Abstract Accurately identifying orthogroups is crucial for precise phylogenetic reconstruction, but clustering-based methods often generate complex, many-to-many orthogroups that …
Abstract Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies …
Transitions from canonical outcrossing to rare, cryptic, or noncanonical reproduction are widespread in fungi, but how mating-type ( MAT ) systems are reorganized at the genomic …
Abstract Background Alternative splicing is a pivotal mechanism of post-transcriptional modification that contributes to the transcriptome plasticity and proteome diversity in …
Abstract Background Many long non-coding RNAs (lncRNAs) have been extensively identified in higher eukaryotic species. The function of lncRNAs has been reported to play important …
Abstract Integrating omics data with quantification of biological traits provides unparalleled opportunities for discovery of genetic regulators by in silico inference. However, …
Abstract Transcription-replication conflicts (TRCs) occur when intensive transcriptional activity compromises replication fork stability, potentially leading to gene mutations. …