The 3DGD: A database of genome 3D structure

Chao Li; Xiao Dong; Haiwei Fan; Chuan Wang; Guohui Ding; Yixue Li

doi:10.1093/bioinformatics/btu081

The 3DGD: A database of genome 3D structure

Chao Li, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding, Yixue Li

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

Summary: The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines. We built 3DGD (3D Genome Database), a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein-DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions.

Original language	English (US)
Pages (from-to)	1640-1642
Number of pages	3
Journal	Bioinformatics
Volume	30
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btu081
State	Published - Jun 1 2014
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btu081

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@article{35ec11c9b4064d149287c0cdfdf022e0,

title = "The 3DGD: A database of genome 3D structure",

abstract = "Summary: The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines. We built 3DGD (3D Genome Database), a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein-DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions.",

author = "Chao Li and Xiao Dong and Haiwei Fan and Chuan Wang and Guohui Ding and Yixue Li",

note = "Funding Information: Funding: State key basic research program (973) (2011CB910204, 2010CB529206, 2010CB912702, 2011CBA00801), Research Program of CAS (KSCX2-EW-R-04, KSCX2-YW-R-190, 2011KIP204), National Natural Science Foundation of China (30900272, 31070752), Chinese Ministry for Science and Technology Grant (2008BAI64B01), Chinese High-Tech R&D Program [(863)-2009AA02Z304] and SA-SIBS Scholarship Programme.",

year = "2014",

month = jun,

day = "1",

doi = "10.1093/bioinformatics/btu081",

language = "English (US)",

volume = "30",

pages = "1640--1642",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "11",

}

TY - JOUR

T1 - The 3DGD

T2 - A database of genome 3D structure

AU - Li, Chao

AU - Dong, Xiao

AU - Fan, Haiwei

AU - Wang, Chuan

AU - Ding, Guohui

AU - Li, Yixue

N1 - Funding Information: Funding: State key basic research program (973) (2011CB910204, 2010CB529206, 2010CB912702, 2011CBA00801), Research Program of CAS (KSCX2-EW-R-04, KSCX2-YW-R-190, 2011KIP204), National Natural Science Foundation of China (30900272, 31070752), Chinese Ministry for Science and Technology Grant (2008BAI64B01), Chinese High-Tech R&D Program [(863)-2009AA02Z304] and SA-SIBS Scholarship Programme.

PY - 2014/6/1

Y1 - 2014/6/1

N2 - Summary: The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines. We built 3DGD (3D Genome Database), a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein-DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions.

AB - Summary: The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines. We built 3DGD (3D Genome Database), a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein-DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions.

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DO - 10.1093/bioinformatics/btu081

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JO - Bioinformatics

JF - Bioinformatics

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ER -

The 3DGD: A database of genome 3D structure

Abstract

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