发表状态 | 已发表Published |
题名 | A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns |
作者 | |
发表日期 | 2017-12-01 |
发表期刊 | Scientific Reports
![]() |
卷号 | 7期号:1 |
摘要 | Variations in DNA copy number carry important information on genome evolution and regulation of DNA replication in cancer cells. The rapid development of single-cell sequencing technology enables exploration of gene-expression heterogeneity among single cells, providing important information on cell evolution. Evolutionary relationships in accumulated sequence data can be visualized by adjacent positioning of similar cells so that similar copy-number profiles are shown by block patterns. However, single-cell DNA sequencing data usually have low amount of starting genome, which requires an extra step of amplification to accumulate sufficient samples, introducing noise and making regular pattern-finding challenging. In this paper, we will propose to tackle this issue of recovering the hidden blocks within single-cell DNA-sequencing data through continuous sample permutations such that similar samples are positioned adjacently. The permutation is guided by the total variational norm of the recovered copy number profiles, and is continued until the total variational norm is minimized when similar samples are stacked together to reveal block patterns. An efficient numerical scheme for finding this permutation is designed, tailored from the alternating direction method of multipliers. Application of this method to both simulated and real data demonstrates its ability to recover the hidden structures of single-cell DNA sequences. |
DOI | 10.1038/s41598-017-09139-8 |
URL | 查看来源 |
收录类别 | SCIE |
语种 | 英语English |
WOS研究方向 | Science & Technology - Other Topics |
WOS类目 | Multidisciplinary Sciences |
WOS记录号 | WOS:000408535700011 |
Scopus入藏号 | 2-s2.0-85028473008 |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | https://repository.uic.edu.cn/handle/39GCC9TT/6345 |
专题 | 理工科技学院 |
通讯作者 | Cheung, Yiu-ming |
作者单位 | 1.Electrical and Information College of Jinan,University,Zhuhai,China 2.Department of Computer Science,Hong Kong Baptist University China,Hong Kong,China 3.HKBU Institute of Research and Continuing Education,Shenzhen,China 4.BNU-HKBU United International College,Zhuhai,China |
通讯作者单位 | 北师香港浸会大学 |
推荐引用方式 GB/T 7714 | Zhang, Yue,Cheung, Yiu-ming,Su, Weifeng. A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns[J]. Scientific Reports, 2017, 7(1). |
APA | Zhang, Yue, Cheung, Yiu-ming, & Su, Weifeng. (2017). A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns. Scientific Reports, 7(1). |
MLA | Zhang, Yue,et al."A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns". Scientific Reports 7.1(2017). |
条目包含的文件 | 条目无相关文件。 |
除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。
修改评论