14 Result(s)

Article

A unified solution for different scenarios of predicting drug-target interactions via triple matrix factorization

During the identification of potential candidates, computational prediction of drug-target interactions (DTIs) is important to subsequent expensive validation in wet-lab. DTI screening considers four scenarios...

Jian-Yu Shi, An-Qi Zhang, Shao-Wu Zhang, Kui-Tao Mao, Siu-Ming Yiu in BMC Systems Biology (2018)

Article

TMFUF: 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...

Jian-Yu Shi, Hua Huang, Jia-**n Li, Peng Lei, Yan-Ning Zhang… in BMC Bioinformatics (2018)

Article

BMCMDA: 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...

Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Jiang-Bo Cao, Siu-Ming Yiu in BMC Bioinformatics (2018)

Article

Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization

Drug-drug interactions (DDIs) always cause unexpected and even adverse drug reactions. It is important to identify DDIs before drugs are used in the market. However, preclinical identification of DDIs requires...

Hui Yu, Kui-Tao Mao, Jian-Yu Shi, Hua Huang, Zhi Chen, Kai Dong… in BMC Systems Biology (2018)

Article

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, a...

Le Li, Alden King-Yung Leung, Tsz-Piu Kwok, Yvonne Y. Y. Lai… in Genome Biology (2017)

Article

Predicting 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...

Jian-Yu Shi, Jia-**n Li, Ke Gao, Peng Lei, Siu-Ming Yiu in BMC Bioinformatics (2017)

Article

GIW 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...

Christian Schönbach, Paul Horton, Siu-Ming Yiu, Tin Wee Tan… in BMC Bioinformatics (2015)

Article

misFinder: 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...

**ao Zhu, Henry C. M. Leung, Rongjie Wang, Francis Y. L. Chin… in BMC Bioinformatics (2015)

Article

Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Ruibang Luo, Binghang Liu, Yinlong **e, Zhenyu Li, Weihua Huang… in GigaScience (2015)

Article

Improving 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...

Qing Zhan, Yongtao Ye, Tak-Wah Lam, Siu-Ming Yiu, Yadong Wang… in BMC Bioinformatics (2015)

Article

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many ...

Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay… in GigaScience (2013)

Article

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accu...

Ruibang Luo, Binghang Liu, Yinlong **e, Zhenyu Li, Weihua Huang… in GigaScience (2012)

Article

Unsupervised 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...

Bin Yang, Yu Peng, Henry Chi-Ming Leung, Siu-Ming Yiu, **g-Chi Chen… in BMC Bioinformatics (2010)

Article

Finding 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...

Francis YL Chin, Henry CM Leung, Wei-Lin Li, Siu-Ming Yiu in BMC Bioinformatics (2009)