The most popular approaches for reconstructing phylogenetic trees attempt to solve NP-hard optimization criteria such as maximum parsimony (MP). Currently, the bestperforming heur...
Despite its state-of-the-art performance, the Data Oriented Parsing (DOP) model has been shown to suffer from biased parameter estimation, and the good performance seems more the ...
Background: Co-evolution is the process in which two (or more) sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn abo...
Background: We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called...
Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chr...
Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. Because no g...