6,411 research outputs found
RNAhybrid: microRNA target prediction easy, fast, and flexible
Get PDFKrüger J, Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast, and flexible. Nucleic Acids Research. 2006;34(Web Server):W451-W454
Complete probabilistic analysis of RNA shapes
Get PDFVoß B, Giegerich R, Rehmsmeier M. Complete probabilistic analysis of RNA shapes. BMC Biology. 2006;4(1): 5.Background: Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived. Results: In this paper we extend the approach of abstract shape analysis. We show how to compute the accumulated probabilities of all structures that share the same shape. While this implies a complete (non-heuristic) analysis of the folding space, the computational effort depends only on the size of the shape space, which is much smaller. This approach has been integrated into the tool RNAshapes, and we apply it to various RNAs. Conclusion: Analyses of conformational switches show the existence of two shapes with probabilities approximately 2/3 vs. 1/3, whereas the analysis of a microRNA precursor reveals one shape with a probability near to 1.0. Furthermore, it is shown that a shape can outperform an energetically more favourable one by achieving a higher probability. From these results, and the fact that we use a complete and exact analysis of the folding space, we conclude that this approach opens up new and promising routes for investigating and understanding RNA secondary structure
Phylogeny meets sequence search
No full textRehmsmeier M, Vingron M. Phylogeny meets sequence search. In: Proceedings of the German Conference on Bioinformatics GCB. 1999: 66-72
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana
Get PDFAlves jun. L, Niemeier S, Hauenschild A, Rehmsmeier M, Merkle T. Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Research. 2009;37(12):4010-4021
Phylogenetic Information Improves Homology Detection
No full textRehmsmeier M, Vingron MV. Phylogenetic Information Improves Homology Detection. Proteins: Structure, Function, and Genetics. 2001;45:360-371
The Future of Canadian Climate Policy — with Marc Lee
No full textMarc Lee is a Senior Economist at the Canadian Centre for Policy Alternatives\u27 BC Office. In addition to tracking federal and provincial budgets and economic trends, Marc has published on a range of topics from poverty and inequality to globalization and international trade to public services and regulation. Marc is the Co-Director of the Climate Justice Project, a research partnership with UBC\u27s School of Community and Regional Planning that examines the links between climate change policies and social justice.Resources:Climate Justice Project: www.policyalternatives.ca/projects/cli…tice-projectMarc Lee\u27s Posts on Policy Note: www.policynote.ca/author/marclee/Canadian Centre for Policy Alternatives: www.policyalternatives.ca/Marc\u27s Twitter: twitter.com/MarcLeeCCPA International Panel on Climate Change, 2021 report: www.ipcc.ch/report/ar6/wg1
Genome Wide Prediction of Polycomb/Trithorax Response Elements in Drosophila melanogaster
No full textRingrose L, Rehmsmeier M, Dura J-M, Paro R. Genome Wide Prediction of Polycomb/Trithorax Response Elements in Drosophila melanogaster. Developmental Cell. 2003;5:759-771
Sequence Database Search Using Jumping Alignments
No full textSpang R, Rehmsmeier M, Stoye J. Sequence Database Search Using Jumping Alignments. In: Proc. of ISMB 2000. 2000: 367-375
Automatic clustering of large sequence databases
No full textKrause A, Nicodeme P, Rehmsmeier M, Vingron M. Automatic clustering of large sequence databases. In: Proceedings of the German Conference on Bioinformatics GCB. 1998
Climate Justice & Inequality: The Future of Canadian Climate Policy — with Marc Lee
No full textMarc Lee is a Senior Economist at the Canadian Centre for Policy Alternatives\u27 BC Office. In addition to tracking federal and provincial budgets and economic trends, Marc has published on a range of topics from poverty and inequality to globalization and international trade to public services and regulation. Marc is the Co-Director of the Climate Justice Project, a research partnership with UBC\u27s School of Community and Regional Planning that examines the links between climate change policies and social justice.Resources: Climate Justice Project: https://www.policyalternatives.ca/projects/climate-justice-projectMarc Lee\u27s Posts on Policy Note: https://www.policynote.ca/author/marclee/Canadian Centre for Policy Alternatives: https://www.policyalternatives.ca/Marc\u27s Twitter: https://twitter.com/MarcLeeCCPA International Panel on Climate Change, 2021 report: https://www.ipcc.ch/report/ar6/wg1
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