Multiple alignment and structure prediction of non-coding RNA sequences (2007)
Lindgreen, Stinus, Gardner, Paul P, Krogh, Anders
No abstract available.
Weile, Christian, Gardner, Paul P, Hedegaard, Mads M, Vinther, Jeppe
Abstract Background Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of...
A hidden Markov model approach for determining expression from genomic tiling micro arrays (2006)
Munch, Kasper, Gardner, Paul P, Arctander, Peter, Krogh, Anders
Abstract Background Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have...
A comparison of RNA folding measures (2005)
Freyhult, Eva, Gardner, Paul P, Moulton, Vincent
Abstract Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random...
A comprehensive comparison of comparative RNA structure prediction approaches (2004)
Gardner, Paul P, Giegerich, Robert
Abstract Background An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent...
Rakonjac, Jasna, Ward, Lawrence J. H., Schiemann, Anja H., Gardner, Paul P., Lubbers, Mark W., O'Toole, Paul W.
Prolate or c2-like phages are a large homologous group of viruses that infect the bacterium Lactococcus lactis. In a collection of 122 prolate phages, three distinct, non-cross-hybridizing groups of...
A benchmark of multiple sequence alignment programs upon structural RNAs
Gardner, Paul P., Wilm, Andreas, Washietl, Stefan
To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents...
A hidden Markov model approach for determining expression from genomic tiling micro arrays
Munch, Kasper, Gardner, Paul P, Arctander, Peter, Krogh, Anders
Identification of miRNA targets with stable isotope labeling by amino acids in cell culture
Vinther, Jeppe, Hedegaard, Mads M., Gardner, Paul P., Andersen, Jens S., Arctander, Peter
miRNAs are small noncoding RNAs that regulate gene expression. We have used stable isotope labeling by amino acids in cell culture (SILAC) to investigate the effect of miRNA-1 on the HeLa cell...
Rakonjac, Jasna, Ward, Lawrence J. H., Schiemann, Anja H., Gardner, Paul P., Lubbers, Mark W., O'Toole, Paul W.
Prolate or c2-like phages are a large homologous group of viruses that infect the bacterium Lactococcus lactis. In a collection of 122 prolate phages, three distinct, non-cross-hybridizing groups of...
A benchmark of multiple sequence alignment programs upon structural RNAs
Gardner, Paul P., Wilm, Andreas, Washietl, Stefan
To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents...
A hidden Markov model approach for determining expression from genomic tiling micro arrays
Munch, Kasper, Gardner, Paul P, Arctander, Peter, Krogh, Anders
Identification of miRNA targets with stable isotope labeling by amino acids in cell culture
Vinther, Jeppe, Hedegaard, Mads M., Gardner, Paul P., Andersen, Jens S., Arctander, Peter
miRNAs are small noncoding RNAs that regulate gene expression. We have used stable isotope labeling by amino acids in cell culture (SILAC) to investigate the effect of miRNA-1 on the HeLa cell...
Optimal alphabets for an RNA world.
Gardner, Paul P, Holland, Barbara R, Moulton, Vincent, Hendy, Mike, Penny, David
Experiments have shown that the canonical AUCG genetic alphabet is not the only possible nucleotide alphabet. In this work we address the question 'is the canonical alphabet optimal?' We make the...
Freyhult, Eva K., Bollback, Jonathan P., Gardner, Paul P.
Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use...
Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes
Weile, Christian, Gardner, Paul P, Hedegaard, Mads M, Vinther, Jeppe
Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
Mourier, Tobias, Carret, Celine, Kyes, Sue, Christodoulou, Zoe, Gardner, Paul P., Jeffares, Daniel C., ...
We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P....