Wei Chen

Summary

Country: China

Publications

  1. doi Prediction of replication origins by calculating DNA structural properties
    Wei Chen
    Department of Physics, School of Sciences, Hebei United University, Tangshan, China
    FEBS Lett 586:934-8. 2012
  2. doi Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine
    Wei Chen
    Department of Physics, College of Sciences, Hebei United University, Tangshan 063000, China
    Comput Biol Med 42:504-7. 2012
  3. doi Prediction of ketoacyl synthase family using reduced amino acid alphabets
    Wei Chen
    Department of Physics, College of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China
    J Ind Microbiol Biotechnol 39:579-84. 2012
  4. ncbi Recognition of DNase I hypersensitive sites in multiple cell lines
    Wei Chen
    Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
    Int J Bioinform Res Appl 5:378-84. 2009
  5. doi Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information
    Wei Chen
    Department of Physics, School of Basic Medical Sciences, North China Coal Medical University, Tangshan 063000, China
    Biochem Biophys Res Commun 401:382-4. 2010
  6. pmc iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition
    Wei Chen
    Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan, China
    Nucleic Acids Res 41:e68. 2013
  7. doi iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
    Shou Hui Guo
    Key Laboratory for Neuro Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research CEGMR, King Abdulaziz University, Jeddah, Saudi Arabia
    Bioinformatics 30:1522-9. 2014
  8. pmc Identification of antioxidants from sequence information using naïve Bayes
    Peng Mian Feng
    School of Public Health, Hebei United University, Tangshan, China
    Comput Math Methods Med 2013:567529. 2013
  9. pmc Naïve Bayes classifier with feature selection to identify phage virion proteins
    Peng Mian Feng
    School of Public Health, Hebei United University, Tangshan 063000, China
    Comput Math Methods Med 2013:530696. 2013
  10. doi iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition
    Wei Chen
    Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China Gordon Life Science Institute, Boston, MA 02478, USA Electronic address
    Anal Biochem 462:76-83. 2014

