Yi Pan

Summary

Affiliation: Georgia State University
Country: USA

Publications

  1. pmc Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering
    Xuan Guo
    Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, USA
    BMC Bioinformatics 15:102. 2014
  2. ncbi request reprint Using hybrid hierarchical K-means (HHK) clustering algorithm for protein sequence motif super-rule-tree (SRT) structure construction
    Bernard Chen
    Department of Computer Science, University of Central Arkansas, 201 Donaghey Avenue, Conway, AR 72035, USA
    Int J Data Min Bioinform 4:316-30. 2010
  3. ncbi request reprint Understandable learning machine system design for transmembrane or embedded membrane segments prediction
    Hae Jin Hu
    Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
    Int J Data Min Bioinform 5:38-51. 2011
  4. ncbi request reprint Prediction of the disulphide bridges in proteins using SVM
    Aiguo Du
    Department of Computer Science, Georgia State University, 30303 Atlanta, GA, USA
    Int J Bioinform Res Appl 3:223-33. 2007
  5. doi request reprint Novel efficient granular computing models for protein sequence motifs and structure information discovery
    Bernard Chen
    Department of Computer Science, University of Central Arkansas, 201 Donaghey Ave MCST304, Conway, AR 72035, USA
    Int J Comput Biol Drug Des 2:168-86. 2009
  6. pmc DIME: a novel framework for de novo metagenomic sequence assembly
    Xuan Guo
    1 Departments of Computer Science and Biology, Georgia State University, Atlanta, Georgia
    J Comput Biol 22:159-77. 2015
  7. ncbi request reprint To be or not to be: predicting soluble SecAs as membrane proteins
    Hae Jin Hu
    Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
    IEEE Trans Nanobioscience 6:168-79. 2007
  8. pmc Nonclassical protein secretion by Bacillus subtilis in the stationary phase is not due to cell lysis
    Chun Kai Yang
    Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
    J Bacteriol 193:5607-15. 2011
  9. doi request reprint EPGA: de novo assembly using the distributions of reads and insert size
    Junwei Luo
    School of Information Science and Engineering, Central South University, Changsha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA School of Information Science and Engineering, Central South University, Changsha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA
    Bioinformatics 31:825-33. 2015
  10. ncbi request reprint Multiple sequence alignment based on dynamic weighted guidance tree
    Ken D Nguyen
    Department of Computer Science, Georgia State University, Atlanta, GA 30303 3994, USA
    Int J Bioinform Res Appl 7:168-82. 2011

