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RECOMB
2010
Springer
14 years 2 months ago
Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs
Abstract. In this paper, we focus on finding complex annotation patterns representing novel and interesting hypotheses from gene annotation data. We define a generalization of th...
Barna Saha, Allison Hoch, Samir Khuller, Louiqa Ra...
ISMB
2003
13 years 9 months ago
Deriving phylogenetic trees from the similarity analysis of metabolic pathways
Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type ...
Maureen Heymans, Ambuj K. Singh
BMCBI
2004
115views more  BMCBI 2004»
13 years 7 months ago
An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage
Background: Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed...
Gary W. Stuart, Michael W. Berry
BIOINFORMATICS
2002
100views more  BIOINFORMATICS 2002»
13 years 7 months ago
Optimal algorithms for local vertex quartet cleaning
Reconstructing evolutionary trees is an important problem in biology. A response to the computational intractability of most of the traditional criteria for inferring evolutionary...
Gianluca Della Vedova, Todd Wareham
BMCBI
2010
143views more  BMCBI 2010»
13 years 7 months ago
ETE: a python Environment for Tree Exploration
Background: Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relations...
Jaime Huerta-Cepas, Joaquín Dopazo, Toni Ga...