title: iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.
abstract: Regulatory DNA elements are associated with DNase I hypersensitive sites (DHSs). Accordingly, identification of DHSs will provide useful insights for in-depth investigation into the function of noncoding genomic regions.
  
  
  
  In this study, using the strategy of ensemble learning framework, we proposed a new predictor called iDHS-EL for identifying the location of DHS in human genome. It was formed by fusing three individual Random Forest (RF) classifiers into an ensemble predictor. The three RF operators were respectively based on the three special modes of the general pseudo nucleotide composition (PseKNC): (i) kmer, (ii) reverse complement kmer and (iii) pseudo dinucleotide composition. It has been demonstrated that the new predictor remarkably outperforms the relevant state-of-the-art methods in both accuracy and stability.
  
  
  
  For the convenience of most experimental scientists, a web server for iDHS-EL is established at http://bioinformatics.hitsz.edu.cn/iDHS-EL, which is the first web-server predictor ever established for identifying DHSs, and by which users can easily get their desired results without the need to go through the mathematical details. We anticipate that IDHS-EL: will become a very useful high throughput tool for genome analysis.
  
  
  
  bliu@gordonlifescience.org or bliu@insun.hit.edu.cn
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China Gordon Life Science Institute, Belmont, MA 02478, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
authors.forename: Ren
authors.initials: R
authors.lastname: Long
authors.affiliation: Gordon Life Science Institute, Belmont, MA 02478, USA Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D004247:DNA; D003850:Deoxyribonuclease I; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009711:Nucleotides; D017422:Sequence Analysis, DNA
chemical_list: D009711:Nucleotides; D004247:DNA; D003850:Deoxyribonuclease I