Ngoc Tam L. Tran

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ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for(More)
The detection of network motifs has recently become an important part of network analysis across all disciplines. In this work, we detected and analyzed network motifs from undirected and directed networks of several different disciplines, including biological network, social network, ecological network, as well as other networks such as airlines, power(More)
Network motif detection is the search for statistically overrepresented subgraphs present in a larger target network. They are thought to represent key structure and control mechanisms. Although the problem is exponential in nature, several algorithms and tools have been developed for efficiently detecting network motifs. This work analyzes 11 network motif(More)
Currently, there are a number of motif detection tools available that possess unique functionality. These tools often report different motifs, and therefore use of multiple tools is generally advised since common motifs reported by multiple tools are more likely to be biologically significant. However, results produced by these different tools need to be(More)
Finding binding site motifs plays an important role in bioinformatics as it reveals the transcription factors that control the gene expression. The development for motif finders has flourished in the past years with many tools have been introduced to the research community. Although these tools possess exceptional features for detecting motifs, they report(More)
We developed the cloud-based MOTIFSIM on Amazon Web Services (AWS) cloud. The tool is an extended version from our web-based tool version 2.0, which was developed based on a novel algorithm for detecting similarity in multiple DNA motif data sets. This cloud-based version further allows researchers to exploit the computing resources available from AWS to(More)
Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we(More)
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