Xin-Yi Chua

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Culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. Recently, changes in microbial community structure and dynamics have been associated with a growing list of human diseases. The identification and comparison of bacteria driving those changes(More)
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone(More)
The Regulog assumption has been widely used as a method to reconstruct transcriptional regulatory networks (TRNs) in uncharacterized genomes by mapping from a model organism whose regulatory interactions are well studied [1, 8]. Under this assumption, if orthologs of a transcription factor (TF) known to regulate a target gene (TG) in a model organism are(More)
We sought to explore how knowledge of videogames could inform the design of complex digital interfaces for bioinformatics visualization tools. Aquaria is an open-source web resource for visual exploration of protein structures. We present the results of a series of workshops conducted with participants who have expertise in videogame design and development.(More)
The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex(More)
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