De novo prediction of structured RNAs from genomic sequences
Growing recognition of the numerous, diverse and important roles played by non-coding
RNA in all organisms motivates better elucidation of these cellular components …
RNA in all organisms motivates better elucidation of these cellular components …
Sequence assembly
K Scheibye-Alsing, S Hoffmann, A Frankel… - … Biology and Chemistry, 2009 - Elsevier
Despite the rapidly increasing number of sequenced and re-sequenced genomes, many
issues regarding the computational assembly of large-scale sequencing data have remain …
issues regarding the computational assembly of large-scale sequencing data have remain …
[PDF][PDF] A comparative assessment of the pig, mouse and human genomes
HD Dawson - The minipig in biomedical research, 2011 - academia.edu
Mice are arguably the experimental workhorse of immunological research and mouse
models have paved the way for the discovery of numerous important mechanisms related to …
models have paved the way for the discovery of numerous important mechanisms related to …
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions
E Torarinsson, Z Yao, ED Wiklund, JB Bramsen… - Genome …, 2008 - genome.cshlp.org
Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have
relied on existing multiple sequence alignments. However, as sequence similarity drops, a …
relied on existing multiple sequence alignments. However, as sequence similarity drops, a …
Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes
Z Qu, DL Adelson - 2012 - journals.plos.org
It is apparent that non-coding transcripts are a common feature of higher organisms and
encode uncharacterized layers of genetic regulation and information. We used public bovine …
encode uncharacterized layers of genetic regulation and information. We used public bovine …
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum
Background Schistosomes are trematode parasites of the phylum Platyhelminthes. They are
considered the most important of the human helminth parasites in terms of morbidity and …
considered the most important of the human helminth parasites in terms of morbidity and …
Nematode sbRNAs: homologs of vertebrate Y RNAs
Stem-bulge RNAs (sbRNAs) are a group of small, functionally yet uncharacterized
noncoding RNAs first described in C. elegans, with a few homologous sequences …
noncoding RNAs first described in C. elegans, with a few homologous sequences …
Structured RNAs and synteny regions in the pig genome
C Anthon, H Tafer, JH Havgaard, B Thomsen… - BMC genomics, 2014 - Springer
Background Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial
since far from all ncRNAs are known and the computational models are resource …
since far from all ncRNAs are known and the computational models are resource …
Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements
Abstract Background Long non-coding RNAs (lncRNA) are a major class of non-coding
RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding …
RNAs. They are involved in diverse intra-cellular mechanisms like molecular scaffolding …
Identification and analysis of intermediate size noncoding RNAs in the human fetal brain
The involvement of noncoding RNAs (ncRNAs) in the development of the human brain
remains largely unknown. Applying a cloning strategy for detection of intermediate size (50 …
remains largely unknown. Applying a cloning strategy for detection of intermediate size (50 …