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NAR
2011
198views Computer Vision» more  NAR 2011»
14 years 4 months ago
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralo
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large col...
Jaime Huerta-Cepas, Salvador Capella-Gutiér...
UAI
2008
15 years 3 months ago
Tightening LP Relaxations for MAP using Message Passing
Linear Programming (LP) relaxations have become powerful tools for finding the most probable (MAP) configuration in graphical models. These relaxations can be solved efficiently u...
David Sontag, Talya Meltzer, Amir Globerson, Tommi...
BMCBI
2006
101views more  BMCBI 2006»
15 years 1 months ago
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives
Background: Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the ...
Petras J. Kundrotas, Emil Alexov
CMSB
2009
Springer
15 years 8 months ago
Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network
Circadian clocks are biochemical networks, present in nearly all living organisms, whose function is to regulate the expression of specific mRNAs and proteins to synchronise rhyth...
Ozgur E. Akman, Federica Ciocchetta, Andrea Degasp...
BMCBI
2005
100views more  BMCBI 2005»
15 years 1 months ago
Evolutionary models for insertions and deletions in a probabilistic modeling framework
Background: Probabilistic models for sequence comparison (such as hidden Markov models and pair hidden Markov models for proteins and mRNAs, or their context-free grammar counterp...
Elena Rivas