A5003280938- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Protein Structure and Dynamics
- Bacteriophages and microbial interactions
- Cancer-related gene regulation
- Epigenetics and DNA Methylation
- DNA and Nucleic Acid Chemistry
- DNA Repair Mechanisms
- CRISPR and Genetic Engineering
- Advanced biosensing and bioanalysis techniques
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Biochemical and Molecular Research
- Genetics, Bioinformatics, and Biomedical Research
- Cancer-related molecular mechanisms research
- RNA Interference and Gene Delivery
- Amino Acid Enzymes and Metabolism
- RNA regulation and disease
- Genomics and Chromatin Dynamics
- Trypanosoma species research and implications
- interferon and immune responses
International Institute of Molecular and Cell Biology
2016-2025
Adam Mickiewicz University in Poznań
2013-2022
Stanford University
2019
Institute of Molecular Biology and Biotechnology
2011-2015
Faculty (United Kingdom)
2014
Institute of Bioorganic Chemistry, Polish Academy of Sciences
2013
Poznań University of Technology
2013
Nationwide Children's Hospital
2013
Instytut Biologii Doświadczalnej im. Marcelego Nenckiego
2013
Johannes Gutenberg University Mainz
2012
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures modified ribonucleosides, their biosynthetic pathways, location residues in sequences, and RNA-modifying enzymes. In current version, we included following new features data: extended mass spectrometry liquid chromatography data for nucleosides; links between human tRNA sequences MINTbase - framework interactive exploration mitochondrial nuclear fragments; new,...
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location residues in sequences. In current version, accessible at http://modomics.genesilico.pl, we included new features: census human yeast snoRNAs involved RNA-guided modification, section covering 5′-end capping process, catalogue ‘building blocks’ for synthesis large variety nucleosides....
The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of ribonucleosides, their biosynthetic pathways, location residues in RNA sequences, RNA-modifying enzymes. Over years, prompted by accumulation new knowledge types data, been updated with functionalities. In this release, we have created catalog modifications...
Abstract Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected extensive clinical, pathologic, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. To characterize processes underlying transformation of normal colonic epithelium, we compared transcriptomes 32 prospectively collected adenomas with those mucosa same individuals. Important differences...
RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of 3D structures is laborious challenging, therefore, majority known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational structure prediction, which uses coarse-grained representation, relies Monte Carlo sampling...
Intrinsically unstructured proteins (IUPs) lack a well-defined three-dimensional structure. Some of them may assume locally stable structure under specific conditions, e.g. upon interaction with another molecule, while others function in permanently state. The discovery IUPs challenged the traditional protein paradigm, which stated that defines protein. As December 2011, approximately 60 methods for computational prediction disorder from sequence have been made publicly available. They are...
We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess leading edge techniques; compare existing methods and tools; evaluate their relative strengths, weaknesses, limitations terms sequence length structural complexity. should give potential users insight into suitability available for different applications facilitate efforts community ongoing improve tools. also...
The YTH (YT521-B homology) domain was identified by sequence comparison and is found in 174 different proteins expressed eukaryotes. It characterized 14 invariant residues within an alpha-helix/beta-sheet structure. Here we show that the a novel RNA binding binds to short, degenerated, single-stranded motif. presence of motif alternative exons necessary for YT521-B directly influence splice site selection vivo. Array analyses demonstrate predominantly regulates vertebrate-specific exons. An...
Abstract SARS-CoV-2 is a betacoronavirus with linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes development effective durable therapeutic strategies challenging urgent need. As for other viruses, genomic structures are expected play crucial roles in several steps coronavirus replication cycle. Despite this, only handful functionally-conserved...
RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function depends on its structure and dynamics, which in turn encoded linear sequence. However, while there are numerous methods for computational prediction protein three-dimensional (3D) from sequence, with comparative modeling being most reliable approach, very few such RNA. Here, we present ModeRNA, software tool 3D structures. As an input, ModeRNA requires template molecule, sequence...
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...
Protein–RNA and protein–DNA interactions play fundamental roles in many biological processes. A detailed understanding of these requires knowledge about protein–nucleic acid complex structures. Because the experimental determination complexes is time-consuming perhaps futile some instances, we have focused on computational docking methods starting from separate Docking are widely employed to study protein–protein interactions; however, only a few been made available model complexes. Here,...
This paper is a report of second round RNA-Puzzles, collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, 10, represented sequences three large structures with limited or no homology previously solved molecules. A lariat-capping ribozyme, as well riboswitches complexed to adenosylcobalamin tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, AMBER refinement. Some derived models...
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures riboswitch aptamers and puzzle 7, ribozyme structure, are included this the experiment. The include biological binding sites for small molecules ( S -adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5′-triphosphate, glutamine) proteins (YbxF), one set describes large conformational...
The MODOMICS database was updated with recent data and now includes new types related to RNA modifications. Changes the include an expanded modification catalog, encompassing both natural synthetic residues identified in structures. This addition aids representing sequences from RCSB PDB more effectively. To manage increased number of modifications, adjustments nomenclature system were made. Updates section reintroduction sequence alignments for tRNAs rRNAs. protein connected structures...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, structures are predicted by various groups before publication crystal structures. We now report prediction for six sequences: four nucleolytic ribozymes two riboswitches. Systematic protocols comparing models described analyzed. In these puzzles, we discuss (i) comparison between automated web servers human experts; (ii) coaxial stacking;...
Abstract During recent years many protein fold recognition methods have been developed, based on different algorithms and using various kinds of information. To examine the performance these several evaluation experiments conducted. These include blind tests in CASP/CAFASP, large scale benchmarks, long‐term, continuous assessment with newly solved structures. studies confirm expectation that for targets produce best predictions, final prediction accuracy could be improved if available were...
The Structure Prediction Meta Server offers a convenient way for biologists to utilize various high quality structure prediction servers available worldwide. meta server translates the results obtained from remote services into uniform format, which are consequently used request jury consensus Pcons.The is freely at http://BioInfo.PL/meta/, some have however restrictions non-academic users, respected by server.Results of several sessions CAFASP and LiveBench programs assessment performance...
Combination of biochemical and bioinformatic analyses led to the discovery oxidative demethylation – a novel DNA repair mechanism catalyzed by Escherichia coli AlkB protein its two human homologs, hABH2 hABH3. This was based on prediction made Aravind Koonin that is member 2OG-Fe2+ oxygenase superfamily. In this article, we report identification sequence analysis five members (2OG-Fe2+) superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized poorly annotated...
MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected substantial improvements. It provides comprehensive information on chemical structure modified nucleosides, pathways their biosynthesis, sequences RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also cross-references other databases literature. In addition previously available manually curated tRNA from few model organisms, we have now included additional tRNAs rRNAs, all with...
The collagens are a family of animal proteins containing segments repeated Gly-Xaa-Yaa (GXY) motifs that form characteristic triple-helical structure. Genes encoding with GXY have also been reported in bacteria and phages; however, it is unclear whether these prokaryotic can collagen-like Here we used two recently identified streptococcal proteins, Scl1 Scl2, extended sequence repeats as model proteins. First observed prior to heat denaturation recombinant Scl migrated homotrimers gel...