A5060684278- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Plant Disease Resistance and Genetics
- Plant and Fungal Interactions Research
- RNA Research and Splicing
- PI3K/AKT/mTOR signaling in cancer
- interferon and immune responses
- RNA regulation and disease
- Parasites and Host Interactions
- Omental and Epiploic Conditions
- Hippo pathway signaling and YAP/TAZ
- vaccines and immunoinformatics approaches
- Diabetes and associated disorders
- Tumors and Oncological Cases
- Influenza Virus Research Studies
- MicroRNA in disease regulation
- Cancer-related gene regulation
- Wildlife Ecology and Conservation
- Endometriosis Research and Treatment
- Histiocytic Disorders and Treatments
- Cardiovascular Disease and Adiposity
- FOXO transcription factor regulation
- Adipose Tissue and Metabolism
Leipzig University
2009-2023
Institute of Bioinformatics
2016
Max Planck Institute for Mathematics in the Sciences
2009-2010
University of Vienna
2009-2010
Ingo Braasch, John Postlethwait and colleagues report the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before duplication. Their data provide insights into evolution genes involved in immunity, mineralization development facilitate comparison cis-regulatory elements between humans. To connect human biology to fish biomedical models, we sequenced teleost duplication (TGD). The slowly evolving has conserved content size many entire chromosomes bony...
Ning Li and colleagues report the whole-genome sequence of duck, Anas platyrhynchos, a natural host avian influenza viruses. They examine response to infection by comparing lung transcriptomes ducks that were infected with A The duck (Anas platyrhynchos) is one principal hosts We present genome perform deep transcriptome analyses investigate immune-related genes. Our data indicate possesses contractive immune gene repertoire, as in chicken zebra finch, this repertoire has been shaped through...
Small nucleolar RNAs (snoRNAs) are a class of non-coding that guide the post-transcriptional processing other (mostly ribosomal RNAs), but have also been implicated in processes ranging from microRNA-dependent gene silencing to alternative splicing. In order construct an up-to-date catalog human snoRNAs we combined data various databases, de novo prediction and extensive literature review. total, list more than 750 curated genomic loci give rise snoRNA snoRNA-like genes. Utilizing small...
Abstract Motivation: Small nucleolar RNAs (snoRNAs) are an abundant class of non-coding with a wide variety cellular functions including chemical modification RNA, telomere maintanance, pre-rRNA processing and regulatory activities in alternative splicing. The main role box C/D snoRNAs is to determine the targets for 2′-O-ribose methylation, which important rRNA maturation splicing regulation some mRNAs. still unknown, however, many ‘orphan’ snoRNAs. While fast efficient target predictor...
Ribosomal and small nuclear RNAs (snRNAs) comprise numerous modified nucleotides. The modification patterns are retained during evolution, making it even possible to project them from yeast onto human. stringent conservation of sites the slow evolution rRNAs snRNAs contradicts rapid nucleolar RNA (snoRNA) sequences. To explain this discrepancy, we investigated coevolution snoRNAs their targeted throughout vertebrates. measure evaluate RNA-RNA interactions, defined interaction index (ICI). It...
Abstract Background Schistosomes are trematode parasites of the phylum Platyhelminthes. They considered most important human helminth in terms morbidity and mortality. Draft genome sequences now available for Schistosoma mansoni japonicum . Non-coding RNA (ncRNA) plays a crucial role gene expression regulation, cellular function defense, homeostasis, pathogenesis. The genome-wide annotation ncRNAs is non-trivial task unless well-annotated genomes closely related species already available....
Abstract Motivation: Small nucleolar RNAs are an abundant class of non-coding that guide chemical modifications rRNAs, snRNAs and some mRNAs. In the case many ‘orphan’ snoRNAs, targeted nucleotides remain unknown, however. The box H/ACA subclass determines uridine residues to be converted into pseudouridines via specific complementary binding in a well-defined secondary structure configuration is outside scope common RNA (co-)folding algorithms. Results: RNAsnoop implements dynamic...
