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Chimira
UNLABELLED: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates...
MapMi
BACKGROUND: A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs...
Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies...
Detecting and comparing non-coding RNAs in the high-throughput era.
In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes and of the finding that many of these transcripts are...
Annotation of mammalian primary microRNAs.
BACKGROUND: MicroRNAs (miRNAs) are important regulators of gene expression and have been implicated in development, differentiation and pathogenesis. Hundreds of miRNAs have been discovered in mammalian genomes. Approximately...
Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation.
BACKGROUND: Synapse formation and the development of neural networks are known to be controlled by a coordinated program of mRNA synthesis. microRNAs are now recognized to be important regulators of mRNA translation and...
Evolutionary and functional insights into Leishmania META1
BACKGROUND: Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear....
Amino Acid Sequence Bacterial Proteins Base Composition DNA Protozoan evolution Molecular Gene Transfer Horizontal Leishmania Models Molecular Molecular Sequence Data Mutagenesis Site-Directed Phylogeny Protein Structure Tertiary Protozoan Proteins selection Genetic Sequence Alignment Sequence Analysis DNA Virulence
Large-scale analysis of microRNA evolution.
BACKGROUND: In animals, microRNAs (miRNA) are important genetic regulators. Animal miRNAs appear to have expanded in conjunction with an escalation in complexity during early bilaterian evolution. Their small size and...
Detecting microRNA binding and siRNA off-target effects from expression data.
Sylamer is a method for detecting microRNA target and small interfering RNA off-target signals in 3' untranslated regions from a ranked gene list, sorted from upregulated to downregulated, after a microRNA perturbation or RNA...
spongeScan
Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has...
miRBase
miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature...
The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/U-rich transcriptome.
Plasmodium falciparum, a protozoan parasite and causative agent of human malaria, has one of the most A/T-biased genomes sequenced to date. This may give the genome and the transcriptome unusual structural features. Recent...
The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A/U-rich transcriptome.
Plasmodium falciparum, a protozoan parasite and causative agent of human malaria, has one of the most A/T-biased genomes sequenced to date. This may give the genome and the transcriptome unusual structural features. Recent...
Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.
BACKGROUND: RNA inhibition by siRNAs is a frequently used approach to identify genes required for specific biological processes. However RNAi screening using siRNAs is hampered by non-specific or off target effects of the...
Visualisation of BioPAX Networks using BioLayout Express (3D).
BioLayout Express (3D) is a network analysis tool designed for the visualisation and analysis of graphs derived from biological data. It has proved to be powerful in the analysis of gene expression data, biological pathways and...
Visualizing genome and systems biology
Georgios A Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J Enright, Ioannis Iliopoulos
Jan 22, 2018
"Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information....
Defective germline reprogramming rewires the spermatogonial transcriptome.
Lina Vasiliauskaitė, Rebecca V Berrens, Ivayla Ivanova, Claudia Carrieri, Wolf Reik, Anton J Enright, Dónal O'Carroll
Dec 18, 2018
Defective germline reprogramming in Piwil4 (Miwi2)- and Dnmt3l-deficient mice results in the failure to reestablish transposon silencing, meiotic arrest and progressive loss of spermatogonia. Here we sought to understand the...
MicroRNA targets in Drosophila.
BACKGROUND: The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of a...
High-density P300 enhancers control cell state transitions.
BACKGROUND: Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise...
miRBase
Sam Griffiths-Jones, Russell J Grocock, Stijn van Dongen, Alex Bateman, Anton J Enright
Nov 16, 2017
The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles...
Denoising inferred functional association networks obtained by gene fusion analysis.
Atanas Kamburov, Leon Goldovsky, Shiri Freilich, Aliki Kapazoglou, Victor Kunin, Anton J Enright, Athanasios Tsaftaris, Christos A Ouzounis
Jan 22, 2018
BACKGROUND: Gene fusion detection - also known as the 'Rosetta Stone' method - involves the identification of fused composite genes in a set of reference genomes, which indicates potential interactions between its un-fused...
Human MicroRNA targets.
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted target sites on the 3'...
3' Untranslated Regions Algorithms Amino Acid Motifs Amyloid beta-Protein Precursor Animals Chromosome Mapping Computational Biology Conserved Sequence DNA Complementary Disks Large Homolog 4 Protein Fragile X Mental Retardation Protein Gene Expression Regulation Gene Silencing Humans Intracellular Signaling Peptides and Proteins Introns Membrane Proteins MicroRNAs Models Genetic Models Statistical Molecular Sequence Data Polyadenylation Protein Binding Protein Biosynthesis Protein Structure Tertiary RNA RNA Messenger Rats Software
Smallpox vaccination induces a substantial increase in commensal skin bacteria that promote pathology and influence the host response.
Evgeniya V Shmeleva, Mercedes Gomez de Agüero, Josef Wagner, Anton J Enright, Andrew J Macpherson, Brian J Ferguson, Geoffrey L Smith
May 22, 2022
Interactions between pathogens, host microbiota and the immune system influence many physiological and pathological processes. In the 20th century, widespread dermal vaccination with vaccinia virus (VACV) led to the eradication...
MiR-221 influences effector functions and actin cytoskeleton in mast cells.
Ramon J Mayoral, Lorenzo Deho, Nicole Rusca, Nenad Bartonicek, Harpreet Kaur Saini, Anton J Enright, Silvia Monticelli
Jan 23, 2018
Mast cells have essential effector and immunoregulatory functions in IgE-associated allergic disorders and certain innate and adaptive immune responses, but the role of miRNAs in regulating mast cell functions is almost...
3T3 Cells Actin Cytoskeleton Actins Animals Base Sequence Bone Marrow Cells Cell Adhesion Cell Degranulation Cell Differentiation Cell Movement Cell Proliferation Cyclin-Dependent Kinase Inhibitor p27 Down-Regulation FIBROBLASTS Gene Knockdown Techniques Lentivirus Mast Cells Mice Mice Inbred C57BL MicroRNAs Molecular Sequence Data Oligonucleotide Array Sequence Analysis Up-Regulation
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