgdorferi (Bb). It is believed that the robust inflammatory response induced by the host’s innate immune system is responsible for the clinical manifestations associated with Bb infection. The macrophage plays a central role in the immune response to many bacterial infections and is thought to play a central role in activation of the innate immune response to Bb. Previous studies have shown that following phagocyto...
Source
#1Meizhen ZhengH-Index: 5
Last.Yijun Ruan (University of Connecticut Health Center)H-Index: 63
view all 16 authors...
The genomes of multicellular organisms are extensively folded into 3D chromosome territories within the nucleus1. Advanced 3D genome-mapping methods that combine proximity ligation and high-throughput sequencing (such as chromosome conformation capture, Hi-C)2, and chromatin immunoprecipitation techniques (such as chromatin interaction analysis by paired-end tag sequencing, ChIA-PET)3, have revealed topologically associating domains4 with frequent chromatin contacts, and have identified chromati...
24 CitationsSource
#1Zhizhuo Zhang (MIT: Massachusetts Institute of Technology)H-Index: 10
#2Kern Rei Chng (Genome Institute of Singapore)H-Index: 12
Last.Edwin Cheung (Genome Institute of Singapore)H-Index: 22
view all 20 authors...
4 CitationsSource
12345678910