Refining transcriptional regulatory networks using network evolutionary models and gene histories
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An entomopathogenic, Gram-negative bacterium isolated from a female specimen of the fruit fly Drosophila melanogaster was taxonomically characterised. Strain L48(T) was strictly aerobic, non-fermentative, oxidase and catalase positive, rod-shaped, and moti ...
The determination of transcriptional regulatory networks is key to the understanding of biological systems. However, the experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while current ...
Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed ...
The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...
Transcription factor binding site(s) (TFBS) gain and loss (i.e., turnover) is a well-documented feature of cis-regulatory module (CRM) evolution, yet little attention has been paid to the evolutionary force(s) driving this turnover process. The predominant ...
Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals - some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite ...
The study of genorne rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed ...
The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while computational methods to infer these networks provide only modest accuracy. The latter can be attributed in part to the limi ...
The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal “DNA barcode” for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses h ...
Background: Scleractinian corals are currently a focus of major interest because of their ecological importance and the uncertain fate of coral reefs in the face of increasing anthropogenic pressure. Despite this, remarkably little is known about the evolu ...