A5081056569- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Bacteriophages and microbial interactions
- Microbial Community Ecology and Physiology
- Retinal Development and Disorders
- Peptidase Inhibition and Analysis
- Cellular transport and secretion
- Barrier Structure and Function Studies
- Hedgehog Signaling Pathway Studies
- Multi-Agent Systems and Negotiation
- Privacy, Security, and Data Protection
- Antibiotics Pharmacokinetics and Efficacy
- Parasitic Infections and Diagnostics
- Plant and Fungal Species Descriptions
- Bacterial Identification and Susceptibility Testing
- Escherichia coli research studies
- Data Stream Mining Techniques
- Mobile Crowdsensing and Crowdsourcing
- Yersinia bacterium, plague, ectoparasites research
- Cerebrovascular and genetic disorders
- Health and Conflict Studies
- Molecular Biology Techniques and Applications
University of California, Santa Cruz
2014-2025
University of Wisconsin–Madison
2023
City of Knowledge
2020
Council for Scientific and Industrial Research
2020
Capital Medical University
2018
University of Pennsylvania
2018
New York University
2015
Santa Cruz County Office of Education
2012
Western University
2005
Canadian Blood Services
2005
High-throughput genome sequencing continues to grow the need for rapid, accurate annotation and tRNA genes constitute largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced state-of-the-art methodology in gene detection functional prediction, captured by rich new content companion Genomic Database. Previously, web-server was isolated from knowledge existing tRNAs their annotation. In this update On-line resource, we tie together...
tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction over twenty years, developed just as the first genomes were decoded. With massive increase in quantity and phylogenetic diversity of genomes, accurate detection functional tRNAs become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype- clade-specific models, greatly improving tRNAscan-SE's ability to identify classify both typical atypical tRNAs. We employ new...
Transfer RNAs represent the largest, most ubiquitous class of non-protein coding RNA genes found in all living organisms. The tRNAscan-SE search tool has become de facto standard for annotating tRNA genomes, and Genomic Database (GtRNAdb) was created as a portal interactive exploration these gene predictions. Since its published description 2009, GtRNAdb steadily grown content, remains commonly cited web-based source information. In this update, we describe not only major increase number...
Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments now thought to be significant contributors carbon nitrogen cycling. The isolation of Candidatus “ Nitrosopumilus maritimus ” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory globally distributed archaea. Here we report 1,645,259-bp closed genome SCM1, revealing highly copper-dependent systems ammonia oxidation electron transport that distinctly different...
Transfer RNAs (tRNAs) represent the single largest, best-understood class of non-protein coding RNA genes found in all living organisms. By far, major source new tRNAs is computational identification within newly sequenced genomes. To organize rapidly growing collection and enable systematic analyses, we created Genomic tRNA Database (GtRNAdb), currently including over 74,000 predicted from 740 species. The web resource provides overview statistics each analyzed genome, information by...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides single access point to 44 resources and >18 million ncRNA from wide range organisms types. now also includes secondary (2D) structure information for >13 sequences, making the world's largest 2D database. The diagrams are displayed using R2DT, new visualization method uses consistent, reproducible recognizable layouts related RNAs. sequence similarity search has been updated with faster interface...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences all types from broad range organisms. We have recently added new genome mapping pipeline that identifies genomic locations for in 296 species. also several functional annotations, such as tRNA secondary structures, Gene Ontology and miRNA-target interactions. A quality control mechanism based Rfam family assignments potential contamination, incomplete more. The has become...
RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides single entry point for accessing all types organisms. Since its launch in 2014, has integrated twelve new resources, taking the total number collaborating to 22, began importing data, such as modified nucleotides MODOMICS PDB. We created species-specific identifiers refer unique within context species. The website been subject continuous improvements focusing on...
The field of non-coding RNA biology has been hampered by the lack availability a comprehensive, up-to-date collection accessioned sequences. Here we present first release RNAcentral, database that collates and integrates information from an international consortium established sequence databases. initial contains over 8.1 million sequences, including representatives all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality,...
Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on secondary (2D) tertiary structure. Despite the abundance of software visualisation ncRNAs, few automatically generate consistent recognisable 2D layouts, which makes it challenging users to construct, compare analyse structures. Here, we present R2DT, a method predicting visualising wide range RNA structures in standardised layouts. R2DT is based library 3,647 templates representing majority known...
Abstract The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints distinct responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that transfer RNA‐derived small RNAs (tDRs) play pivotal roles in responses. However, RNA modifications present on tDRs are barriers accurately quantifying using traditional sequencing. Here, AlkB‐facilitated methylation sequencing used...
RNA secondary (2D) structure visualization is an essential tool for understanding function. R2DT a software package designed to visualize 2D structures in consistent, recognizable, and reproducible layouts. The latest release, 2.0, introduces multiple significant features, including the ability display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers new template-free mode allowing of RNAs without pre-existing templates, alongside...
The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal other selected microbial genomes. By bringing together existing gene annotations, expression data, multiple-genome alignments, pre-computed sequence comparisons specialized analysis tracks, the genome browser is powerful aggregator of varied genomic information. environment maintains current look-and-feel vertebrate Browser, but also integrates...
Abstract Recent high-throughput sequencing protocols have facilitated increased accuracy in measurements of transfer tRNAs (tRNAs) and tRNA-derived small RNAs (tDRs) from biological samples. However, commonly used RNA-seq analysis pipelines overlook special considerations given the unique features tRNA metabolism. We present tRAX (tRNA Analysis eXpression), a user-friendly analytic package for streamlined processing graphic presentation small-RNA data. Here, we apply it to both tDRs mouse...
We present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications standard protocols directly impact read length total output. The goal is help those interested in generating data determine which steps may be necessary optimizing output results.
Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide variants in their cognate tRNAs can lead to mistranslation. Human genomes include both rare more common mistranslating tRNA variants. We investigated three human tRNALeu that mis-incorporate Leu at phenylalanine or tryptophan codons. Expression...
Type III secretion systems (T3SS) are essential for virulence in dozens of pathogens, but not required growth outside the host. Therefore, T3SS many bacterial species under tight regulatory control. To increase our understanding molecular mechanisms behind regulation, we performed a transposon screen to identify genes important function food-borne pathogen Yersinia pseudotuberculosis. We identified two unique insertions YPTB2860, gene that displays 79% identity with E. coli iron-sulfur...
ABSTRACT tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction over twenty years, developed just as the first genomes were decoded. With massive increase in quantity and phylogenetic diversity of genomes, accurate detection functional tRNAs become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype-and clade-specific models, greatly improving tRNAscan-SE’s ability to identify classify both typical atypical tRNAs. We...
As in eukaryotes, precursor transfer RNAs Archaea often contain introns that are removed tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity the form of split genes, which two to three segments tRNAs transcribed from different loci, then trans-spliced a mature tRNA. Another rare type pre-tRNA, found only eukaryotic algae, is permuted, where 3' half encoded upstream 5' half, and must be processed functional. Using an improved version gene-finding...
Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all can be grouped in sets common acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis alignments shows that, despite the high number genes, specific sequence motifs highly conserved across multicellular eukaryotes. conservation often extends throughout isoacceptors isodecoders with, some cases, two isodecoders. This study is focused on non-Watson-Crick...