OpenLooper (OLP)


Previous research efforts have advanced our understanding of specific chromosomal events, such as DNA transcription,replication, recombination, partitioning, and epigenetic modification. One of the major future challenges in chromosome biology will be to provide an overall framework of how these individual activities are orchestrated and coordinated to maximize their effects in a variety of biological processes that evolve over time.

OpenLooper (OLP) collects genome-wide data on chromatin structures investigated by various high-throughput experimental assays, such as Hi-C, ChIA-PET, ChIP-seq, and RNA-seq. Simultaneously, OLP provides a platform that supports opening and sharing high-throughput sequencing datasets.
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In Focus Articles (last modified: 2018-05-25 17:12:37)

[1] Investigation of Spatial Organization of Chromosome Territories in Chromosome Exchange Aberrations A...  (Health Phys. 2018 Jul;115(1):77-89)

Investigation of Spatial Organization of Chromosome Territories in Chromosome Exchange Aberrations After Ionizing Radiation Exposure.


Balajee AS, Sanders JT, Golloshi R, Shuryak I, McCord RP, Dainiak N (Health Phys. 2018 Jul;115(1):77-89)
Higher-order organization of the human genome is well established with chromosomes occupying distinct domains or territories in the interphase nucleus. Spatial organization of chromosome territories in the interphase nucleus occurs in a cell-type-specific manner. Since both stable and unstable aberrations induced by ionizing radiation involve the exchange of material between two or more chromosome......
PubMed:29787433
[2] Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray ...  (BMC Genomics. 2017 Oct 12;18(1):778)

Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice.


Pan X, Fang Y, Yang X, Zheng D, Chen L, Wang L, Xiao J, Wang XE, Wang K, Cheng Z, Yu H, Zhang W (BMC Genomics. 2017 Oct 12;18(1):778)
BACKGROUND: The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response....
PubMed:29025389
[3] 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double a...  (Methods. 2018 May 14;:)

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.


Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE (Methods. 2018 May 14;:)
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput co......
PubMed:29772275
[4] HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.  (Bioinformatics. 2017 Jul 15;33(14):2199-2201)

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.


Yan KK, Yardimci GG, Yan C, Noble WS, Gerstein M (Bioinformatics. 2017 Jul 15;33(14):2199-2201)
Summary: Genome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of the genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit the 2D nature of Hi-C contact maps, matrix techniques like spectral analysis are particularly useful. Here, we present HiC-spector, a collection of matrix-related functio......
PubMed:28369339
[5] GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.  (BMC Genomics. 2018 May 08;19(Suppl 5):308)

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.


Schulz T, Stoye J, Doerr D (BMC Genomics. 2018 May 08;19(Suppl 5):308)
BACKGROUND: Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of genes with associated functionality that exhibit close proximity to each other in the spatial conformation of chromosomes across several related species....
PubMed:29745835