Patho-finder-A fast and accurate program for pathogen identification through RNA-seq

Chin Ting Wu; Tzu Hung Hsiao; Yu Chiao Chiu; Yu Ching Hsu; Eric Y. Chuang; Yidong Chen

doi:10.1109/BIBM.2015.7359843

Patho-finder-A fast and accurate program for pathogen identification through RNA-seq

Chin Ting Wu, Tzu Hung Hsiao, Yu Chiao Chiu, Yu Ching Hsu, Eric Y. Chuang, Yidong Chen

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

Abstract

Technology of next generation sequencing to detect pathogens of sample can impact human health by revealing pathogens which cause disease. Several workflow has developed in purposed to detect pathogens in next generation sequencing data. However, the requirement of computation power of these workflows limited the application. The time consuming problem make the workflow difficult to detect datasets with large sample size. Here we presented Patho-finder, a fast and accurate workflow designed for detecting pathogen in RNA sequencing data. We have evaluated performance of Patho-finder by three aspects. First, we evaluate performance by alter the data features, to see how Patho-finder work under different simulation conditions. Next, we compare the time consuming and accuracy between Patho-finder and existing workflow. At last, we used Patho-finder on the RNA-seq of cell lines with known virus-infected. The validation result demonstrated our approach could finish the task in real datasets.

Original language	English (US)
Title of host publication	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editors	lng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	1148-1151
Number of pages	4
ISBN (Electronic)	9781467367981
DOIs	https://doi.org/10.1109/BIBM.2015.7359843
State	Published - Dec 16 2015
Event	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States Duration: Nov 9 2015 → Nov 12 2015

Publication series

Name	Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

Other	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Country/Territory	United States
City	Washington
Period	11/9/15 → 11/12/15

Keywords

RNA-seq
next generation sequencing
pathogen

ASJC Scopus subject areas

Software
Artificial Intelligence
Health Informatics
Biomedical Engineering

Access to Document

10.1109/BIBM.2015.7359843

Cite this

Wu, C. T., Hsiao, T. H., Chiu, Y. C., Hsu, Y. C., Chuang, E. Y., & Chen, Y. (2015). Patho-finder-A fast and accurate program for pathogen identification through RNA-seq. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 1148-1151). Article 7359843 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359843

Patho-finder-A fast and accurate program for pathogen identification through RNA-seq. / Wu, Chin Ting; Hsiao, Tzu Hung; Chiu, Yu Chiao et al.
Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. ed. / lng. Matthieu Schapranow; Jiayu Zhou; Xiaohua Tony Hu; Bin Ma; Sanguthevar Rajasekaran; Satoru Miyano; Illhoi Yoo; Brian Pierce; Amarda Shehu; Vijay K. Gombar; Brian Chen; Vinay Pai; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. p. 1148-1151 7359843 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

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

Wu, CT, Hsiao, TH, Chiu, YC, Hsu, YC, Chuang, EY & Chen, Y 2015, Patho-finder-A fast and accurate program for pathogen identification through RNA-seq. in LM Schapranow, J Zhou, XT Hu, B Ma, S Rajasekaran, S Miyano, I Yoo, B Pierce, A Shehu, VK Gombar, B Chen, V Pai & J Huan (eds), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359843, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 1148-1151, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359843

Wu CT, Hsiao TH, Chiu YC, Hsu YC, Chuang EY, Chen Y. Patho-finder-A fast and accurate program for pathogen identification through RNA-seq. In Schapranow LM, Zhou J, Hu XT, Ma B, Rajasekaran S, Miyano S, Yoo I, Pierce B, Shehu A, Gombar VK, Chen B, Pai V, Huan J, editors, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 1148-1151. 7359843. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). doi: 10.1109/BIBM.2015.7359843

Wu, Chin Ting ; Hsiao, Tzu Hung ; Chiu, Yu Chiao et al. / Patho-finder-A fast and accurate program for pathogen identification through RNA-seq. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. editor / lng. Matthieu Schapranow ; Jiayu Zhou ; Xiaohua Tony Hu ; Bin Ma ; Sanguthevar Rajasekaran ; Satoru Miyano ; Illhoi Yoo ; Brian Pierce ; Amarda Shehu ; Vijay K. Gombar ; Brian Chen ; Vinay Pai ; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 1148-1151 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

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abstract = "Technology of next generation sequencing to detect pathogens of sample can impact human health by revealing pathogens which cause disease. Several workflow has developed in purposed to detect pathogens in next generation sequencing data. However, the requirement of computation power of these workflows limited the application. The time consuming problem make the workflow difficult to detect datasets with large sample size. Here we presented Patho-finder, a fast and accurate workflow designed for detecting pathogen in RNA sequencing data. We have evaluated performance of Patho-finder by three aspects. First, we evaluate performance by alter the data features, to see how Patho-finder work under different simulation conditions. Next, we compare the time consuming and accuracy between Patho-finder and existing workflow. At last, we used Patho-finder on the RNA-seq of cell lines with known virus-infected. The validation result demonstrated our approach could finish the task in real datasets.",

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AU - Chuang, Eric Y.

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AB - Technology of next generation sequencing to detect pathogens of sample can impact human health by revealing pathogens which cause disease. Several workflow has developed in purposed to detect pathogens in next generation sequencing data. However, the requirement of computation power of these workflows limited the application. The time consuming problem make the workflow difficult to detect datasets with large sample size. Here we presented Patho-finder, a fast and accurate workflow designed for detecting pathogen in RNA sequencing data. We have evaluated performance of Patho-finder by three aspects. First, we evaluate performance by alter the data features, to see how Patho-finder work under different simulation conditions. Next, we compare the time consuming and accuracy between Patho-finder and existing workflow. At last, we used Patho-finder on the RNA-seq of cell lines with known virus-infected. The validation result demonstrated our approach could finish the task in real datasets.

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Patho-finder-A fast and accurate program for pathogen identification through RNA-seq

Abstract

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Keywords

ASJC Scopus subject areas

Access to Document

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