3D genome reconstruction from chromosomal contacts

被引：5

作者：

Lesne, Annick ^{[1
,2
]}

Riposo, Julien ^{[1
]}

Roger, Paul ^{[1
]}

Cournac, Axel ^{[3
]}

Mozziconacci, Julien ^{[1
]}

机构：

[1] Univ Paris 06, Sorbonne Univ, Lab Phys Theor Matiere Condensee, CNRS UMR 7600, Paris, France

[2] Univ Montpellier, CNRS UMR 5535, Inst Genet Mol Montpellier, F-34059 Montpellier, France

[3] Inst Pasteur, Grp Spatial Regulat Genomes, Dept Genomes & Genet, Paris, France

来源：

NATURE METHODS | 2014年 / 11卷 / 11期

关键词：

CHROMATIN INTERACTIONS; INTERACTION FREQUENCY; REVEALS; CONFORMATION;

D O I：

10.1038/NMETH.3104

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A computational challenge raised by chromosome conformation capture (3C) experiments is to reconstruct spatial distances and three-dimensional genome structures from observed contacts between genomic loci. We propose a two-step algorithm, ShRec3D, and assess its accuracy using both in silico data and human genome-wide 3C (Hi-C) data. This algorithm avoids convergence issues, accommodates sparse and noisy contact maps, and is orders of magnitude faster than existing methods.

引用

页码：1141 / 1143

页数：3

共 50 条

[21] 3D Reconstruction from Plenoptic Image
Murgia, Francesca
Giusto, Daniele
Perra, Cristian
[J]. 2015 23RD TELECOMMUNICATIONS FORUM TELFOR (TELFOR), 2015, : 448 - 451
[22] ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction
Collins, Brandon
Oluwadare, Oluwatosin
Brown, Philip
[J]. GENES, 2021, 12 (11)
[23] 3D RECONSTRUCTION FROM LINE DRAWINGS
Wendt, Lars H.
Stork, Andre
Kuijper, Arjan
Fellner, Dieter W.
[J]. GRAPP 2010: PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTER GRAPHICS THEORY AND APPLICATIONS, 2010, : 65 - 71
[24] 3D Reconstruction from Image Sequence
Liu, Ji-zhong
Zheng, En-tao
Wang, Guang-hui
Chen, Cai-ying
[J]. 2015 INTERNATIONAL CONFERENCE ON SOFTWARE, MULTIMEDIA AND COMMUNICATION ENGINEERING (SMCE 2015), 2015, : 117 - 122
[25] OVERVIEW ON 3D RECONSTRUCTION FROM IMAGES
Aharchi, Moncef
Kbir, M'hamed Ait
[J]. 4TH INTERNATIONAL CONFERENCE ON SMART CITY APPLICATIONS (SCA' 19), 2019,
[26] 3D RECONSTRUCTION FROM MRI IMAGES
Anderla, Andras
Brkljac, Branko
Stefanovic, Darko
Krsmanovic, Cvijan
Sladojevic, Srdan
Culibrk, Dubravko
[J]. METALURGIA INTERNATIONAL, 2013, 18 : 17 - 21
[27] 3D Reconstruction from Hyperspectral Images
Zia, Ali
Liang, Jie
Zhou, Jun
Gao, Yongsheng
[J]. 2015 IEEE WINTER CONFERENCE ON APPLICATIONS OF COMPUTER VISION (WACV), 2015, : 318 - 325
[28] 3D Reconstruction from A Single Image
Ping, Guiju
Wang, Han
[J]. PROCEEDINGS OF THE IEEE 2019 9TH INTERNATIONAL CONFERENCE ON CYBERNETICS AND INTELLIGENT SYSTEMS (CIS) ROBOTICS, AUTOMATION AND MECHATRONICS (RAM) (CIS & RAM 2019), 2019, : 47 - 52
[29] Can 3D diploid genome reconstruction from unphased Hi-C data be salvaged?
Segal, Mark R.
[J]. NAR GENOMICS AND BIOINFORMATICS, 2022, 4 (02)
[30] Reconstruction of 3D genome architecture via a two-stage algorithm
Mark R. Segal
Henrik L. Bengtsson
[J]. BMC Bioinformatics, 16

← 1 2 3 4 5 →