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: 2020-01-12 09:01:14)

[1] Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?  (Gigascience. 2020 Jan 01;9(1):)

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?


Kadota M, Nishimura O, Miura H, Tanaka K, Hiratani I, Kuraku S (Gigascience. 2020 Jan 01;9(1):)
BACKGROUND: Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for H......
PubMed:31919520
[2] Identification of significant chromatin contacts from HiChIP data by FitHiChIP.  (Nat Commun. 2019 09 17;10(1):4221)

Identification of significant chromatin contacts from HiChIP data by FitHiChIP.


Bhattacharyya S, Chandra V, Vijayanand P, Ay F (Nat Commun. 2019 09 17;10(1):4221)
HiChIP/PLAC-seq is increasingly becoming popular for profiling 3D chromatin contacts among regulatory elements and for annotating functions of genetic variants. Here we describe FitHiChIP, a computational method for loop calling from HiChIP/PLAC-seq data, which jointly models the non-uniform coverage and genomic distance scaling of contact counts to compute statistical significance estimates. We a......
PubMed:31530818
[3] Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data.  (Genes (Basel). 2019 07 18;10(7):)

Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data.


Hansen P, Gargano M, Hecht J, Ibn-Salem J, Karlebach G, Roehr JT, Robinson PN (Genes (Basel). 2019 07 18;10(7):)
Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacti......
PubMed:31323892
[4] Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequen...  (Mol Ecol Resour. 2019 Dec 30;:)

Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequencing and Hi-C analysis.


Kang S, Kim JH, Jo E, Lee SJ, Jung J, Kim BM, Lee JH, Oh TJ, Yum S, Rhee JS, Park H (Mol Ecol Resour. 2019 Dec 30;:)
The Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mecha......
PubMed:31887246
[5] Topological structure analysis of chromatin interaction networks.  (BMC Bioinformatics. 2019 Dec 27;20(Suppl 23):618)

Topological structure analysis of chromatin interaction networks.


Viksna J, Melkus G, Celms E, Čerāns K, Freivalds K, Kikusts P, Lace L, Opmanis M, Rituma D, Rucevskis P (BMC Bioinformatics. 2019 Dec 27;20(Suppl 23):618)
BACKGROUND: Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis of Hi-C data to identify biologically significant features, many questions still remain open, in particular regarding potential biological significance of various topological feat......
PubMed:31881819