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3DIV: A 3D-genome Interaction Viewer and database
Yang, Dongchan,Jang, Insu,Choi, Jinhyuk,Kim, Min-Seo,Lee, Andrew J,Kim, Hyunwoong,Eom, Junghyun,Kim, Dongsup,Jung, Inkyung,Lee, Byungwook Oxford University Press 2018 Nucleic acids research Vol.46 No.d1
<P><B>Abstract</B></P><P>Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C data and the large size of raw sequencing data. In order to overcome these limitations, we constructed a database named 3DIV (a 3D-genome Interaction Viewer and database) that provides a list of long-range chromatin interaction partners for the queried locus with genomic and epigenomic annotations. 3DIV is the first of its kind to collect all publicly available human Hi-C data to provide 66 billion uniformly processed raw Hi-C read pairs obtained from 80 different human cell/tissue types. In contrast to other databases, 3DIV uniquely provides normalized chromatin interaction frequencies against genomic distance dependent background signals and a dynamic browsing visualization tool for the listed interactions, which could greatly advance the interpretation of chromatin interactions. ‘3DIV’ is available at http://kobic.kr/3div.</P>
Multi-slice imAGe generation using intra-slice paraLLel imaging and Inter-slice shifting (MAGGULLI)
Kim, Dongchan,Seo, Hyunseok,Oh, Changheun,Han, Yeji,Park, HyunWook IOP 2016 Physics in medicine & biology Vol.61 No.4
<P>For acceleration of imaging time, multi-band imaging techniques (e.g. CAIPIRINHA) use the sensitivity differences of the multi-channel RF coils in the slice selection direction. To more effectively utilize the RF coil characteristics than the conventional multi-band imaging techniques, we propose a new imaging technique, called multi-slice image generation using intra-slice parallel imaging and inter-slice shifting (MAGGULLI). The proposed technique used an inter-slice shifting gradient in slice selection direction to make multi-slice images shift in the frequency encoding direction. Thus, aliasing caused by sub-sampling in the phase encoding direction is orthogonal to that by multi-band imaging with the inter-slice shifting, both of which are resolved by using the sensitivity information of the RF coil. Phantom and <I>in vivo</I> imaging experiments for the acceleration factors up to 10 demonstrate that the quality of the images reconstructed by MAGGULLI are better than that of CAIPIRINHA for high acceleration factors in the qualitative and quantitative analysis.</P>