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Article
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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Article
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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Article
Open AccessSOAPdenovo2: 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...
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Article
Open AccessAssemblathon 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 ...
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Article
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 AccessErratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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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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Article
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 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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Article
Open AccessOMSV 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...
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Open AccessPredicting 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...
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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 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 AccessA 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...