Research ExplorerPublicationsOasis 2: improved online analysis of small RNA-seq data

Oasis 2: improved online analysis of small RNA-seq data

Standard

Oasis 2: improved online analysis of small RNA-seq data. / Rahman, Raza-Ur; Gautam, Abhivyakti; Bethune, Jörn; Sattar, Abdul; Fiosins, Maksims; Magruder, Daniel Sumner; Capece, Vincenzo; Shomroni, Orr; Bonn, Stefan.

In: BMC BIOINFORMATICS, Vol. 19, No. 1, 14.02.2018, p. 54.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Rahman, R-U, Gautam, A, Bethune, J, Sattar, A, Fiosins, M, Magruder, DS, Capece, V, Shomroni, O & Bonn, S 2018, 'Oasis 2: improved online analysis of small RNA-seq data', BMC BIOINFORMATICS, vol. 19, no. 1, pp. 54. https://doi.org/10.1186/s12859-018-2047-z

APA

Rahman, R-U., Gautam, A., Bethune, J., Sattar, A., Fiosins, M., Magruder, D. S., Capece, V., Shomroni, O., & Bonn, S. (2018). Oasis 2: improved online analysis of small RNA-seq data. BMC BIOINFORMATICS, 19(1), 54. https://doi.org/10.1186/s12859-018-2047-z

Vancouver

Rahman R-U, Gautam A, Bethune J, Sattar A, Fiosins M, Magruder DS et al. Oasis 2: improved online analysis of small RNA-seq data. BMC BIOINFORMATICS. 2018 Feb 14;19(1):54. https://doi.org/10.1186/s12859-018-2047-z

Bibtex

@article{8436be740594488cabb5119323e59073,
title = "Oasis 2: improved online analysis of small RNA-seq data",
abstract = "BACKGROUND: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing.RESULTS: Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module.CONCLUSIONS: Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.AVAILABILITY AND IMPLEMENTATION: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.",
keywords = "Base Sequence, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, MicroRNAs, RNA, Small Untranslated, Sequence Analysis, RNA, Software, Statistics as Topic, Journal Article, Research Support, Non-U.S. Gov't",
author = "Raza-Ur Rahman and Abhivyakti Gautam and J{\"o}rn Bethune and Abdul Sattar and Maksims Fiosins and Magruder, {Daniel Sumner} and Vincenzo Capece and Orr Shomroni and Stefan Bonn",
year = "2018",
month = feb,
day = "14",
doi = "10.1186/s12859-018-2047-z",
language = "English",
volume = "19",
pages = "54",
journal = "BMC BIOINFORMATICS",
issn = "1471-2105",
publisher = "BioMed Central Ltd.",
number = "1",

}

RIS

TY - JOUR

T1 - Oasis 2: improved online analysis of small RNA-seq data

AU - Rahman, Raza-Ur

AU - Gautam, Abhivyakti

AU - Bethune, Jörn

AU - Sattar, Abdul

AU - Fiosins, Maksims

AU - Magruder, Daniel Sumner

AU - Capece, Vincenzo

AU - Shomroni, Orr

AU - Bonn, Stefan

PY - 2018/2/14

Y1 - 2018/2/14

N2 - BACKGROUND: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing.RESULTS: Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module.CONCLUSIONS: Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.AVAILABILITY AND IMPLEMENTATION: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.

AB - BACKGROUND: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing.RESULTS: Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module.CONCLUSIONS: Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.AVAILABILITY AND IMPLEMENTATION: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.

KW - Base Sequence

KW - Gene Expression Profiling

KW - High-Throughput Nucleotide Sequencing

KW - MicroRNAs

KW - RNA, Small Untranslated

KW - Sequence Analysis, RNA

KW - Software

KW - Statistics as Topic

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1186/s12859-018-2047-z

DO - 10.1186/s12859-018-2047-z

M3 - SCORING: Journal article

C2 - 29444641

VL - 19

SP - 54

JO - BMC BIOINFORMATICS

JF - BMC BIOINFORMATICS

SN - 1471-2105

IS - 1

ER -