Cross-kingdom patterns of alternative splicing and splice recognition (2008)
McGuire, Abigail M, Pearson, Matthew D, Neafsey, Daniel E, Galagan, James E
Abstract Background Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of...
Jade P. Vinson, Stacey Luoma, David Decaprio, Matthew D. Pearson, James E. Galagan
Computational gene prediction using generative models has reached a plateau, with several groups converging to a generalized hidden Markov model (GHMM) incorporating phylogenetic models of nucleotide...
Fast Out-of-Core Sorting on Parallel Disk Systems (1999)
Matthew Pearson Mdp, Matthew D. Pearson
This paper discusses our implementation of Rajasekaran's (l,m)-mergesort algorithm (LMM) for sorting on parallel disks. LMM is asymptotically optimal for large problems and has the additional...
Includes abstract.
Conrad: Gene prediction using conditional random fields
DeCaprio, David, Vinson, Jade P., Pearson, Matthew D., Montgomery, Philip, Doherty, Matthew, Galagan, James E.
We present Conrad, the first comparative gene predictor based on semi-Markov conditional random fields (SMCRFs). Unlike the best standalone gene predictors, which are based on generalized hidden...
Cross-kingdom patterns of alternative splicing and splice recognition
McGuire, Abigail M, Pearson, Matthew D, Neafsey, Daniel E, Galagan, James E
A comprehensive survey of alternate splicing across 42 eukaryotes so as to gain insight into how spliceosomal introns are recognized.