Manuel E Lladser
Affiliation: University of Colorado
- Multiple pattern matching: a Markov chain approachManuel E Lladser
Department of Applied Mathematics, University of Colorado at Boulder, 526 UCB, Boulder, CO 80309 0526, USA
J Math Biol 56:51-92. 2008..The applications we present focus on the concept of synchronization of automata, as well as automata used to search for a finite number of keywords (including sets of patterns generated according to base pairing rules) in a general text...
- Extrapolation of urn models via poissonization: accurate measurements of the microbial unknownManuel E Lladser
Department of Applied Mathematics, University of Colorado, Boulder, Colorado, United States of America
PLoS ONE 6:e21105. 2011....
- Natural and artificial RNAs occupy the same restricted region of sequence spaceRyan Kennedy
Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA
RNA 16:280-9. 2010..These universal evolved sequence features are therefore intrinsic in RNA molecules that bind small-molecule targets or catalyze reactions...
- Comparison of methods for estimating the nucleotide substitution matrixMaribeth Oscamou
Department of Applied Mathematics, University of Colorado, Boulder, CO, USA
BMC Bioinformatics 9:511. 2008..However, the speed and accuracy of these methods has not been compared...
- Estimation of distribution overlap of urn modelsJerrad Hampton
Department of Applied Mathematics, University of Colorado, Boulder, Colorado, USA
PLoS ONE 7:e42368. 2012..The dissimilarity of these pools is then related to the probability of finding binding site solutions in one pool that are absent in the other...
- Information, probability, and the abundance of the simplest RNA active sitesRyan Kennedy
Department of Computer Science, University of Colorado at Boulder, 430 UCB, Boulder, CO 80309 0430, USA
Front Biosci 13:6060-71. 2008..We show that all of the methods that take modularity into account provide far more accurate estimates of this probability than the informational methods, and that fast approximate methods are suitable for a wide range of RNA motifs...