18 Result(s)
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Siu Ming Yiu
Microarrays
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Article
Open AccessDeep analysis and optimization of CARD antibiotic resistance gene discovery models
Identification of antibiotic resistance genes from environmental samples has been a critical sub-domain of gene discovery which is directly connected to human health. However, it is drawing extraordinary atten...
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Open AccessTMFUF: a triple matrix factorization-based unified framework for predicting comprehensive drug-drug interactions of new drugs
A significant number of adverse drug reactions is caused by unexpected Drug-drug interactions (DDIs). The identification of DDIs becomes crucial before the co-prescription of multiple drugs is made. Such a tas...
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Open AccessBMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion
Human Microbiome Project reveals the significant mutualistic influence between human body and microbes living in it. Such an influence lead to an interesting phenomenon that many noninfectious diseases are clo...
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Open AccessPredicting binary, discrete and continued lncRNA-disease associations via a unified framework based on graph regression
In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) st...
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Open AccessImproving somatic variant identification through integration of genome and exome data
Cost-effective high-throughput sequencing technologies, together with efficient map** and variant calling tools, have made it possible to identify somatic variants for cancer study. However, integrating soma...
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Open AccessPredicting combinative drug pairs towards realistic screening via integrating heterogeneous features
Drug Combination is one of the effective approaches for treating complex diseases. However, determining combinative drug pairs in clinical trials is still costly. Thus, computational approaches are used to ide...
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Open AccessBASE: a practical de novo assembler for large genomes using long NGS reads
De novo genome assembly using NGS data remains a computation-intensive task especially for large genomes. In practice, efficiency is often a primary concern and favors using a more eff...
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Open AccessGIW and InCoB are advancing bioinformatics in the Asia-Pacific
GIW/InCoB2015 the joint 26th International Conference on Genome Informatics (GIW) and 14th International Conference on Bioinformatics (InCoB) held in Tokyo, September 9-11, 2015 was attended by over 200 delega...
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Open AccessGIW and InCoB, two premier bioinformatics conferences in Asia with a combined 40 years of history
Knowledge discovery in bioinformatics thrives on joint and inclusive efforts of stakeholders. Similarly, knowledge dissemination is expected to be more effective and scalable through joint efforts. Therefore, ...
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Open AccessmisFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Because of the short read length of high throughput sequencing data, assembly errors are introduced in genome assembly, which may have adverse impact to the downstream data analysis. Several tools have been de...
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Open AccessImproving multiple sequence alignment by using better guide trees
Progressive sequence alignment is one of the most commonly used method for multiple sequence alignment. Roughly speaking, the method first builds a guide tree, and then aligns the sequences progressively accor...
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Open AccessGlobal small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars
In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP an...
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Open AccessMetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning
Taxonomic annotation of reads is an important problem in metagenomic analysis. Existing annotation tools, which rely on the approach of aligning each read to the taxonomic structure, are unable to annotate man...
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Open AccessDe novo assembly and characterization of Camelina sativatranscriptome by paired-end sequencing
Biofuels extracted from the seeds of Camelina sativa have recently been used successfully as environmentally friendly jet-fuel to reduce greenhouse gas emissions. Camelina sativa is genetically very close to Arab...
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Open AccessRefining orthologue groups at the transcript level
Orthologues are genes in different species that are related through divergent evolution from a common ancestor and are expected to have similar functions. Many databases have been created to describe orthologo...
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Open AccessUnsupervised binning of environmental genomic fragments based on an error robust selection of l-mers
With the rapid development of genome sequencing techniques, traditional research methods based on the isolation and cultivation of microorganisms are being gradually replaced by metagenomics, which is also kno...
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Open AccessFinding optimal threshold for correction error reads in DNA assembling
DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DN...
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Open AccessPromoter-sharing by different genes in human genome – CPNE1 and RBM12 gene pair as an example
Regulation of gene expression plays important role in cellular functions. Co-regulation of different genes may indicate functional connection or even physical interaction between gene products. Thus analysis o...
