The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Exome-based analysis for RNA epigenome sequencing data
Open accessAbstract
Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach ‘exomePeak’ for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome. Availability: The MATLAB package ‘exomePeak’ and additional details are available at http://compgenomics.utsa.edu/exomePeak/. Contact: yufei.huang@utsa.edu or jmeng@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Landscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
Meyer, K. D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C. E., & Jaffrey, S. R. (2012) · Cell · doi:10.1016/j.cell.2012.05.003 · Cited by 4,223
The accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679
Bernstein, B. E., Meissner, A., & Lander, E. S. (2007) · Cell · doi:10.1016/j.cell.2007.01.033 · Cited by 2,086
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Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L. M., Hulse-Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0614-5 · Cited by 462
Meng, J., Lu, Z., Liu, H., Zhang, L., Zhang, S., Chen, Y., Rao, M. K., & Huang, Y. (2014) · Methods · doi:10.1016/j.ymeth.2014.06.008 · Cited by 375
Self-citationTumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance
Liu, Y., Liang, G., Xu, H., Dong, W., Dong, Z., Qiu, Z., Zhang, Z., Li, F., Huang, Y., Li, Y., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.04.001 · Cited by 361
Self-citationDynamic landscape and evolution of m6A methylation in human
Zhang, H., Shi, X., Huang, T., Zhao, X., Chen, W., Gu, N., & Zhang, R. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa347 · Cited by 359
Metadata
- Authors
- Meng, J., Cui, X., Rao, M. K., Chen, Y., & Huang, Y.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-04-14
- Volume
- 29
- Issue
- 12
- Pages
- 1565-1567
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2166153887
- Cited by
- 193
- References
- 4
- FWCI
- 2.42
- Type
- journal article
- Language
- en
- Open access
- bronze
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