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 proceedingConference 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 languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1148-1151
Number of pages4
ISBN (Electronic)9781467367981
DOIs
StatePublished - Dec 16 2015
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: Nov 9 2015Nov 12 2015

Other

OtherIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period11/9/1511/12/15

Fingerprint

Workflow
Pathogens
RNA
RNA Sequence Analysis
Viruses
Sample Size
Cells
Health
Technology
Cell Line

Keywords

  • next generation sequencing
  • pathogen
  • RNA-seq

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence
  • Health Informatics
  • Biomedical Engineering

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 Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 1148-1151). [7359843] 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; Hsu, Yu Ching; Chuang, Eric Y.; Chen, Yidong.

Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc., 2015. p. 1148-1151 7359843.

Research output: Chapter in Book/Report/Conference proceedingConference 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 Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359843, 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 Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 1148-1151. 7359843 https://doi.org/10.1109/BIBM.2015.7359843
Wu, Chin Ting ; Hsiao, Tzu Hung ; Chiu, Yu Chiao ; Hsu, Yu Ching ; Chuang, Eric Y. ; Chen, Yidong. / Patho-finder-A fast and accurate program for pathogen identification through RNA-seq. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 1148-1151
@inproceedings{1188001aa5b4414492af5398bee152b7,
title = "Patho-finder-A fast and accurate program for pathogen identification through RNA-seq",
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.",
keywords = "next generation sequencing, pathogen, RNA-seq",
author = "Wu, {Chin Ting} and Hsiao, {Tzu Hung} and Chiu, {Yu Chiao} and Hsu, {Yu Ching} and Chuang, {Eric Y.} and Yidong Chen",
year = "2015",
month = "12",
day = "16",
doi = "10.1109/BIBM.2015.7359843",
language = "English (US)",
pages = "1148--1151",
booktitle = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
address = "United States",

}

TY - GEN

T1 - Patho-finder-A fast and accurate program for pathogen identification through RNA-seq

AU - Wu, Chin Ting

AU - Hsiao, Tzu Hung

AU - Chiu, Yu Chiao

AU - Hsu, Yu Ching

AU - Chuang, Eric Y.

AU - Chen, Yidong

PY - 2015/12/16

Y1 - 2015/12/16

N2 - 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.

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.

KW - next generation sequencing

KW - pathogen

KW - RNA-seq

UR - http://www.scopus.com/inward/record.url?scp=84962359226&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84962359226&partnerID=8YFLogxK

U2 - 10.1109/BIBM.2015.7359843

DO - 10.1109/BIBM.2015.7359843

M3 - Conference contribution

AN - SCOPUS:84962359226

SP - 1148

EP - 1151

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

PB - Institute of Electrical and Electronics Engineers Inc.

ER -