Article-Journal

Genomic rearrangements at the MAT locus suggest reproductive shifts in Rhodotorula yeasts

Rhodotorula, a red yeast genus inhabiting diverse environmental and clinical niches, is a promising microbial source for carotenoid and lipid production. Despite the coexistence of …

xin-zhan-liu

Phyling: phylogenetic inference from annotated genomes

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies …

cheng-hung-tsai

Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning

BACKGROUND: Alternative splicing is a pivotal mechanism of post-transcriptional modification that contributes to the transcriptome plasticity and proteome diversity in metazoan …

tzu-chieh-lin

Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states

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 roles in …

cheng-hung-tsai

iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover

Integrating omics data with quantification of biological traits provides unparalleled opportunities for discovery of genetic regulators by in silico inference. However, current …

jia-hsin-huang

H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress

Transcription-replication conflicts (TRCs) occur when intensive transcriptional activity compromises replication fork stability, potentially leading to gene mutations. …

shin-yen-chong