The DNA motif discovery is a primary step in many systems for studying gene function. Motif
discovery plays a vital role in identification of Transcription Factor Binding Sites (TFBSs) that …

Identifying master regulators of biological processes and mapping their downstream gene
networks are key challenges in systems biology. We developed a computational method …

ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for
finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site …

We present CisFinder software, which generates a comprehensive list of motifs enriched in a
set of DNA sequences and describes them with position frequency matrices (PFMs). A new …

A major challenge in analyzing the data from high-throughput next-generation sequencing
(NGS) is how to handle the huge amounts of data and variety of NGS tools and visualize the …

Background The gene doublesex (dsx) is known as a key factor regulating genetic sex
determination in many organisms. We previously identified two dsx genes (DapmaDsx1 and …

Background Upstream open reading frames (uORFs) can down-regulate the translation of
the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling …

Some plants like Arabidopsis thaliana increase in freezing tolerance when exposed to low
nonfreezing temperatures, a process known as cold acclimation. Other plants including …

By using genome in situ hybridization (GISH) on root somatic chromosomes of allotetraploid
derived from the cross Gossypium arboreum× G. bickii with genomic DNA (gDNA) of G. bickii …

Plants contain more genes encoding core cell cycle regulators than other organisms but it is
unclear whether these represent distinct functions. D-type cyclins (CYCD) play key roles in …