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MODOMICS: a database of RNA modification pathways
- S. Dunin-Horkawicz, A. Czerwoniec, M. Gajda, M. Feder, H. Grosjean, J. Bujnicki
- Biology, ChemistryNucleic Acids Res.
- 28 December 2005
MODOMICS is the first comprehensive database resource for systems biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in…
MODOMICS: a database of RNA modification pathways—2013 update
New features are included: a census of human and yeast snoRNAs involved in RNA-guided RNA modification, a new section covering the 5′-end capping process, and a catalogue of ‘building blocks’ for chemical synthesis of a large variety of modified nucleosides.
Transcriptome Profile of Human Colorectal Adenomas
- Jacob Sabates-Bellver, Laurens G. van der Flier, G. Marra
- Biology, MedicineMolecular Cancer Research
- 1 December 2007
Significant differences emerged not only between the expression profiles of normal and adenomatous tissues but also between those of small and large adenomas, and KIAA1199 was identified as a novel target of the Wnt signaling pathway and a putative marker of colorectal adenOMatous transformation.
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
It is proposed that the Last Universal Common Ancestor of all extant organisms contained at least three SPOUT members, ancestors of contemporary RNA MTases that carry out m1G, m3U, and 2'O-ribose methylation, respectively.
GeneSilico protein structure prediction meta-server
This work has developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input.
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins
A series of disorder predictors were combined into a meta-meta predictor called GSmetaDisorderMD, which was the top scoring method in the subsequent CASP9 benchmark and also developed a disorder predictor GS metaDisorder3D that used no third-party Disorder predictors, but alignments to known protein structures, reported by the protein fold-recognition methods.
MetaMQAP: A meta-server for the quality assessment of protein models
MetaMQAP is a meta-predictor based on a multivariate regression model, which uses scores of the above-mentioned methods, but in which trivial parameters are controlled, and is the best among methods capable of evaluating just single models.
Trm7p catalyses the formation of two 2′‐O‐methylriboses in yeast tRNA anticodon loop
- L. Pintard, François Lecointe, J. Bujnicki, C. Bonnerot, H. Grosjean, B. Lapeyre
- BiologyThe EMBO journal
- 2 April 2002
Evidence is presented that Trm7p methylates the 2′‐O‐ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop, both in vivo and in vitro, indicating that these tRNA modifications could be important for translation efficiency.
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements
This work identifies a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics, and lays the foundation for the developed of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.
MODOMICS: a database of RNA modification pathways. 2017 update
In the current database version of MODOMICS, the following new features and data are included: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.