Chengpeng (Charlie) Bi
Ph.D. 2002 The Pennsylvania State University

Assistant Professor of Pediatrics
Division of Clinical Pharmacology and Toxicology
The Children's Mercy Hospitals and Clinics
Kansas City, MO 64108, USA

Faculty appointments with UMKC:
Assistant Professor of Pediatrics, School of Medicine
Adjunct Professor of Computer Science, School of Computing & Engineering
University of Missouri - Kansas City (UMKC)
Kansas City, Missouri 64108 USA
Web Hyperlink to here

      C Bi

Contact: cbi at cmh dot edu

Link: curriculum vitae (short version | long version)

Servers: BiPad | Bilogo plotter | GEMFA | WebSIDD | PMC | SpliceSite Scanner |

Teaching: Advanced Algorithms in Bioinformatics (graduate course)

Publications:

Listed in: PubMed | DBLP | BioInfoBank | ResearchGate | Google Scholar |

    [Submitted]
  1. Deciphering Sequence Signals by Particle Swarm Optimized Motif Alignment Clustering (Submitted)
  2. Memetic Algorithms for Motif-Finding in Biomedical Sequences (In Revision)

    [2012]

  3. Large-Scale Computation of Pediatric Growth Percentiles with Fuzzy Logic Justification of Parameter Selection. (Accepted, joint work with Steve Leeder)

    [2011]

  4. The Xla (X-linked anemia) mouse: A transient neonatal anemia caused by a Gata1 splicing mutation.
    Blood, 118, 1366-1367 (2011) [ PubMed ]
    ** Joint work with K Miller, M Silvey, D Logsdon, F Balch, N Nsumu, I Sokolovsky, M Gibson, D Heruth, and RA White)
  5. Derivation of minimum best sample size from microarray data Sets: A Monte Carlo approach. Proceedings of The 2011 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB). IEEE Press, Piscataway, NJ, pp. 129-134 (2011). [ IEEE Xplore ]
    ** Joint work with Mara Becker and Steve Leeder.
  6. Tackling the Challenging Motif Problem through Hybrid Particle Swarm Optimized Alignment Clustering. Proceedings of The 2011 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB). IEEE Press, Piscataway, NJ, pp. 84-89 (2011) [ IEEE Xplore ]
    ***Winner of Best Paper Award received from The 2011 IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2011, Paris, France).

    [2010]

  7. Allele drop-out in the MECP2 gene due to G-quadruplex and i-motif sequences when using PCR-based diagnosis for Rett syndrome. Genetic Testing and Molecular Biomarkers, 14 (2), 241-247 (2010). [ PubMed ]
  8. Determinisitc local alignment methods improved by a simple genetic algorithm. Neurocomputing, 73, 2394-2406 (2010). doi:10.1016/j.neucom.2010.01.023
  9. Supervised learning of maternal cigarette-smoking signatures from placental gene expression data: A case study. Proc. 2010 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB), Montreal, Canada, pp. 1-6 (2010). (with Carrie Vyhlidal and Steve Leeder) [ IEEEXplore ]
  10. Comparison of optimization techniques for sequence pattern discovery by maximum-likelihood. Pattern Recognition Letters, 31, 2147-2160 (2010). doi:10.1016/j.patrec.2009.09.005

    [2009]

  11. A Monte Carlo EM algorithm for motif discovery in biomolecular sequences. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6 (3), 370-386 (2009). [ PubMed ]
  12. DNA motif alignment by evolving a population of Markov chains. BMC Bioinformatics, 10, S13 (2009). [ PubMed | PDF ]
  13. Genome-wide screening SNPs with arginine vs tryptophan change associated with allergy. Journal of Allergy and Clinical Immunology, 123, S167 (2009).
    ** Joint work with J Meng and LJ Rosenwasser
  14. DNA motif alignment by evolving a population of Markov chains. Proc. the 7th Asia-Pacific Bioinformatics Conference ,vol 7, pp. 126-137. Tsinghua University Press, Beijing, CHINA (2009) [book chapter]

    [2008]

