Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and
gain or loss of sequence conservation can be used to infer changes in function across a …
gain or loss of sequence conservation can be used to infer changes in function across a …
Co-evolution based machine-learning for predicting functional interactions between human genes
Over the next decade, more than a million eukaryotic species are expected to be fully
sequenced. This has the potential to improve our understanding of genotype and phenotype …
sequenced. This has the potential to improve our understanding of genotype and phenotype …
CladeOScope: functional interactions through the prism of clade-wise co-evolution
Map** co-evolved genes via phylogenetic profiling (PP) is a powerful approach to
uncover functional interactions between genes and to associate them with pathways …
uncover functional interactions between genes and to associate them with pathways …
Optimization of co-evolution analysis through phylogenetic profiling reveals pathway-specific signals
The exponential growth in available genomic data is expected to reach full sequencing of a
million genomes in the coming decade. Improving and develo** methods to analyze these …
million genomes in the coming decade. Improving and develo** methods to analyze these …
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level
Background Phylogenetic profiling is widely used to predict novel members of large protein
complexes and biological pathways. Although methods combined with phylogenetic trees …
complexes and biological pathways. Although methods combined with phylogenetic trees …
Multimodal bioinformatic analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles
Background Loss of tectonin β-propeller repeat-containing 2 (TECPR2) function has been
implicated in an array of neurodegenerative disorders, yet its physiological function remains …
implicated in an array of neurodegenerative disorders, yet its physiological function remains …
Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families
Motivation Reconstruction of gene copy number evolution is an essential approach for
understanding how complex biological systems have been organized. Although various …
understanding how complex biological systems have been organized. Although various …
A hierarchical Bayesian model for detecting convergent rate changes of conserved noncoding elements on phylogenetic trees
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and
thus gain or loss of sequence conservation can be used to infer putative changes in function …
thus gain or loss of sequence conservation can be used to infer putative changes in function …
Integrative functional analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles
Background Loss of tectonin β-propeller repeat-containing 2 (TECPR2) function has been
implicated in an array of neurodegenerative disorders, yet its physiological function remains …
implicated in an array of neurodegenerative disorders, yet its physiological function remains …
Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model
Reconstruction of gene-content evolutionary history is an essential approach for
understanding how complex biological systems have been organized. However, the existing …
understanding how complex biological systems have been organized. However, the existing …