Journal
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Volume 16, Issue 5, Pages 1620-1626Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TCBB.2018.2814995
Keywords
Three-dimensional displays; Sociology; Statistics; Genomics; Bioinformatics; Sparse matrices; Optimization; Chromosome conformation capture; 3D reconstruction; genetic algorithm; ShRec3D
Categories
Funding
- JSPS KAKENHI [15K00402, 16H03261, 262801060, 16K125250]
- Grants-in-Aid for Scientific Research [15K00402, 15K00403, 16H03261] Funding Source: KAKEN
Ask authors/readers for more resources
Recent epigenetics research has demonstrated that chromatin conformation plays an important role in various aspects of gene regulation. Chromosome Conformation Capture (3C) technology makes it possible to analyze the spatial organization of chromatin in a cell. Several algorithms for three-dimensional reconstruction of chromatin structure from 3C experimental data have been proposed. Compared to other algorithms, ShRec3D, one of the most advanced algorithms, can reconstruct a chromatin model in the shortest time for high-resolution whole-genome experimental data. However, ShRec3D employs a graph shortest path algorithm, which introduces errors in the resulting model. We propose an improved algorithm that optimizes shortest path distances using a genetic algorithm approach. The proposed algorithm and ShRec3D were compared using in silico 3C experimental data. Compared to ShRec3D, the proposed algorithm demonstrated significant improvement relative to the similarity between the algorithm's output and the original model with a reasonable increase to calculation time.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available