Huai Kuang Tsai

..Here, we conducted a comprehensive investigation to depict the emergence and establishment of cis-regulatory elements in de novo yeast genes...

..In this study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues...

..MYBS also allows users to identify target gene sets of each TF pair, which could be used as a starting point for further explorations of TF combinatorial regulation. MYBS is available at http://cg1.iis.sinica.edu.tw/~mybs/...

..iis.sinica.edu.tw/~mybs/, the ratios of TF-sharing pairs among all the adjacent pairs in yeast genomes were analyzed. The levels of co-expression in different adjacent patterns were also compared...

..Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes' co-expression are also discussed...

..For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods. AVAILABILITY: http://cg1.iis.sinica.edu.tw/~TFBSfinder/...

..After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams...

..Our analysis suggests that genes in a divergent pair tend to be co-regulated in at least one condition; however, in most conditions, they may not be co-regulated...

..e., highly co-localized). Moreover, such associations were highly conserved between sensu stricto yeasts and also influenced gene expression, which were consistent with enriched functional categories...

..Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites...

..Moreover, MIM genes are, on average, subject to stronger trans effects than SIM genes, though the difference between the two types of genes is not conspicuous...

..This article aims at improving the accuracy of inferring TF-TF interactions by incorporating motif discovery as a fundamental step when detecting overlapping targets of TFs based on ChIP-chip data...

..In addition to the cell cycle, our methods are also applicable to other functions...

..However, such estimated abundances might deviate from the true abundances in habitats due to sampling biases and other systematic artifacts in metagenomic data processing...

..Our analysis supports the importance of nucleotide variants at variable positions of TFBSs in gene regulation...

..We also compared the consistency between our taxonomic binning and those reported in the original studies...

..It may be also combined with other algorithms for further improvements in protein structure prediction. AVAILABILITY: The program and datasets are available from the authors upon request. CONTACT: ...

..These results indicate that HeSGA has potential in analyzing gene expression patterns...

..0074% above the optimum for each test problem. These findings imply that the proposed method can find tours robustly with a fixed small population and a limited family competition length in reasonable time, when used to solve large TSPs...

..Predictions on additional 54 TFs successfully discover 11 gapped and 38 ungapped motifs supported by literature. Our method achieves high sensitivity and specificity for predicting experimentally verified TFBSs...

..These results suggest that GEM is robust and can be used to examine the factors limiting the accuracy of protein side-chain prediction methods. Furthermore, it can be used to systematically evaluate and thus improve scoring functions...