A5044386095- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Enzyme Production and Characterization
- Neurogenesis and neuroplasticity mechanisms
- Bacteriophages and microbial interactions
- RNA regulation and disease
- Distributed and Parallel Computing Systems
- Epigenetics and DNA Methylation
- Viral Infections and Outbreaks Research
- Axon Guidance and Neuronal Signaling
- Enzyme Structure and Function
- Platelet Disorders and Treatments
- Machine Learning in Bioinformatics
- MicroRNA in disease regulation
- Antioxidant Activity and Oxidative Stress
- Viral Infections and Immunology Research
- Methane Hydrates and Related Phenomena
- Evolution and Genetic Dynamics
- Chromosomal and Genetic Variations
- Memory and Neural Mechanisms
University of Copenhagen
2016-2025
Herzog August Library
2024
Catholic University of Eichstätt-Ingolstadt
2024
Boehringer Ingelheim (Egypt)
2024
Technologies pour la Santé
2017
Martin Luther University Halle-Wittenberg
2017
German Centre for Integrative Biodiversity Research
2017
Helmholtz Centre for Environmental Research
2017
Cancer Genetics (United States)
2012
Sidney Kimmel Cancer Center
2012
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...
Abstract We currently have limited knowledge of the involvement long non-coding RNAs (lncRNAs) in normal cellular processes and pathologies. Here, we identify characterize SNHG5 as a stable cytoplasmic lncRNA with up-regulated expression colorectal cancer. Depletion induces cell cycle arrest apoptosis vitro limits tumour outgrowth vivo , whereas overexpression counteracts oxaliplatin-induced apoptosis. Using an unbiased approach, 121 transcript sites interacting cytoplasm. Importantly,...
Structural characteristics are essential for the functioning of many noncoding RNAs and cis-regulatory elements mRNAs. SNPs may disrupt these structures, interfere with their molecular function, hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects SNPs. The global measures employed so far suffer from limited accuracy programs on large computationally too demanding genome-wide applications. Here, we present strategy that focuses local...
The function of many non-coding RNA genes and cis-regulatory elements messenger largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) other mutations may disrupt interfere with molecular hence cause a phenotypic effect. RNAsnp an efficient method to predict effect SNPs local secondary structure based folding algorithms implemented Vienna package. SNP effects are quantified terms empirical P-values, which, for computational...
Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is no approach that combines both sources information in a single optimization problem. Here, we present model formally integrates energy-based and evolution-based approaches to predict folding multiple aligned sequences. We have implemented an extended version Pfold identifies...
Structured elements of RNA molecules are essential in, e.g., stabilization, localization, and protein interaction, their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction sequence identity GC content, we predict ∼516,000 human genomic regions containing CRSs. find that substantial fraction human-mouse CRS (1)...
Abstract The unprecedented outbreak of Ebola in West Africa resulted over 28,000 cases and 11,000 deaths, underlining the need for a better understanding biology this highly pathogenic virus to develop specific counter strategies. Two filoviruses, Marburg viruses, result severe often fatal infection humans. However, bats are natural hosts survive filovirus infections without obvious symptoms. molecular basis striking difference response is not well understood. We report systematic overview...
Predicting RNA-RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods prediction are all based on single sequences. Since comparative have already been useful in RNA structure determination, we assume that conserved also imply function. Of these, further a non-negligible amount existing acquired compensating base changes throughout evolution. We implement method, PETcofold, can take covariance information intra-molecular and inter-molecular...
The original article to which this Erratum refers was published in Human Mutation 34(4):546–556 (DOI 10.1002/humu.22273). In the cited above, symbols for Mik and were inadvertently changed during production process. corrected text appears below. Publisher sincerely regrets error. At face value, minimization is rather expensive because each index pair u,v, values of πi[u,v] need be determined. naïve evaluation Eq. (7) can replaced by a recursive scheme (Supp. Fig. S1). Consider sequence...
Abstract One strategy for CO 2 mitigation is using photosynthetic microorganisms to sequester under high concentrations, such as in flue gases. While elevated levels generally promote growth, excessively inhibit growth through uncertain mechanisms. This study investigated the physiology of cyanobacterium Synechocystis sp. PCC 6803 very concentrations and yet stable pH around 7.5. The rate wild type (WT) at 200 µmol photons m −2 s −1 a gas phase containing 30% was 2.7-fold lower compared 4% ....
