Pathogen detection using short-RNA deep sequencing subtraction and assembly

Ofer Isakov; Shira Modai; Noam Shomron

doi:10.1093/bioinformatics/btr349

Pathogen detection using short-RNA deep sequencing subtraction and assembly

Ofer Isakov, Shira Modai, Noam Shomron

Tel Aviv University

Research output: Contribution to journal › Article › peer-review

Abstract

Motivation: Early and accurate detection of human pathogen infection is critical for treatment and therapeutics. Here we describe pathogen identification using short RNA subtraction and assembly (SRSA), a detection method that overcomes the requirement of prior knowledge and culturing of pathogens, by using degraded small RNA and deep sequencing technology. We prove our approach's efficiency through identification of a combined viral and bacterial infection in human cells.

Original language	English
Article number	btr349
Pages (from-to)	2027-2030
Number of pages	4
Journal	Bioinformatics
Volume	27
Issue number	15
DOIs	https://doi.org/10.1093/bioinformatics/btr349
State	Published - Aug 2011

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr349

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title = "Pathogen detection using short-RNA deep sequencing subtraction and assembly",

abstract = "Motivation: Early and accurate detection of human pathogen infection is critical for treatment and therapeutics. Here we describe pathogen identification using short RNA subtraction and assembly (SRSA), a detection method that overcomes the requirement of prior knowledge and culturing of pathogens, by using degraded small RNA and deep sequencing technology. We prove our approach's efficiency through identification of a combined viral and bacterial infection in human cells.",

author = "Ofer Isakov and Shira Modai and Noam Shomron",

note = "Funding Information: Funding: The Shomron laboratory is supported by the Chief Scientist Office, Ministry of Health, Israel; Kunz-Lion Foundation; Ori Levi Foundation for Mitochondrial Research; Israel Cancer Association; the Wolfson family Charitable Fund. O.I. is supported by a fellowship from the Edmond J. Safra Bioinformatics program at Tel-Aviv University.",

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doi = "10.1093/bioinformatics/btr349",

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AB - Motivation: Early and accurate detection of human pathogen infection is critical for treatment and therapeutics. Here we describe pathogen identification using short RNA subtraction and assembly (SRSA), a detection method that overcomes the requirement of prior knowledge and culturing of pathogens, by using degraded small RNA and deep sequencing technology. We prove our approach's efficiency through identification of a combined viral and bacterial infection in human cells.

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Pathogen detection using short-RNA deep sequencing subtraction and assembly

Abstract

All Science Journal Classification (ASJC) codes

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