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» Hybrid Tree Reconstruction Methods
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BMCBI
2008
104views more  BMCBI 2008»
13 years 7 months ago
Comparison of methods for estimating the nucleotide substitution matrix
Background: The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different math...
Maribeth Oscamou, Daniel McDonald, Von Bing Yap, G...
BMCBI
2010
164views more  BMCBI 2010»
13 years 7 months ago
Gene regulatory networks modelling using a dynamic evolutionary hybrid
Background: Inference of gene regulatory networks is a key goal in the quest for understanding fundamental cellular processes and revealing underlying relations among genes. With ...
Ioannis A. Maraziotis, Andrei Dragomir, Dimitris T...
BMCBI
2010
118views more  BMCBI 2010»
13 years 7 months ago
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Background: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Ph...
Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent...
WABI
2004
Springer
100views Bioinformatics» more  WABI 2004»
14 years 23 days ago
Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data
In the last few years, it has become routine to use gene-order data to reconstruct phylogenies, both in terms of edge distances (parsimonious sequences of operations that transform...
Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard...
RECOMB
2012
Springer
11 years 9 months ago
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem
Signaling networks are essential for cells to control processes such as growth and response to stimuli. Although many “omic” data sources are available to probe signaling pathw...
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani...