Chengpeng Bi

Summary

Publications

  1. doi request reprint Memetic algorithms for de novo motif-finding in biomedical sequences
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Lab, Division of Clinical Pharmacology, Children s Mercy Hospitals and Clinics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA
    Artif Intell Med 56:1-17. 2012
  2. doi request reprint A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Laboratory, Division of Clinical Pharmacology, Children s Mercy Hospitals and Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA
    IEEE/ACM Trans Comput Biol Bioinform 6:370-86. 2009
  3. pmc BIPAD: a web server for modeling bipartite sequence elements
    Chengpeng Bi
    Laboratory of Human Molecular Genetics, Children s Mercy Hospital and Clinics, Kansas City, MO 64108, USA
    BMC Bioinformatics 7:76. 2006
  4. ncbi request reprint SEAM: a Stochastic EM-type Algorithm for Motif-finding in biopolymer sequences
    Chengpeng Bi
    Children s Mercy Hospitals and Clinics, 2401 Gillham Road, Pediatrics Research Building, Third Floor, Kansas City, Missouri 64108, USA
    J Bioinform Comput Biol 5:47-77. 2007
  5. ncbi request reprint Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Lab, Children s Mercy Hospitals and Clinics Schools of Medicine, Computing and Engineering University of Missouri, Kansas City, Missouri 64108, USA
    J Proteome Res 7:192-201. 2008
  6. pmc DNA motif alignment by evolving a population of Markov chains
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Lab, Division of Clinical Pharmacology, Children s Mercy Hospitals, Kansas City, Missouri, USA
    BMC Bioinformatics 10:S13. 2009
  7. ncbi request reprint A comparative study on computational two-block motif detection: algorithms and applications
    Chengpeng Bi
    Bioinformatics and Intelligent Computing, Division of Clinical Pharmacology and Toxicology, Children s Mercy Hospitals and Clinics, 2401 Gillham Road, Kansas City, Missouri 64108, USA
    Mol Pharm 5:3-16. 2008
  8. doi request reprint Allele drop-out in the MECP2 gene due to G-quadruplex and i-motif sequences when using polymerase chain reaction-based diagnosis for Rett syndrome
    Carol J Saunders
    Department of Pathology and Laboratory Medicine, The Children s Mercy Hospitals and Clinics, Kansas City, Missouri 64108, USA
    Genet Test Mol Biomarkers 14:241-7. 2010
  9. pmc Bipartite pattern discovery by entropy minimization-based multiple local alignment
    Chengpeng Bi
    Laboratory of Human Molecular Genetics, Children s Mercy Hospital and Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA
    Nucleic Acids Res 32:4979-91. 2004

Collaborators

Detail Information

Publications9

  1. doi request reprint Memetic algorithms for de novo motif-finding in biomedical sequences
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Lab, Division of Clinical Pharmacology, Children s Mercy Hospitals and Clinics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA
    Artif Intell Med 56:1-17. 2012
    ..The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences...
  2. doi request reprint A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Laboratory, Division of Clinical Pharmacology, Children s Mercy Hospitals and Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA
    IEEE/ACM Trans Comput Biol Bioinform 6:370-86. 2009
    ..Finally, MCEMDA is applied to detect large blocks of conserved domains using protein benchmarks and exhibits its excellent capacity while compared with other multiple sequence alignment methods...
  3. pmc BIPAD: a web server for modeling bipartite sequence elements
    Chengpeng Bi
    Laboratory of Human Molecular Genetics, Children s Mercy Hospital and Clinics, Kansas City, MO 64108, USA
    BMC Bioinformatics 7:76. 2006
    ..Many dimeric protein complexes bind cooperatively to families of bipartite nucleic acid sequence elements, which consist of pairs of conserved half-site sequences separated by intervening distances that vary among individual sites...
  4. ncbi request reprint SEAM: a Stochastic EM-type Algorithm for Motif-finding in biopolymer sequences
    Chengpeng Bi
    Children s Mercy Hospitals and Clinics, 2401 Gillham Road, Pediatrics Research Building, Third Floor, Kansas City, Missouri 64108, USA
    J Bioinform Comput Biol 5:47-77. 2007
    ..The convergence of the new algorithm is shown by simulation. The in silico experiments using simulated and biological examples illustrate the power and robustness of the new algorithm SEAM in de novo motif discovery...
  5. ncbi request reprint Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Lab, Children s Mercy Hospitals and Clinics Schools of Medicine, Computing and Engineering University of Missouri, Kansas City, Missouri 64108, USA
    J Proteome Res 7:192-201. 2008
    ..As a result, four DA motif discovery algorithms are described, evaluated, and compared by aligning real and simulated protein sequences...
  6. pmc DNA motif alignment by evolving a population of Markov chains
    Chengpeng Bi
    Bioinformatics and Intelligent Computing Lab, Division of Clinical Pharmacology, Children s Mercy Hospitals, Kansas City, Missouri, USA
    BMC Bioinformatics 10:S13. 2009
    ..Hence it would be worth a new algorithm design enabling such information exchange...
  7. ncbi request reprint A comparative study on computational two-block motif detection: algorithms and applications
    Chengpeng Bi
    Bioinformatics and Intelligent Computing, Division of Clinical Pharmacology and Toxicology, Children s Mercy Hospitals and Clinics, 2401 Gillham Road, Kansas City, Missouri 64108, USA
    Mol Pharm 5:3-16. 2008
    ..We demonstrate how to use this suite of methods and apply them to human nuclear receptor response elements (i.e., protein binding sites of several relevant nuclear receptors, HNF4alpha, CAR/RXR, and PXR/RXR)...
  8. doi request reprint Allele drop-out in the MECP2 gene due to G-quadruplex and i-motif sequences when using polymerase chain reaction-based diagnosis for Rett syndrome
    Carol J Saunders
    Department of Pathology and Laboratory Medicine, The Children s Mercy Hospitals and Clinics, Kansas City, Missouri 64108, USA
    Genet Test Mol Biomarkers 14:241-7. 2010
    ..We identify factors in both the polymerase chain reaction amplification and the sequencing steps that help overcome ADO...
  9. pmc Bipartite pattern discovery by entropy minimization-based multiple local alignment
    Chengpeng Bi
    Laboratory of Human Molecular Genetics, Children s Mercy Hospital and Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA
    Nucleic Acids Res 32:4979-91. 2004
    ..Finally, a new bipartite information weight matrix for vitamin D3 receptor/retinoid X receptor alpha (VDR/RXRalpha) binding sites was derived that comprehensively models the natural variability inherent in these sequence elements...