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BMCBI
2006
116views more  BMCBI 2006»
13 years 7 months ago
Gene annotation and network inference by phylogenetic profiling
Background: Phylogenetic analysis is emerging as one of the most informative computational methods for the annotation of genes and identification of evolutionary modules of functi...
Jie Wu, Zhenjun Hu, Charles DeLisi
STOC
2006
ACM
129views Algorithms» more  STOC 2006»
14 years 7 months ago
Optimal phylogenetic reconstruction
One of the major tasks of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on the true evolu...
Constantinos Daskalakis, Elchanan Mossel, Sé...
ICCS
2001
Springer
13 years 12 months ago
High-Performance Algorithm Engineering for Computational Phylogenetics
Abstract. Phylogeny reconstruction from molecular data poses complex optimization problems: almost all optimization models are NP-hard and thus computationally intractable. Yet app...
Bernard M. E. Moret, David A. Bader, Tandy Warnow
BMCBI
2008
118views more  BMCBI 2008»
13 years 7 months ago
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
Background: The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints) has become a common strategy to predict cis-acting regulatory elements. S...
Rekin's Janky, Jacques van Helden
BMCBI
2010
83views more  BMCBI 2010»
13 years 7 months ago
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins
Background: Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in...
William P. Kelly, Michael P. H. Stumpf