The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
MODOMICS: a database of RNA modifications and related information. 2023 update
Open accessAbstract
The MODOMICS database was updated with recent data and now includes new data types related to RNA modifications. Changes to the database include an expanded modification catalog, encompassing both natural and synthetic residues identified in RNA structures. This addition aids in representing RNA sequences from the RCSB PDB database more effectively. To manage the increased number of modifications, adjustments to the nomenclature system were made. Updates in the RNA sequences section include the addition of new sequences and the reintroduction of sequence alignments for tRNAs and rRNAs. The protein section was updated and connected to structures from the RCSB PDB database and predictions by AlphaFold. MODOMICS now includes a data annotation system, with ‘Evidence’ and ‘Estimated Reliability’ features, offering clarity on data support and accuracy. This system is open to all MODOMICS entries, enhancing the accuracy of RNA modification data representation. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.
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Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · cited 1×
“Whenever available, we linked the MODOMICS entries to 3D structural predictions from the Al-phaFold database ( 25 ).”
MethodInfernal 1.1: 100-fold faster RNA homology searches
Nawrocki, E. P., & Eddy, S. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt509 · Cited by 3,591
Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers
Shi, H., Wei, J., & He, C. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.04.025 · Cited by 1,931
MODOMICS: a database of RNA modification pathways. 2017 update
Boccaletto, P., Machnicka, M. A., Purta, E., Piątkowski, P., Bagiński, B., Wirecki, T. K., de Crécy-Lagard, V., Ross, R., Limbach, P. A., Kotter, A., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1030 · Cited by 1,782
Self-citationRfam 14: expanded coverage of metagenomic, viral and microRNA families
Kalvari, I., Nawrocki, E. P., Ontiveros-Palacios, N., Argasinska, J., Lamkiewicz, K., Marz, M., Griffiths-Jones, S., Toffano-Nioche, C., Gautheret, D., Weinberg, Z., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1047 · Cited by 1,045
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P. A., Crichlow, G. V., Dalenberg, K., Duarte, J. M., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1077 · Cited by 887
MODOMICS: a database of RNA modification pathways. 2021 update
Boccaletto, P., Stefaniak, F., Ray, A., Cappannini, A., Mukherjee, S., Purta, E., Kurkowska, M., Shirvanizadeh, N., Destefanis, E., Groza, P., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1083 · Cited by 813
Self-citationAccurate detection of m6A RNA modifications in native RNA sequences
Liu, H., Begik, O., Lucas, M. C., Ramirez, J. M., Mason, C. E., Wiener, D., Schwartz, S., Mattick, J. S., Smith, M. A., & Novoa, E. M. (2019) · Nature Communications · doi:10.1038/s41467-019-11713-9 · Cited by 518
Visualization of chemical modifications in the human 80S ribosome structure
Natchiar, S. K., Myasnikov, A. G., Kratzat, H., Hazemann, I., & Klaholz, B. P. (2017) · Nature · doi:10.1038/nature24482 · Cited by 362
Self-citationQuantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing
Begik, O., Lucas, M. C., Pryszcz, L. P., Ramirez, J. M., Medina, R., Milenkovic, I., Cruciani, S., Liu, H., Vieira, H. G. S., Sas-Chen, A., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00915-6 · Cited by 312
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TET dioxygenases localize at splicing speckles and promote RNA splicing
Hastert, F. D., Weber, J., Bauer, C., Zhadan, A., Singh, D. N. D., Dix, T. C., Arnold, R., Bessonov, S., Soller, M., Leonhardt, H., et al. (2025) · Nucleus · doi:10.1080/19491034.2025.2536902 · Cited by 5
A comprehensive analysis of the use of nucleoside analogues in RNA therapeutics
Kukushkina-Zvezdova, A. A., Zherebtsova, A. A., Telegina, D. V., Skvortsov, I. A., Ivanov, R. A., & Reshetnikov, V. V. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-08083-4 · Cited by 3
TET dioxygenases localize at splicing speckles and promote RNA splicing
Hastert, F. D., Weber, J., Bauer, C., Zhadan, A., Singh, D. N. D., Dix, T. C., Arnold, R., Bessonov, S., Soller, M., Leonhardt, H., et al. (2025) · doi:10.1101/2025.03.07.641893
Metadata
- Authors
- Cappannini, A., Ray, A., Purta, E., Mukherjee, S., Boccaletto, P., Moafinejad, S. N., Lechner, A., Barchet, C., Klaholz, B. P., Stefaniak, F., & Bujnicki, J. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-11-28
- Volume
- 52
- Issue
- D1
- Pages
- D239-D244
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4389076163
- Cited by
- 406
- References
- 25
- FWCI
- 30.41
- Type
- journal article
- Language
- en
- Open access
- gold
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- Cappannini, A., Ray, A., Purta, E., Mukherjee, S., Boccaletto, P., Moafinejad, S. N., Lechner, A., Barchet, C., Klaholz, B. P., Stefaniak, F., & Bujnicki, J. M. (2024). MODOMICS: a database of RNA modifications and related information. 2023 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad1083
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