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» Reconstruction of Reticulate Networks from Gene Trees
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RECOMB
2004
Springer
14 years 8 months ago
Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response
We present a novel classification-based algorithm called GeneClass for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple orga...
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, ...
BMCBI
2010
191views more  BMCBI 2010»
13 years 7 months ago
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Background: Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabili...
Jan Schellenberger, Junyoung O. Park, Tom M. Conra...
ALMOB
2008
85views more  ALMOB 2008»
13 years 7 months ago
Noisy: Identification of problematic columns in multiple sequence alignments
Motivation: Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Larg...
Andreas W. M. Dress, Christoph Flamm, Guido Fritzs...
WABI
2001
Springer
14 years 3 days ago
A Chemical-Distance-Based Test for Positive Darwinian Selection
There are very few instances in which positive Darwinian selection has been convincingly demonstrated at the molecular level. In this study, we present a novel test for detecting p...
Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Sham...
BIOINFORMATICS
2007
88views more  BIOINFORMATICS 2007»
13 years 7 months ago
Maximum likelihood of phylogenetic networks
Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversiļ¬cation as well as their ability to develop resistance t...
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller