Bioinformatics on Maragkakis Lab

SamQL: A Structured Query Language and filtering tool for the SAM/BAM file format

Sat, 02 Oct 2021 00:00:00 +0000

Summary

SamQL implements a SQL-like query language for filtering and extracting reads from SAM/BAM alignment files based on arbitrary combinations of alignment attributes. The tool enables complex queries that are not possible with existing SAM/BAM filtering utilities, facilitating flexible downstream analysis of sequencing data.

bíogo: a simple high-performance bioinformatics toolkit for the Go language

Sat, 18 Feb 2017 00:00:00 +0000

Summary

bíogo is a bioinformatics library written in the Go programming language, providing high-performance tools for common genomic data processing tasks. The toolkit offers a clean API for sequence manipulation, alignment, and genomic data parsing with the performance characteristics of a compiled language.

CLIPSeqTools — a novel bioinformatics CLIP-seq analysis suite

Fri, 01 Jan 2016 00:00:00 +0000

Summary

CLIPSeqTools is a modular bioinformatics pipeline for the analysis of CLIP-seq data, providing tools for read processing, peak calling, motif analysis, and visualization. The suite enables comprehensive characterization of RNA-binding protein interaction sites across the transcriptome.

DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs

Tue, 01 Jan 2013 00:00:00 +0000

Summary

DIANA-LncBase is the first database dedicated to microRNA interactions with long non-coding RNAs, combining experimentally validated interactions with high-confidence computational predictions. The resource enables systematic study of miRNA-lncRNA regulatory networks.

DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways

Sun, 01 Jul 2012 00:00:00 +0000

Summary

DIANA miRPath v.2.0 enables researchers to study how multiple microRNAs cooperatively regulate biological pathways. The updated tool incorporates improved statistical methods and expanded databases for pathway enrichment analysis based on miRNA target predictions.

Functional microRNA targets in protein coding sequences

Thu, 15 Mar 2012 00:00:00 +0000

Summary

This study demonstrates that microRNAs can regulate gene expression through binding sites located within protein-coding sequences, not only the canonical 3’ UTR sites. Functional coding sequence targets are identified and validated, broadening the scope of miRNA-mediated gene regulation.

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

Sun, 01 Jan 2012 00:00:00 +0000

Summary

TarBase 6.0 is a manually curated database of experimentally validated microRNA targets, significantly expanding the collection of miRNA-target interactions with experimental support from the literature. The database provides a gold standard for benchmarking computational prediction methods.

DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association

Fri, 01 Jul 2011 00:00:00 +0000

Summary

This update to the DIANA-microT web server extends its target prediction capabilities to Drosophila melanogaster and Caenorhabditis elegans microRNAs, and introduces a bibliographic module linking microRNAs to diseases based on the scientific literature.

Online resources for microRNA analysis

Mon, 17 Jan 2011 00:00:00 +0000

Summary

This article provides a curated overview of the online tools, databases, and web servers available for microRNA research, covering target prediction, expression analysis, and pathway analysis resources.

The DIANA-mirExTra web server: from gene expression data to microRNA function

Thu, 11 Feb 2010 00:00:00 +0000

Summary

DIANA-mirExTra identifies microRNAs driving observed gene expression changes by combining miRNA target predictions with gene expression data. Users provide a list of differentially expressed genes and receive ranked microRNAs predicted to regulate that expression signature.

Lost in translation: an assessment and perspective for computational microRNA target identification

Tue, 01 Dec 2009 00:00:00 +0000

Summary

This work provides a systematic assessment of the state of computational microRNA target identification, examining the performance of existing tools and discussing the challenges in translating predictions into biological insight. Guidelines are provided for researchers interpreting computational miRNA target predictions.

Accurate microRNA target prediction correlates with protein repression levels

Fri, 18 Sep 2009 00:00:00 +0000

Summary

This study benchmarks microRNA target prediction methods against protein repression data, showing that the DIANA-microT algorithm achieves high correlation with experimentally measured protein repression. The work provides a framework for evaluating and improving computational miRNA target prediction.

DIANA-mirPath: Integrating human and mouse microRNAs in pathways

Sat, 01 Aug 2009 00:00:00 +0000

Summary

DIANA-mirPath is a web-based tool that integrates microRNA target predictions with KEGG pathway data to identify biological pathways regulated by user-specified microRNAs. The tool supports both human and mouse miRNAs and provides statistical analysis of pathway enrichment.

DIANA-microT web server: elucidating microRNA functions through target prediction

Wed, 01 Jul 2009 00:00:00 +0000

Summary

The DIANA-microT web server provides access to the DIANA-microT algorithm for microRNA target prediction. The server enables researchers to identify genes regulated by specific microRNAs, query microRNAs targeting specific genes, and perform pathway-level analysis of miRNA regulatory networks.