Irmtraud M Meyer
Affiliation: University of Oxford
- Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAsIrmtraud M Meyer
European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
Nucleic Acids Res 33:6338-48. 2005....
- Gene structure conservation aids similarity based gene predictionIrmtraud M Meyer
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nucleic Acids Res 32:776-83. 2004..It is more accurate than Genewise for genes whose proteins are <80% identical, and is suitable for use in a combined gene prediction system where other methods identify well conserved and non-conserved genes, and pseudogenes...
- Co-transcriptional folding is encoded within RNA genesIrmtraud M Meyer
University of Oxford, Oxford OX1 3QB, UK
BMC Mol Biol 5:10. 2004..Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription...
- Comparative ab initio prediction of gene structures using pair HMMsIrmtraud M Meyer
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Bioinformatics 18:1309-18. 2002..More information can be found at: http://www.sanger.ac.uk/Software/analysis/doublescan/..
- Moments of the Boltzmann distribution for RNA secondary structuresIstván Miklós
MTA ELTE Theoretical Biology and Ecology Modelling Group, H 1117 Budapest, Pazmany Peter setany 1 C, Hungary
Bull Math Biol 67:1031-47. 2005..These results suggest that biologically functional RNA sequences not only require a thermodynamically stable minimum free energy structure, but also an ensemble of structures whose free energies are close to the minimum free energy...
- SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC frameworkIrmtraud M Meyer
UBC Bioinformatics Centre, University of British Columbia, Vancouver, British Columbia, Canada
PLoS Comput Biol 3:e149. 2007..It is thus likely to have a strong impact, both on the field of RNA structure prediction and on a wide range of data analyses...
- A linear memory algorithm for Baum-Welch trainingIstván Miklós
MTA ELTE Theoretical Biology and Ecology Group, Pázmány Péter sétány 1 c 1117 Budapest, Hungary
BMC Bioinformatics 6:231. 2005..This has so far effectively prevented the automatic parameter training of hidden Markov models that are currently used for biological sequence analyses...
- A practical guide to the art of RNA gene predictionIrmtraud M Meyer
Bioinformatics Centre and Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC, Canada V6T 1Z4
Brief Bioinform 8:396-414. 2007..It discusses our current view of RNA genes as well as recent computational analyses of RNA genes and concludes with an outlook to future directions in algorithm development and data analyses...
- A cross-species comparison of X-chromosome inactivation in EutheriaZiny C Yen
Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
Genomics 90:453-63. 2007....
- Predicting novel RNA-RNA interactionsIrmtraud M Meyer
UBC Bioinformatics Centre and Department of Medical Genetics, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
Curr Opin Struct Biol 18:387-93. 2008..We conclude by discussing the merits of the different approaches and provide an outlook on probably and desirable future developments in the field...