The Experts below are selected from a list of 3828 Experts worldwide ranked by ideXlab platform
Chun Liang - One of the best experts on this subject based on the ideXlab platform.
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mirPRo–a novel Standalone Program for differential expression and variation analysis of miRNAs
Scientific reports, 2015Co-Authors: Jieming Shi, Min Dong, Lin Liu, Agustin Luz-madrigal, Panagiotis A. Tsonis, Katia Del Rio-tsonis, Chun LiangAbstract:Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing Standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new Standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used Standalone Program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source Standalone Program (https://sourceforge.net/projects/mirpro/).
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mirpro a novel Standalone Program for differential expression and variation analysis of mirnas
Scientific Reports, 2015Co-Authors: Jieming Shi, Min Dong, Lin Liu, Panagiotis A. Tsonis, Agustin Luzmadrigal, Katia Del Riotsonis, Chun LiangAbstract:Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing Standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new Standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used Standalone Program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source Standalone Program (https://sourceforge.net/projects/mirpro/).
Daniel H. Huson - One of the best experts on this subject based on the ideXlab platform.
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MAIRA- real-time taxonomic and functional analysis of long reads on a laptop
BMC Bioinformatics, 2020Co-Authors: Benjamin Albrecht, Caner Bağcı, Daniel H. HusonAbstract:Background Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud. Results MAIRA is a new Standalone Program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The Program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph. Conclusions We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.
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MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.
BMC Bioinformatics, 2020Co-Authors: Benjamin Albrecht, Caner Bağcı, Daniel H. HusonAbstract:Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud. MAIRA is a new Standalone Program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The Program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph. We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.
Dario Ghersi - One of the best experts on this subject based on the ideXlab platform.
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FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis
BMC Bioinformatics, 2019Co-Authors: Matthew L. Hale, Ishwor Thapa, Dario GhersiAbstract:BackgroundGene Ontology enrichment analysis provides an effective way to extract meaningful information from complex biological datasets. By identifying terms that are significantly overrepresented in a gene set, researchers can uncover biological features shared by genes. In addition to extracting enriched terms, it is also important to visualize the results in a way that is conducive to biological interpretation.ResultsHere we present FunSet, a new web server to perform and visualize enrichment analysis. The web server identifies Gene Ontology terms that are statistically overrepresented in a target set with respect to a background set. The enriched terms are displayed in a 2D plot that captures the semantic similarity between terms, with the option to cluster terms via spectral clustering and identify a representative term for each cluster. FunSet can be used interactively or Programmatically, and allows users to download the enrichment results both in tabular form and in graphical form as SVG files or in data format as JSON or csv. To enhance reproducibility of the analyses, users have access to historical data for the ontology and the annotations. The source code for the Standalone Program and the web server are made available with an open-source license.
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funset an open source software and web server for performing and displaying gene ontology enrichment analysis
BMC Bioinformatics, 2019Co-Authors: Matthew L. Hale, Ishwor Thapa, Dario GhersiAbstract:Gene Ontology enrichment analysis provides an effective way to extract meaningful information from complex biological datasets. By identifying terms that are significantly overrepresented in a gene set, researchers can uncover biological features shared by genes. In addition to extracting enriched terms, it is also important to visualize the results in a way that is conducive to biological interpretation. Here we present FunSet, a new web server to perform and visualize enrichment analysis. The web server identifies Gene Ontology terms that are statistically overrepresented in a target set with respect to a background set. The enriched terms are displayed in a 2D plot that captures the semantic similarity between terms, with the option to cluster terms via spectral clustering and identify a representative term for each cluster. FunSet can be used interactively or Programmatically, and allows users to download the enrichment results both in tabular form and in graphical form as SVG files or in data format as JSON or csv. To enhance reproducibility of the analyses, users have access to historical data for the ontology and the annotations. The source code for the Standalone Program and the web server are made available with an open-source license.
Jieming Shi - One of the best experts on this subject based on the ideXlab platform.
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mirPRo–a novel Standalone Program for differential expression and variation analysis of miRNAs
Scientific reports, 2015Co-Authors: Jieming Shi, Min Dong, Lin Liu, Agustin Luz-madrigal, Panagiotis A. Tsonis, Katia Del Rio-tsonis, Chun LiangAbstract:Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing Standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new Standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used Standalone Program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source Standalone Program (https://sourceforge.net/projects/mirpro/).
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mirpro a novel Standalone Program for differential expression and variation analysis of mirnas
Scientific Reports, 2015Co-Authors: Jieming Shi, Min Dong, Lin Liu, Panagiotis A. Tsonis, Agustin Luzmadrigal, Katia Del Riotsonis, Chun LiangAbstract:Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing Standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new Standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used Standalone Program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and "arm switching" detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source Standalone Program (https://sourceforge.net/projects/mirpro/).
Benjamin Albrecht - One of the best experts on this subject based on the ideXlab platform.
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MAIRA- real-time taxonomic and functional analysis of long reads on a laptop
BMC Bioinformatics, 2020Co-Authors: Benjamin Albrecht, Caner Bağcı, Daniel H. HusonAbstract:Background Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud. Results MAIRA is a new Standalone Program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The Program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph. Conclusions We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.
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MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.
BMC Bioinformatics, 2020Co-Authors: Benjamin Albrecht, Caner Bağcı, Daniel H. HusonAbstract:Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud. MAIRA is a new Standalone Program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The Program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph. We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.