Detail Information

Publications17

  1. pmc Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering
    Xuan Guo
    Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, USA
    BMC Bioinformatics 15:102. 2014
    ..In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger...
  2. ncbi request reprint Using hybrid hierarchical K-means (HHK) clustering algorithm for protein sequence motif super-rule-tree (SRT) structure construction
    Bernard Chen
    Department of Computer Science, University of Central Arkansas, 201 Donaghey Avenue, Conway, AR 72035, USA
    Int J Data Min Bioinform 4:316-30. 2010
    ..By analysing the motif results generated by our approach, they are significant not only in sequence area but also in secondary structure similarity...
  3. ncbi request reprint Understandable learning machine system design for transmembrane or embedded membrane segments prediction
    Hae Jin Hu
    Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
    Int J Data Min Bioinform 5:38-51. 2011
    ..The prediction server is available at http://bmcc2.cs.gsu.edu/ haeh2/...
  4. ncbi request reprint Prediction of the disulphide bridges in proteins using SVM
    Aiguo Du
    Department of Computer Science, Georgia State University, 30303 Atlanta, GA, USA
    Int J Bioinform Res Appl 3:223-33. 2007
    ..The physical-chemical characteristics of the flanking sequences and the linear distance between the concerned cysteine pairs were also included in the encoding. An overall pair wise accuracy of 92% was obtained for the SP39 dataset...
  5. doi request reprint Novel efficient granular computing models for protein sequence motifs and structure information discovery
    Bernard Chen
    Department of Computer Science, University of Central Arkansas, 201 Donaghey Ave MCST304, Conway, AR 72035, USA
    Int J Comput Biol Drug Des 2:168-86. 2009
    ..We have performed a comprehensive comparison between the two models. In addition, we further combine the results from the FIK and FGK models to generate our best sequence motif information...
  6. pmc DIME: a novel framework for de novo metagenomic sequence assembly
    Xuan Guo
    1 Departments of Computer Science and Biology, Georgia State University, Atlanta, Georgia
    J Comput Biol 22:159-77. 2015
    ..Results indicate that DIME offers great improvement in assembly across a range of sequence abundances and thus is robust to decreasing coverage. ..
  7. ncbi request reprint To be or not to be: predicting soluble SecAs as membrane proteins
    Hae Jin Hu
    Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA
    IEEE Trans Nanobioscience 6:168-79. 2007
    ....
  8. pmc Nonclassical protein secretion by Bacillus subtilis in the stationary phase is not due to cell lysis
    Chun Kai Yang
    Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
    J Bacteriol 193:5607-15. 2011
    ..subtilis is a general phenomenon and is not a consequence of cell lysis or membrane shedding; instead, their secretion is through a process(es) in which protein domain structure plays a contributing factor...
  9. doi request reprint EPGA: de novo assembly using the distributions of reads and insert size
    Junwei Luo
    School of Information Science and Engineering, Central South University, Changsha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA School of Information Science and Engineering, Central South University, Changsha 410083, China, College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, 454000, China, Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan S7N 5A9, Canada and Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA
    Bioinformatics 31:825-33. 2015
    ..All the aforementioned problems prohibit existing assemblers from getting satisfactory assembly results...
  10. ncbi request reprint Multiple sequence alignment based on dynamic weighted guidance tree
    Ken D Nguyen
    Department of Computer Science, Georgia State University, Atlanta, GA 30303 3994, USA
    Int J Bioinform Res Appl 7:168-82. 2011
    ..1994), DIALIGN (Morgenstern, 1999), T-COFFEE (Notredame et al., 2000), MUSCLE (Edgar, 2004), and PROBCONS (Do et al., 2005) of the multiple sequence alignment...
  11. ncbi request reprint 3D Reconstruction Using Image Contour Data Structure
    Yong Li
    Department of Computer Science, Georgia State University, P O Box 3994, Atlanta, GA 30302 3994, USA E mail
    Conf Proc IEEE Eng Med Biol Soc 3:3292-5. 2005
    ..This data structure allows fast 3D object retrieval and 3D component analysis...
  12. ncbi request reprint High performance bio-image database retrieval using MPI
    Yong Li
    Department of Computer Science, Georgia State University, P O Box 3994, Atlanta, GA 30302 3994, USA
    Int J Bioinform Res Appl 4:49-63. 2008
    ..The method has been implemented in MPI on a SGI Origin 2000 machine. The experimental results show a good speedup for sequential object matching and partial 3D component retrieval...
  13. doi request reprint Intussusception after rotavirus vaccines reported to US VAERS, 2006-2012
    Penina Haber
    National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, USA
    Pediatrics 131:1042-9. 2013
    ..In 2006 and 2008, 2 new rotavirus vaccines (RotaTeq [RV5] and Rotarix [RV1]) were introduced in the United States...
  14. pmc Biological network motif detection and evaluation
    Wooyoung Kim
    Department of Computer Science, Georgia State University, Atlanta, GA, USA
    BMC Syst Biol 5:S5. 2011
    ..Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important...
  15. doi request reprint A new permutation-based method for assessing agreement between two observers making replicated quantitative readings
    Yi Pan
    Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
    Stat Med 31:2249-61. 2012
    ....
  16. doi request reprint Assessing non-inferiority to an aggregate response with an application to development of pneumococcal conjugate vaccines
    Yi Pan
    Emory University, Atlanta, GA 30322, USA
    Pharm Stat 10:332-40. 2011
    ..The non-inferiority test p-value and confidence interval are obtained from Miettinen and Nurminen's method, using an effective sample size. The methods are evaluated using simulations and demonstrated with a real clinical trial example...
  17. ncbi request reprint Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property
    Wei Zhong
    Computer Science Department, Georgia State University, Atlanta, GA 30303 4110, USA
    IEEE Trans Nanobioscience 4:255-65. 2005
    ..The satisfactory result of the experiment suggests that this new K-means algorithm may be applied to other areas of bioinformatics research in order to explore the underlying relationships between data samples more effectively...