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IPPS
2006
IEEE
15 years 3 months ago
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L
The Replica Exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. Ho...
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. P...
TSE
2011
134views more  TSE 2011»
14 years 4 months ago
Verifying the Evolution of Probability Distributions Governed by a DTMC
— We propose a new probabilistic temporal logic iLTL which captures properties of systems whose state can be represented by probability mass functions (pmf’s). Using iLTL, we c...
YoungMin Kwon, Gul A. Agha
RECOMB
2009
Springer
15 years 10 months ago
Shared Peptides in Mass Spectrometry Based Protein Quantification
In analyzing the proteome using mass spectrometry, the mass values help identify the molecules, and the intensities help quantify them, relative to their abundance in other sample...
Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Sh...
DATE
2009
IEEE
159views Hardware» more  DATE 2009»
15 years 4 months ago
Design and implementation of a database filter for BLAST acceleration
— BLAST is a very popular Computational Biology algorithm. Since it is computationally expensive it is a natural target for acceleration research, and many reconfigurable archite...
Panagiotis Afratis, Constantinos Galanakis, Euripi...
CLADE
2008
IEEE
15 years 4 months ago
SWARM: a scientific workflow for supporting bayesian approaches to improve metabolic models
With the exponential growth of complete genome sequences, the analysis of these sequences is becoming a powerful approach to build genome-scale metabolic models. These models can ...
Xinghua Shi, Rick Stevens