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WEA
2005
Springer
176views Algorithms» more  WEA 2005»
15 years 11 months ago
High-Performance Algorithm Engineering for Large-Scale Graph Problems and Computational Biology
Abstract. Many large-scale optimization problems rely on graph theoretic solutions; yet high-performance computing has traditionally focused on regular applications with high degre...
David A. Bader
ALGORITHMICA
2008
83views more  ALGORITHMICA 2008»
15 years 6 months ago
Inferring (Biological) Signal Transduction Networks via Transitive Reductions of Directed Graphs
In this paper we consider the p-ary transitive reduction (TRp) problem where p > 0 is an integer; for p = 2 this problem arises in inferring a sparsest possible (biological) sig...
Réka Albert, Bhaskar DasGupta, Riccardo Don...
MMAS
2010
Springer
15 years 29 days ago
Incorporating Active Transport of Cellular Cargo in Stochastic Mesoscopic Models of Living Cells
We propose a new multiscale method to incorporate active transport of cargo particles in biological cells in stochastic, mesoscopic models of reaction-transport processes. Given a...
Andreas Hellander, Per Lötstedt
ICPP
2006
IEEE
16 years 7 days ago
Scalable Time-Parallelization of Molecular Dynamics Simulations in Nano Mechanics
— Molecular Dynamics (MD) is an important atomistic simulation technique, with widespread use in computational chemistry, biology, and materials. An important limitation of MD is...
Yanan Yu, Ashok Srinivasan, Namas Chandra
BMCBI
2005
292views more  BMCBI 2005»
15 years 6 months ago
Atlas - a data warehouse for integrative bioinformatics
Background: We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional a...
Sohrab P. Shah, Yong Huang, Tao Xu, Macaire M. S. ...