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» Computer algebra in systems biology
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SAC
2009
ACM
16 years 1 months ago
GTfold: a scalable multicore code for RNA secondary structure prediction
The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. Among the major obstacles is the fact that a...
Amrita Mathuriya, David A. Bader, Christine E. Hei...
SIAMSC
2010
114views more  SIAMSC 2010»
15 years 5 months ago
Smoothed Aggregation Multigrid for Markov Chains
Abstract. A smoothed aggregation multigrid method is presented for the numerical calculation of the stationary probability vector of an irreducible sparse Markov chain. It is shown...
Hans De Sterck, Thomas A. Manteuffel, Stephen F. M...
EUROPAR
2011
Springer
14 years 6 months ago
A Fully Empirical Autotuned Dense QR Factorization for Multicore Architectures
: Tuning numerical libraries has become more difficult over time, as systems get more sophisticated. In particular, modern multicore machines make the behaviour of algorithms hard ...
Emmanuel Agullo, Jack Dongarra, Rajib Nath, Stanim...
CONCUR
2000
Springer
15 years 11 months ago
Process Spaces
This paper introduces process spaces, a unified theory of interacting systems. The trait, abstract executions, leads to a simple and general set formalism. For concurrent systems ...
Radu Negulescu
BMCBI
2007
158views more  BMCBI 2007»
15 years 7 months ago
Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries
Background: The joint analysis of several categorical variables is a common task in many areas of biology, and is becoming central to systems biology investigations whose goal is ...
Corinne Dahinden, Giovanni Parmigiani, Mark C. Eme...