Collaborators

Detail Information

Publications23

  1. doi Prediction of replication origins by calculating DNA structural properties
    Wei Chen
    Department of Physics, School of Sciences, Hebei United University, Tangshan, China
    FEBS Lett 586:934-8. 2012
    ..The predictive performance of the jackknife cross-validation indicates that DNA bendability and cleavage intensity have the ability to describe core replication regions and our model is effective in ORI prediction...
  2. doi Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine
    Wei Chen
    Department of Physics, College of Sciences, Hebei United University, Tangshan 063000, China
    Comput Biol Med 42:504-7. 2012
    ..These results indicate that VKCPred can be efficiently used to identify and annotate voltage-gated K(+) channels' subfamilies. The VKCPred software and dataset are freely available at http://cobi.uestc.edu.cn/people/hlin/tools/VKCPred/...
  3. doi Prediction of ketoacyl synthase family using reduced amino acid alphabets
    Wei Chen
    Department of Physics, College of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China
    J Ind Microbiol Biotechnol 39:579-84. 2012
    ....
  4. ncbi Recognition of DNase I hypersensitive sites in multiple cell lines
    Wei Chen
    Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
    Int J Bioinform Res Appl 5:378-84. 2009
    ..52%, 96.50%, 99.25% and 97.58%, respectively, and the mean areas under ROC curves (auROC) are all greater than 0.90. The prediction results indicate that the IDQD method is an effective tool for DHSs recognition...
  5. doi Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information
    Wei Chen
    Department of Physics, School of Basic Medical Sciences, North China Coal Medical University, Tangshan 063000, China
    Biochem Biophys Res Commun 401:382-4. 2010
    ..The prediction model and dataset used in this article can be freely downloaded from http://cobi.uestc.edu.cn/people/hlin/tools/MicekiPred/...
  6. pmc iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition
    Wei Chen
    Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan, China
    Nucleic Acids Res 41:e68. 2013
    ..As a user-friendly web-server, iRSpot-PseDNC is freely accessible at http://lin.uestc.edu.cn/server/iRSpot-PseDNC...
  7. doi iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
    Shou Hui Guo
    Key Laboratory for Neuro Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research CEGMR, King Abdulaziz University, Jeddah, Saudi Arabia
    Bioinformatics 30:1522-9. 2014
    ..Although some computational methods were proposed, most of them were species specific and neglected the intrinsic local structural properties that might play important roles in determining the nucleosome positioning on a DNA sequence...
  8. pmc Identification of antioxidants from sequence information using naïve Bayes
    Peng Mian Feng
    School of Public Health, Hebei United University, Tangshan, China
    Comput Math Methods Med 2013:567529. 2013
    ..These results suggest that the proposed method could be an effective and promising high-throughput method for antioxidant protein identification. ..
  9. pmc Naïve Bayes classifier with feature selection to identify phage virion proteins
    Peng Mian Feng
    School of Public Health, Hebei United University, Tangshan 063000, China
    Comput Math Methods Med 2013:530696. 2013
    ..These results indicate that the proposed method could be as an effective and promising high-throughput method in phage proteomics research...
  10. doi iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition
    Wei Chen
    Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China Gordon Life Science Institute, Boston, MA 02478, USA Electronic address
    Anal Biochem 462:76-83. 2014
    ....
  11. pmc iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition
    Wei Chen
    Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China Gordon Life Science Institute, Boston, MA 02478, USA
    Biomed Res Int 2014:623149. 2014
    ....
  12. doi iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
    Peng Mian Feng
    School of Public Health, Hebei United University, Tangshan 063000, China
    Anal Biochem 442:118-25. 2013
    ..As a user-friendly web server, iHSP-PseRAAAC is accessible to the public at http://lin.uestc.edu.cn/server/iHSP-PseRAAAC...
  13. pmc The organization of nucleosomes around splice sites
    Wei Chen
    Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
    Nucleic Acids Res 38:2788-98. 2010
    ....
  14. doi Exon skipping event prediction based on histone modifications
    Wei Chen
    Center for Genomics and Computational Biology, School of Sciences, Hebei United University, Tangshan, 063000, China
    Interdiscip Sci 6:241-9. 2014
    ..It is anticipated that our method may become a useful tool for alternative splicing events prediction and the selected optimal features will provide insights into the regulatory mechanisms of epigenetic factors in alternative splicing. ..
  15. doi PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions
    Wei Chen
    Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063009, China, Department of Computer Science, Virginia Tech, Blacksburg, VA 24060, School of Life Science and Technology, Bioinformatics and Computer Aided Drug Discovery, Gordon Life Science Institute, Boston, MA 02478, Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, Department of Computer Science, Vassar College, Poughkeepsie, NY 12604, USA, Excellence in Genomic Medicine Research, Key Laboratory for Neuro Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China and Excellence in Genomic Medicine Research, Center of Excellence in Genomic Medicine Research CEGMR, King Abdulaziz University, Jeddah 21589, Saudi Arabia Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063009, China, Department of Computer Science, Virginia Tech
    Bioinformatics 31:119-20. 2015
    ..Moreover, it is flexible enough to allow the users to calculate PseKNC with user-defined properties. The package can be run on Linux, Mac and Windows systems and also provides a graphical user interface...
  16. doi Prediction of CpG island methylation status by integrating DNA physicochemical properties
    Pengmian Feng
    School of Public Health, Hebei United University, Tangshan, 063000, China Electronic address
    Genomics 104:229-33. 2014
    ..22%. This result indicates that the proposed model is a useful tool for DNA methylation status prediction...
  17. doi Predicting peroxidase subcellular location by hybridizing different descriptors of Chou' pseudo amino acid patterns
    Yong Chun Zuo
    The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot 010021, China Electronic address
    Anal Biochem 458:14-9. 2014
    ..0% in a jackknife test using a PSSM profile of pattern with width=5. We also demonstrate that the present GO annotation is far from complete or deep enough for annotating proteins with a specific function. ..
  18. doi PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition
    Wei Chen
    School of Sciences, and Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China Gordon Life Science Institute, Belmont, MA 02478, USA Electronic address
    Anal Biochem 456:53-60. 2014
    ..It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis...
  19. pmc Predicting the types of J-proteins using clustered amino acids
    Pengmian Feng
    School of Public Health, Hebei United University, Tangshan 063000, China
    Biomed Res Int 2014:935719. 2014
    ..To enhance the value of the practical applications of the proposed model, an online web server was developed and can be freely accessed. ..
  20. doi A similarity distance of diversity measure for discriminating mesophilic and thermophilic proteins
    Yong Chun Zuo
    School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
    Amino Acids 44:573-80. 2013
    ..The prediction model and dataset used in this article can be freely downloaded from http://wlxy.imu.edu.cn/college/biostation/fuwu/KNN-ID/index.htm ...
  21. pmc The pattern of DNA cleavage intensity around indels
    Wei Chen
    1 Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan, China 063000 2 Department of Computer Science, Virginia Tech, Blacksburg VA 24060
    Sci Rep 5:8333. 2015
    ..These results will provide new insight into indel generation mechanisms. ..
  22. pmc iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties
    Wei Chen
    Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan, China
    PLoS ONE 7:e47843. 2012
    ..It is anticipated that iNuc-PhysChem may become a useful high throughput tool for both basic research and drug design...
  23. doi Classification of antimicrobial peptide using diversity measure with quadratic discriminant analysis
    Wei Chen
    Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
    J Microbiol Methods 78:94-6. 2009
    ..In this work, an excellent algorithm of Increment of Diversity with Quadratic Discriminant analysis (IDQD) was proposed to classify antimicrobial peptides with diverse biological activities...