Motif discovery is a significant problem in Bioinformatics. According to the complexity of most signals in biologic sequences, there are no extremely good models or dependable algorithms to solve this problem. This paper introduces the Uniform Projection and Neighbourhood Thresholding (UPNT) algorithm, which is based on two efficient strategies: Uniform Projection and Neighbourhood-based Thresholding. In the UPNT algorithm, the policy of uniform projection leads to fewer projections, while the strategy of refining the buckets after aggregation results in great abatement of the number of buckets to be refined. This paper further demonstrates its superiority over other projection algorithms by the experiments.
- Inderscience Publishers
- UPNT: uniform projection and neighbourhood thresholding method ...
Big data and hydroinformatics
Big data is popular in the areas of computer science, commerce and bioinformatics, but is in an early stage in hydroinformatics. Big data is originated from the extremely large datasets that cannot be processed in tolerable elapsed time with the traditional data processing methods. Using the analogy from the object-oriented programming, big data should be considered as objects encompassing the data, its characteristics and the processing methods. Hydroinformatics can benefit from the big data technology with...
Is qualitative and quantitative metabarcoding of dung fauna biodiversity feasible?
In biodiversity assessments, especially of small‐bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost‐effective and efficient alternative to traditional identification of species by morphology, ecology and behavior. Here we test the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. We produced eight known mixtures that varied in...
Industrialization of biology report released by the national academies
On March 13, 2015, the National Academies issued Industrialization Of Biology: A Roadmap To Accelerate The Advanced Manufacturing Of Chemicals, a 143-page report prepared in response to a request from the U.S. Department of Energy (DOE) and the National Science Foundation (NSF) to "develop a roadmap of necessary advances in basic science and engineering capabilities, including knowledge, tools and skills" to accelerate the advanced manufacturing of chemicals using biological systems. Thirteen committee members...
Radiobiology worker risk assessment using stress indicators and proteomics
Radiology is an essential technology in medicine and is used for organ diagnosis, radio–tracing and radiotherapy. The risks for the radiobiology workers have not been assessed sufficiently because measuring instruments fail to detect very low doses. This paper presents an investigation on the potential risks for radiobiology workers, due to the occupational exposure to low doses of irradiation. In this respect we used plasma samples from 16 subjects who were supposed to receive very low dose of irradiation in a...
The role of biomarkers in the assessment of aquatic ecosystem health
Ensuring the health of aquatic ecosystems and identifying species at risk from the detrimental effects of environmental contaminants can be facilitated by integrating analytical chemical analysis with carefully selected biological endpoints measured in tissues of species of concern. These biological endpoints include molecular, biochemical and physiological markers (i.e. biomarkers) that when integrated, can clarify issues of contaminant bioavailability, bioaccumulation and ecological effects while enabling a...