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Evidence for human microRNA-offset RNAs in small RNA sequencing data
- David Langenberger, C. Bermúdez-Santana, Jana Hertel, S. Hoffmann, P. Khaitovich, P. Stadler
- 1 September 2009
Using short read sequencing data, it is shown that moRNAs are also produced from human microRNA precursors, albeit at quite low expression levels, and are typically evolutionarily old.
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies
A general framework to distinguish orthologs and paralogs in gene families that are subject to concerted evolution is introduced, based on the use of uniquely aligned adjacent sequence elements as anchors to establish syntenic conservation of sequence intervals.
Genomic organization of eukaryotic tRNAs
The genomic organization of tRNA genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the tRNAs themselves.
Identification and Classification of Small RNAs in Transcriptome Sequence Data
- David Langenberger, C. Bermúdez-Santana, P. Stadler, S. Hoffmann
- BiologyPacific Symposium on Biocomputing
The potential of short read sequence data in the classification and identification of non-coding RNAs is explored and it seems to reflect the processing and thus are specific for the RNA transcripts of which they are derived from.
Evolutionary Genomics of microRNAs and Their Relatives
This work presents a meta-analyses of the tree-ring-like structure of the Higgs boson genome, which shows clear patterns in the response of the immune system to Tournaisian chemotherapy.
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean
This work combines long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean and expects the resources presented here to serve as a solid basis for a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication.
Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum
- Cristian A Velandia-Huerto, A. Gittenberger, Federico D. Brown, P. Stadler, C. Bermúdez-Santana
- BiologyBMC Genomics
- 30 August 2016
A comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians and provides a valuable research for efforts to establish detailed non-Coding RNA annotations for other recently published and recently sequences in tunicate genomes.
Nonprotein-Coding RNAs as Regulators of Development in Tunicates.
- Cristian A Velandia-Huerto, Federico D. Brown, A. Gittenberger, P. Stadler, C. Bermúdez-Santana
- BiologyResults and problems in cell differentiation
The discovery, evolution, and genome organization of the miRNA repertoire, which has been drastically reduced and restructured in tunicates compared to the chordate ancestor, is reviewed.
Dengue virus potentially promotes migratory responses on endothelial cells by enhancing pro-migratory soluble factors and miRNAs.