Human white adipose tissue (AT) is a metabolically active organ with distinct depot-specific functions. Despite their locations close to the gastrointestinal tract, mesenteric AT and epiploic (epiAT) have only scarcely been investigated. Here, we aim characterise these ATs in-depth estimate contribution alterations in whole-body metabolism.Mesenteric, epiploic, omental abdominal subcutaneous were collected from 70 patients obesity undergoing Roux-en-Y gastric bypass surgery. The...
The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence motifs. A group diverse ncRNAs, however, shares the hallmarks one or both snoRNAs but differs substantially from norm in some respects. Here, we compile available information on these exceptional cases, conduct a thorough homology search throughout metazoan genomes, provide improved expanded alignments, investigate evolutionary...
Abstract Motivation: Although small nucleolar RNAs form an important class of non-coding RNAs, no comprehensive annotation efforts have been undertaken, presumably because the task is complicated by both large number distinct RNA families and their relatively rapid pace sequence evolution. Results: With snoStrip we present automatic pipeline developed specifically for comparative genomics RNAs. It makes use conservation, canonical box motifs as well secondary structure predicts putative...
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...
Here we present the results of a large-scale bioinformatics annotation non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models hand-curated families from Rfam database to infer conserved within each genome. We supplement these annotations with predictions tRNA tool, tRNAscan-SE and microRNAs miRBase. identify 34 lncRNA-associated that are between birds mammals validate 12 chicken. report several intriguing cases where reported mammalian lncRNA, but not its function,...
Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They ubiquitous in Archaea and Eukarya but absent bacteria. Their main function is to target chemical modifications ribosomal fall into two classes, box C/D snoRNAs H/ACA snoRNAs, which clearly distinguished by conserved sequence motifs type modification that they govern. Similarly microRNAs, appear distinct homologs affect homologous targets. In animals, their evolution have been studied...
The tumor suppressor phosphatase and tensin homolog (PTEN) negatively regulates the insulin signaling pathway. Germline PTEN pathogenic variants cause hamartoma syndrome (PHTS), associated with lipoma development in children. Adipose progenitor cells (APCs) lose their capacity to differentiate into adipocytes during continuous culture, whereas APCs from lipomas of patients PHTS retain adipogenic potential over a prolonged period. It remains unclear which mechanisms trigger this aberrant...
Adipose tissue inflammation and insulin resistance are hallmarks in the development of metabolic diseases resulting from overweight obesity, such as type 2 diabetes non-alcoholic fatty liver disease. In adipocytes predominantly secrete proinflammatory adipokines that further promote adipose dysfunction with negative effects on local systemic sensitivity. Expression serpin vaspin (SERPINA12) is also increased obesity diabetes, but exhibits compensatory roles resistance. This has part been...
Phospholipid scramblase 4 (PLSCR4) is a member of conserved enzyme family with high relevance for the remodeling phospholipid distribution in plasma membrane and regulation cellular signaling. While PLSCR1 -3 are involved adipose-tissue expansion, role PLSCR4 so far unknown. significantly downregulated an adipose-progenitor-cell model deficiency phosphatase tensin homolog (PTEN). PTEN acts as tumor suppressor antagonist growth survival signaling phosphoinositide 3-kinase (PI3K)/AKT cascade...
Recent advances in the stem cell field allow to obtain many human tissues vitro. However, hepatic differentiation of induced pluripotent cells (iPSCs) still remains challenging. Hepatocyte-like (HLCs) obtained after resemble more fetal liver hepatocytes. MicroRNAs (miRNA) play an important role process. Here, we analysed noncoding RNA profiles from last stages and compare them Our results show that HLCs maintain epithelial character express miRNA which can block hepatocyte maturation by...
Small integral membrane protein 10 like 1 (SMIM10L1) was identified by RNA sequencing as the most significantly downregulated gene in Phosphatase and Tensin Homologue (PTEN) knockdown adipose progenitor cells (APCs). PTEN is a tumor suppressor that antagonizes growth promoting Phosphoinositide 3-kinase (PI3K)/AKT/mechanistic Target of Rapamycin (mTOR) cascade. Diseases caused germline pathogenic variants are summarized Hamartoma Tumor Syndrome (PHTS). This overgrowth syndrome associated with...