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BMCBI
2010
130views more  BMCBI 2010»
13 years 5 months ago
Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors
Background: Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This ...
Karel Zimmermann, Jean-François Gibrat
IPPS
2006
IEEE
13 years 11 months ago
Parallel implementation of a quartet-based algorithm for phylogenetic analysis
This paper describes a parallel implementation of our recently developed algorithm for phylogenetic analysis on the IBM BlueGene/L cluster [15]. This algorithm constructs evolutio...
Bing Bing Zhou, Daniel Chu, Monther Tarawneh, Ping...
BMCBI
2006
116views more  BMCBI 2006»
13 years 5 months ago
Optimized mixed Markov models for motif identification
Background: Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challengi...
Weichun Huang, David M. Umbach, Uwe Ohler, Leping ...
BMCBI
2005
77views more  BMCBI 2005»
13 years 5 months ago
Structural comparison of metabolic networks in selected single cell organisms
Background: There has been tremendous interest in the study of biological network structure. An array of measurements has been conceived to assess the topological properties of th...
Dongxiao Zhu, Zhaohui S. Qin
BMCBI
2005
117views more  BMCBI 2005»
13 years 5 months ago
Graph-representation of oxidative folding pathways
Background: The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative ...
Vilmos Ágoston, Masa Cemazar, Lászl&...