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» Constraint Programming in Structural Bioinformatics
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BMCBI
2005
162views more  BMCBI 2005»
14 years 9 months ago
Accelerated probabilistic inference of RNA structure evolution
Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary...
Ian Holmes
ISBRA
2007
Springer
15 years 3 months ago
Delta: A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice
Abstract. The lattice approach to biological structural analysis was made popular by the HP model for protein folding, but had not been used previously for RNA secondary structure ...
Minghui Jiang, Martin Mayne, Joel Gillespie
PADL
2009
Springer
15 years 10 months ago
Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell
Analysis of biological data often involves large data sets and computationally expensive algorithms. Databases of biological data continue to grow, leading to an increasing demand ...
Ketil Malde, Bryan O'Sullivan
111
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JMLR
2012
12 years 12 months ago
A General Framework for Structured Sparsity via Proximal Optimization
We study a generalized framework for structured sparsity. It extends the well known methods of Lasso and Group Lasso by incorporating additional constraints on the variables as pa...
Luca Baldassarre, Jean Morales, Andreas Argyriou, ...