An optimal method to segment piecewise poisson distributed signals with application to sequencing data

Junbo Duan; Charles Soussen; David Brie; Jérôme Idier; Yu Ping Wang; Mingxi Wan

doi:10.1109/EMBC.2015.7319873

An optimal method to segment piecewise poisson distributed signals with application to sequencing data

Junbo Duan
, Charles Soussen
, David Brie
, Jérôme Idier
, Yu Ping Wang
, Mingxi Wan

School of Life Science and Technology (SLST)

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Abstract

To analyze the next generation sequencing data, the so-called read depth signal is often segmented with standard segmentation tools. However, these tools usually assume the signal to be a piecewise constant signal and contaminated with zero mean Gaussian noise, and therefore modeling error occurs. This paper models the read depth signal with piecewise Poisson distribution, which is more appropriate to the next generation sequencing mechanism. Based on the proposed model, an opti- mal dynamic programming algorithm with parallel computing is proposed to segment the piecewise signal, and furthermore detect the copy number variation.

Original language	English
Title of host publication	2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	6465-6468
Number of pages	4
ISBN (Electronic)	9781424492718
DOIs	https://doi.org/10.1109/EMBC.2015.7319873
State	Published - 4 Nov 2015
Event	37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015 - Milan, Italy Duration: 25 Aug 2015 → 29 Aug 2015

Publication series

Name	Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
Volume	2015-November
ISSN (Print)	1557-170X

Conference

Conference	37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015
Country/Territory	Italy
City	Milan
Period	25/08/15 → 29/08/15

Access to Document

10.1109/EMBC.2015.7319873

Cite this

Duan, J., Soussen, C., Brie, D., Idier, J., Wang, Y. P., & Wan, M. (2015). An optimal method to segment piecewise poisson distributed signals with application to sequencing data. In 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015 (pp. 6465-6468). Article 7319873 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS; Vol. 2015-November). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/EMBC.2015.7319873

Duan, Junbo ; Soussen, Charles ; Brie, David et al. / An optimal method to segment piecewise poisson distributed signals with application to sequencing data. 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 6465-6468 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

@inproceedings{9d6aa8c95bae4d219c45a3cf3fb74d0a,

title = "An optimal method to segment piecewise poisson distributed signals with application to sequencing data",

abstract = "To analyze the next generation sequencing data, the so-called read depth signal is often segmented with standard segmentation tools. However, these tools usually assume the signal to be a piecewise constant signal and contaminated with zero mean Gaussian noise, and therefore modeling error occurs. This paper models the read depth signal with piecewise Poisson distribution, which is more appropriate to the next generation sequencing mechanism. Based on the proposed model, an opti- mal dynamic programming algorithm with parallel computing is proposed to segment the piecewise signal, and furthermore detect the copy number variation.",

author = "Junbo Duan and Charles Soussen and David Brie and J{\'e}r{\^o}me Idier and Wang, \{Yu Ping\} and Mingxi Wan",

note = "Publisher Copyright: {\textcopyright} 2015 IEEE.; 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015 ; Conference date: 25-08-2015 Through 29-08-2015",

year = "2015",

month = nov,

day = "4",

doi = "10.1109/EMBC.2015.7319873",

language = "英语",

series = "Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "6465--6468",

booktitle = "2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015",

}

Duan, J, Soussen, C, Brie, D, Idier, J, Wang, YP & Wan, M 2015, An optimal method to segment piecewise poisson distributed signals with application to sequencing data. in 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015., 7319873, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, vol. 2015-November, Institute of Electrical and Electronics Engineers Inc., pp. 6465-6468, 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015, Milan, Italy, 25/08/15. https://doi.org/10.1109/EMBC.2015.7319873

An optimal method to segment piecewise poisson distributed signals with application to sequencing data. / Duan, Junbo; Soussen, Charles; Brie, David et al.
2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015. Institute of Electrical and Electronics Engineers Inc., 2015. p. 6465-6468 7319873 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS; Vol. 2015-November).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - An optimal method to segment piecewise poisson distributed signals with application to sequencing data

AU - Duan, Junbo

AU - Soussen, Charles

AU - Brie, David

AU - Idier, Jérôme

AU - Wang, Yu Ping

AU - Wan, Mingxi

PY - 2015/11/4

Y1 - 2015/11/4

N2 - To analyze the next generation sequencing data, the so-called read depth signal is often segmented with standard segmentation tools. However, these tools usually assume the signal to be a piecewise constant signal and contaminated with zero mean Gaussian noise, and therefore modeling error occurs. This paper models the read depth signal with piecewise Poisson distribution, which is more appropriate to the next generation sequencing mechanism. Based on the proposed model, an opti- mal dynamic programming algorithm with parallel computing is proposed to segment the piecewise signal, and furthermore detect the copy number variation.

AB - To analyze the next generation sequencing data, the so-called read depth signal is often segmented with standard segmentation tools. However, these tools usually assume the signal to be a piecewise constant signal and contaminated with zero mean Gaussian noise, and therefore modeling error occurs. This paper models the read depth signal with piecewise Poisson distribution, which is more appropriate to the next generation sequencing mechanism. Based on the proposed model, an opti- mal dynamic programming algorithm with parallel computing is proposed to segment the piecewise signal, and furthermore detect the copy number variation.

UR - https://www.scopus.com/pages/publications/84953296881

U2 - 10.1109/EMBC.2015.7319873

DO - 10.1109/EMBC.2015.7319873

M3 - 会议稿件

C2 - 26737773

AN - SCOPUS:84953296881

T3 - Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

SP - 6465

EP - 6468

BT - 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015

Y2 - 25 August 2015 through 29 August 2015

ER -

Duan J, Soussen C, Brie D, Idier J, Wang YP, Wan M. An optimal method to segment piecewise poisson distributed signals with application to sequencing data. In 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 6465-6468. 7319873. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). doi: 10.1109/EMBC.2015.7319873

An optimal method to segment piecewise poisson distributed signals with application to sequencing data

Abstract

Publication series

Conference

Access to Document

Other files and links

Fingerprint

Cite this