The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction RNA–RNA is essential for understanding biological roles pathways associated a specific gene. We present web servers to analyze multiple sequences common sites. are based recent PET (Probabilistic Evolutionary Thermodynamic) models PETfold PETcofold , but add user friendly features ranging from graphical layer interactive usage predictors....
Clustering RNA sequences with common secondary structure is an essential step towards studying function. Whereas structural alignment strategies typically identify for orthologous structured RNAs, clustering seeks to group paralogous RNAs based on similarities. However, existing approaches do not take the compensatory base pair changes obtained from conservation in into account.
A distance constrained secondary structural model of the ≈10 kb RNA genome HIV-1 has been predicted but higher-order structures, involving long interactions, are currently unknown. We present first global structure for genome, which integrates both comparative analysis and information from experimental data in a full-length prediction without constraints. Besides recovering known elements, we predict several novel elements that conserved evolution. Our results also indicate is highly...
A large part of our current understanding gene regulation in Gram-positive bacteria is based on Bacillus subtilis, as it one the most well studied bacterial model systems. The rapid growth data concerning its molecular and genomic biology distributed across multiple annotation resources. Consequently, interpretation from further B. subtilis experiments becomes increasingly challenging both low- large-scale analyses. Additionally, structured RNA non-coding (ncRNA), operon structure, still...
Abstract The CRISPR-Cas9 genome editing tool is used to study genomic variants and gene knockouts, can be combined with transcriptomic analyses measure the effects of such alterations on expression. But how one sure that differential expression due a successful intended edit not an off-target event, without performing often resource-demanding genome-wide sequencing edited cell or strain? To address this question we developed CRISPRroots: CRISPR–Cas9-mediated edits accompanying RNA-seq data...
Abstract Background Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models resource demanding. Currently, human genome holds best ncRNA annotation, a result of numerous efforts by several groups. However, more direct strategy desired increasing number sequenced which some, such as pig, relevant disease production animals. Results We present comprehensive annotation structured in pig genome. Combining sequence...
The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification their biological functions. Sparse sequence conservation non-coding sequences and unreliable nature RNA structure predictions further exacerbate this conundrum. Here, we describe computational method, DotAligner, unsupervised discovery homologous motifs from set interest. Our approach outperforms comparable algorithms at clustering known families, both speed accuracy. It identifies clusters...
Bacillus subtilis is a Gram-positive bacterium used as cell factory for protein production. Over the last decades, continued optimization of production strains has increased yields enzymes, such amylases, and made commercial applications feasible. However, current are still significantly lower than theoretically possible yield based on available carbon sources. In its natural environment, B. can respond to unfavorable growth conditions by differentiating into motile cells that use flagella...
Abstract Summary: With the increasing amount of newly discovered non-coding RNAs, interactions between RNA molecules become an increasingly important aspect for characterizing their functionality. Many computational tools have been developed to predict formation duplexes two either based on single sequences or alignments homologous sequences. Here, we present RILogo, a program visualize inter- and intramolecular base pairing molecules. The input RILogo is pair structure-annotated alignments....
The production of the alpha-amylase (AMY) enzyme in
Alzheimer's disease (AD) is a progressive and irreversible brain disorder, which can occur either sporadically, due to complex combination of environmental, genetic, epigenetic factors, or because rare genetic variants in specific genes (familial AD, fAD). A key hallmark AD the accumulation amyloid beta (Aβ) Tau hyperphosphorylated tangles brain, but underlying pathomechanisms interdependencies remain poorly understood. Here, we identify characterise gene expression changes related two fAD...
Abstract Background Post-transcriptional control of gene expression is mostly conducted by specific elements in untranslated regions (UTRs) mRNAs, collaboration with binding proteins and RNAs. In several well characterized cases, these RNA are known to form stable secondary structures. structures also may have major functional implications for long noncoding RNAs (lncRNAs). Recent transcriptional data has indicated the importance lncRNAs brain development function. However, no methodical...