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MODOMICS specifications

Information


Unique identifier OMICS_02724
Name MODOMICS
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Henri Grosjean
  • person_outline Janusz Bujnicki

Additional information


http://modomics.genesilico.pl/help/

Publications for MODOMICS

MODOMICS citations

 (8)
library_books

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

2017
Nucleic Acids Res
PMCID: 5753253
PMID: 29316735
DOI: 10.1093/nar/gkx1235

[…] DIP (), as well as new databases such as miRCarta (). The new MSDD () links miRNA SNPs to diseases while EVLncRNAs () and MNDR () also major on disease links for non-coding RNAs. The well-established MODOMICS database of RNA modifications () is the subject of an update paper which, among other developments, reports on the availability of liquid chromatography/mass spectrometry data for modified nu […]

library_books

tRNA mediated codon biased translation in mycobacterial hypoxic persistence

2016
Nat Commun
PMCID: 5114619
PMID: 27834374
DOI: 10.1038/ncomms13302

[…] s by taking into account the 40 modifications identified in BCG tRNA (; ), predicted modifications by tRNAmod (http://crdd.osdd.net/raghava/trnamod/) and comparisons with tRNA sequences catalogued in Modomics (http://modomics.genesilico.pl/). The exact masses of these potential modified oligomers and their c1 and y1 ion fragments were calculated. Selected reaction monitoring (SRM) worklists were c […]

library_books

The reverse transcription signature of N 1 methyladenosine in RNA Seq is sequence dependent

2015
Nucleic Acids Res
PMCID: 4787781
PMID: 26365242
DOI: 10.1093/nar/gkv895

[…] ated signatures in thus prepared RNA-seq libraries, the reads were mapped onto a minimal target genome consisting only of rRNA and tRNA sequences. The respective sequences have been obtained from the Modomics database () and do thus not contain any unspliced or unprocessed sequences, but, importantly, sequences of known modifications status. This is in some contrast to the previously published HAM […]

library_books

ARM Seq: AlkB facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

2015
Nat Methods
PMCID: 4553111
PMID: 26237225
DOI: 10.1038/nmeth.3508

[…] owed evidence for demethylation of both an expected m3C32 modification, and an unexpected m1A58.ARM-Seq also predicted m1A58 modifications for five yeast tRNAs in isodecoder groups not represented in Modomics and unmodified A58 for three others, with primer extensions confirming m1A58 for Leu-GAG and unmodified A58 for Arg-CCG and Gly-CCC (, ). The final tRNA not represented in Modomics, Pro-AGG, […]

library_books

Enhanced Detection of Post Transcriptional Modifications Using a Mass Exclusion List Strategy for RNA Modification Mapping by LC MS/MS

2015
Anal Chem
PMCID: 4542202
PMID: 26176336
DOI: 10.1021/acs.analchem.5b01826

[…] Xcaliber software. The tRNA genomic sequences were obtained from the Genomic tRNA Database (http://gtrnadb.ucsc.edu/).E. coli tRNA sequences with post-transcriptional modifications were obtained from Modomics (http://modomics.genesilico.pl/). Two approaches were used to analyze the LC-MS/MS data. Manual annotation of MS/MS spectra was performed by calculating expected m/z values of all RNase T1 di […]

library_books

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

2013
Nucleic Acids Res
PMCID: 3627593
PMID: 23435231
DOI: 10.1093/nar/gkt101

[…] al modifications (e.g. pseudouridines, inosines, methylated nucleosides and so forth), such nucleotides are replaced by their unmodified counterparts, according to the RNA modification table from the MODOMICS database (). The removal of modifications from 3D structures is done by the ModeRNA program (). This step is critical because many bioinformatics methods used for RNA secondary structure pred […]


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MODOMICS institution(s)
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland; Institute of Informatics, University of Warsaw, Warsaw, Poland; Microbiology and Cell Science Department, University of Florida, Gainesville, FL, USA; Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH, USA; Institut fur Pharmazie und Biochemie, Johannes Gutenberg-Universitat, Mainz, Germany; Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
MODOMICS funding source(s)
Polish National Science Center [NCN, 2012/04/A/ NZ2/00455, 2011/03/D/NZ1/03247]; IIMCB [statutory funds]; National Institutes of Health [NIH, GM70641, GM058843]; COST action [CA16120 ’EPITRAN’]; Deutsche Forschungsgemeinschaft [DFG, SPP1784/HE3397/13-1].

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