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TCBB
2008
122views more  TCBB 2008»
15 years 2 months ago
Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference
Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new adva...
Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ra...
JCB
2007
92views more  JCB 2007»
15 years 2 months ago
Neighbor Joining Algorithms for Inferring Phylogenies via LCA Distances
Reconstructing phylogenetic trees efficiently and accurately from distance estimates is an ongoing challenge in computational biology from both practical and theoretical consider...
Ilan Gronau, Shlomo Moran
PVLDB
2010
174views more  PVLDB 2010»
15 years 1 months ago
x-RDF-3X: Fast Querying, High Update Rates, and Consistency for RDF Databases
The RDF data model is gaining importance for applications in computational biology, knowledge sharing, and social communities. Recent work on RDF engines has focused on scalable p...
Thomas Neumann, Gerhard Weikum
BIOCOMP
2010
15 years 1 months ago
A Model Reduction Technique for Stochastic Biochemical Kinetics
Abstract-- Modeling the intermolecular reactions in a single cell is a critical problem in computational biology. Biochemical reaction systems often involve species in both low and...
Silvana Ilie, Ekaterina Kudashkina
INFORMS
2010
147views more  INFORMS 2010»
15 years 9 days ago
Exact Algorithms for the Quadratic Linear Ordering Problem
The quadratic linear ordering problem naturally generalizes various optimization problems, such as bipartite crossing minimization or the betweenness problem, which includes linear...
Christoph Buchheim, Angelika Wiegele, Lanbo Zheng