  15. Data augmentation algorithms for detecting conserved domains in protein sequences: A comparative study. Journal of Proteome Research, 7 (1), 192-201 (2008) [ PubMed ]
  16. A comparative study on structured motif detection: algorithms and applications. Molecular Pharmaceutics, 5 (1), 3-16 (2008) [ PubMed ]
  17. Computational intelligence in multiple sequence alignment. Intl. J. Intelligent Computing and Cybernetics, 1 (1), 8-24 (2008)
  18. Evolutionary Metropolis sampling in sequence alignment space. Proc. 2008 IEEE Congress on Evolutionary Computation (CEC), Hong Kong, CHINA, pp. 189-194 (2008) [ IEEEXplore ]
  19. Neuro-Fuzzy classification of the Rhagoletis pomonella species group using digitized wing structure. Proc. 2008 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB), Idaho, USA, pp. 159-165 (2008) [ IEEEXplore ]

    [2007]

  20. SEAM: A stochastic EM-type algorithm for motif-finding in biopolymer sequences. Journal of Bioinformatics and Computational Biology, 5 (1), 47-77 (2007) [ PubMed ]
  21. Wing pattern-based classification of the Rhagoletis pomonella species complex using genetic neural networks. Intl J. Computer Sci. & Appl., 4 (3), 1-14 (2007) [ PDF ]
  22. A genetic-based EM motif-finding algorithm for biological sequence analysis. Proc. 2007 IEEE Computational Intelligence Symposium on Bioinformatics & Computational Biology (CIBCB), pp. 275-282, Hawaii, USA (2007) [ IEEEXplore ]
    *** Winner of Best Overall Paper Award received from IEEE SSCI'2007.
  23. A survey of in silico motif discovery and computational intelligence applications. Proc. 2007 International Conference on Artificial Intelligence, pp. 147-153. Las Vegas, USA. CSREA Press
  24. Multiple sequence local alignment using Monte Carlo EM algorithm. Lecture Notes in Bioinformatics, vol 4463, pp. 465-476, Springer-Verlag (2007) [ Book Chapter ]

    [2006]

  25. Correlation between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex Destabilization energy. Journal of Molecular Biology, 358 (2), 597-613 (2006) [ PubMed ]
  26. BIPAD: A web server for modeling bipartite sequence elements. BMC Bioinformaitcs, 7:76 (2006) [ PubMed | PDF ]
  27. Computational model of the antioxidant response element. ISSX-2006 (abstract)
  28. A Monte Carlo EM algorithm for motif discovery problem. Proc. 2005 ISMB Bioinformatics Rocky Conference, Snowmass/Aspen, CO, USA (abstract)

    [2005]

  29. Information theory as a model of genomic sequences. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, vol 7, pp. 2868-2880, John Wiley & Sons Ltd. (2005) [ Book Chapter ]
  30. Determining thresholds for binding site sequence models using information theory. Proc. 6th International Symposium on Computational Biology and Genome Informatics, pp. 1285-1290. Utah, USA (2005)

    [2004]

  31. The analysis of stress-induced duplex destabilization in long genomic DNA sequences. Journal of Computational Biology, 11 (4), 519-543 (2004) [ PubMed | PDF ]
  32. Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Research, 32 (17), 4979-4991 (2004) [ PubMed | PDF ]
  33. WebSIDD: Server for prediction of the stress-induced duplex destabilized (SIDD) sites in superhelical DNA. Bioinformatics, 20 (9), 1477-1479 (2004) [ PubMed | PDF ]
  34. A minimization entropy-based bipartite algorithm with application to PXR/RXRa binding sites. Proc. 8th Ann. Conference on Research in Computational Molecular Biology (RECOMB) , San Diego, California USA, pp. 453-454 (2004)

    [2003]

  35. The approximate algorithm for analysis of the strand separation transition in superhelical DNA using nearest neighbor energetics. Proc. IEEE Computer Society for Bioinformatics, pp. 460-461. Stanford University, California USA. IEEE Publisher. (2003) [ IEEEXplore ]

    [2002]

  36. Pattern Classification of the Rhagoletis pomonella Species Complex.
    Ph.D. Dissertation: Graduate School of The Pennsylvania State University, University Park, PA, USA.
Last modified: August 9, 2010