The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
PsRobot: a web-based plant small RNA meta-analysis toolbox
Open accessAbstract
Small RNAs (smRNAs) in plants, mainly microRNAs and small interfering RNAs, play important roles in both transcriptional and post-transcriptional gene regulation. The broad application of high-throughput sequencing technology has made routinely generation of bulk smRNA sequences in laboratories possible, thus has significantly increased the need for batch analysis tools. PsRobot is a web-based easy-to-use tool dedicated to the identification of smRNAs with stem-loop shaped precursors (such as microRNAs and short hairpin RNAs) and their target genes/transcripts. It performs fast analysis to identify smRNAs with stem-loop shaped precursors among batch input data and predicts their targets using a modified Smith-Waterman algorithm. PsRobot integrates the expression data of smRNAs in major plant smRNA biogenesis gene mutants and smRNA-associated protein complexes to give clues to the smRNA generation and functional processes. Besides improved specificity, the reliability of smRNA target prediction results can also be evaluated by mRNA cleavage (degradome) data. The cross species conservation statuses and the multiplicity of smRNA target sites are also provided. PsRobot is freely accessible at http://omicslab.genetics.ac.cn/psRobot/.
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Cites
Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634
Cited by
A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome
The International Wheat Genome Sequencing Consortium (IWGSC), Mayer, K. F. X., Rogers, J., Doležel, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A. J., et al. (2014) · Science · doi:10.1126/science.1251788 · Cited by 1,583
Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants
Wu, H.-J., Wang, Z.-M., Wang, M., & Wang, X.-J. (2013) · Plant Physiology · doi:10.1104/pp.113.215962 · Cited by 428
Self-citationLi, G., Zhou, J., Jia, H., Gao, Z., Fan, M., Luo, Y., Zhao, P., Xue, S., Li, N., Yuan, Y., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0426-7 · Cited by 299
Self-citationTang, C., Han, R., Zhou, Z., Yang, Y., Zhu, M., Xu, T., Wang, A., Li, Z., & Dong, T. (2020) · Journal of Plant Physiology · doi:10.1016/j.jplph.2020.153224 · Cited by 24
Tian, X., Wang, R., Liu, Z., Lu, S., Chen, X., Zhang, Z., Liu, F., Li, H., Zhang, X., & Wang, M. (2025) · Genome Biology · doi:10.1186/s13059-025-03534-5 · Cited by 16
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Metadata
- Authors
- Wu, H.-J., Ma, Y.-K., Chen, T., Wang, M., & Wang, X.-J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-06-12
- Volume
- 40
- Issue
- W1
- Pages
- W22-W28
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2133613866
- Cited by
- 568
- References
- 3
- FWCI
- 1.50
- Type
- journal article
- Language
- en
- Open access
- gold
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