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Chengpeng Bi, PhD

TitleSenior Bioinformatics Scientist
InstitutionChildren's Mercy Kansas City
DepartmentClinical Pharmacology and Toxicology
Address2401 Gillham Rd
Kansas City MO 64108
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    Other Positions
    TitleAssistant Professor
    InstitutionUniversity of Missouri-Kansas City
    DepartmentPediatrics


    Collapse Biography 
    Collapse education and training
    University of California Davis Genome Center, Davis, CAFellowshipClinical Pharmacology
    Pennsylvania State University, State College, PAPhD

    Collapse Bibliography 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Keskus AG, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Bi C, Walter A, Gibson M, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing. Nat Biotechnol. 2025 Apr 04. PMID: 40185952.
      View in: PubMed
    2. Lansdon LA, Yoo B, Keskus A, Pushel I, Bi C, Ahmad T, Bryant A, Walter A, Gibson M, Rindler M, Li W, Habeebu SM, Cooley LD, Herriges J, Repnikova E, Zhang L, August KJ, Flatt TG, Gamis AS, Guest EM, Hays JA, Hetherington M, Lewing K, Pastinen T, Kolmogorov M, Farooqi MS. Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing. medRxiv. 2024 Nov 05. PMID: 39802758.
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    3. Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus A, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Yoo B, Pushel I, Lansdon LA, Bi C, Walter A, Gibson M, Pastinen T, Farooqi MS, Robine N, Miga KH, Carroll A, Kolmogorov M, Paten B, Shafin K. DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies. bioRxiv. 2024 Aug 19. PMID: 39229187.
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    4. Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Mart?nez-Cerde?o V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol. 2024 Oct; 42(10):1606-1614. PMID: 38168995.
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    5. Cheung WA, Johnson AF, Rowell WJ, Farrow E, Hall R, Cohen ASA, Means JC, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Truong TK, Schwendinger-Schreck C, Yoo B, Johnston JJ, Gibson M, Evrony G, Rizzo WB, Thiffault I, Younger ST, Curran T, Wenger AM, Grundberg E, Pastinen T. Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort. Nat Commun. 2023 05 29; 14(1):3090. PMID: 37248219.
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    6. Hosey CM, Halpin K, Shakhnovich V, Bi C, Sweeney B, Yan Y, Leeder JS. Pediatric growth patterns in youth-onset type 2 diabetes mellitus: Implications for physiologically-based pharmacokinetic models. Clin Transl Sci. 2022 04; 15(4):912-922. PMID: 35297172.
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    7. van Groen BD, Bi C, Gaedigk R, Staggs VS, Tibboel D, de Wildt SN, Leeder JS. Alternative Splicing of the SLCO1B1 Gene: An Exploratory Analysis of Isoform Diversity in Pediatric Liver. Clin Transl Sci. 2020 05; 13(3):509-519. PMID: 31917523.
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    8. van Groen BD, van de Steeg E, Mooij MG, van Lipzig MMH, de Koning BAE, Verdijk RM, Wortelboer HM, Gaedigk R, Bi C, Leeder JS, van Schaik RHN, van Rosmalen J, Tibboel D, Vaes WH, de Wildt SN. Proteomics of human liver membrane transporters: a focus on fetuses and newborn infants. Eur J Pharm Sci. 2018 Nov 01; 124:217-227. PMID: 30171984.
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    9. Meier R, Bi C, Gaedigk R, Heruth DP, Ye SQ, Leeder JS, Fridley BL. Ontogeny-related pharmacogene changes in the pediatric liver transcriptome. Pharmacogenet Genomics. 2018 03; 28(3):86-94. PMID: 29360682.
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    10. Li Q Zhang, Leon Van Haandel, Min Xiong, Peixin Huang, Daniel P Heruth, Charlie Bi, Roger Gaedigk, Xun Jiang, Ding-You Li, Gerald Wyckoff, Dmitry N Grigoryev, Li Gao, Linheng Li, Min Wu, J Steven Leeder, Shui Qing Ye. Metabolic and molecular insights into an essential role of nicotinamide phosphoribosyltransferase. Cell death & disease. 2017; (3).
    11. Abdel-Rahman SM, Bi C, Thaete K. Construction of Lambda, Mu, Sigma Values for Determining Mid-Upper Arm Circumference z Scores in U.S. Children Aged 2 Months Through 18 Years. Nutr Clin Pract. 2017 Feb; 32(1):68-76. PMID: 27856693.
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    12. Abdel-Rahman SM, Breitkreutz ML, Bi C, Matzuka BJ, Dalal J, Casey KL, Garg U, Winkle S, Leeder JS, Breedlove J, Rivera B. Design and Testing of an EHR-Integrated, Busulfan Pharmacokinetic Decision Support Tool for the Point-of-Care Clinician. Front Pharmacol. 2016; 7:65. PMID: 27065859.
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    13. Vyhlidal CA, Bi C, Ye SQ, Leeder JS. Dynamics of Cytosine Methylation in the Proximal Promoters of CYP3A4 and CYP3A7 in Pediatric and Prenatal Livers. Drug Metab Dispos. 2016 07; 44(7):1020-6. PMID: 26772622.
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    14. Chengpeng Bi. Methylome-Seq Data Analysis. Big Data Analysis for Bioinformatics and Biomedical Discoveries. 2016.
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    15. Chengpeng Bi. A MAXIMUM FRAMEWORK LIKELIHOOD FOR MULTIPLE SEQUENCE LOCAL ALIGNMENT. Pattern Recognition in Computational Molecular Biology: Techniques and Approaches. 2015.
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    16. Bi C. Memetic algorithms for de novo motif-finding in biomedical sequences. Artif Intell Med. 2012 Sep; 56(1):1-17. PMID: 22613029.
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    17. Chengpeng Bi, J Steve Leeder. Large-scale computation of pediatric growth percentiles with fuzzy logic justification of parameter selection. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2012 IEEE Symposium on. 2012; 43-46.
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    18. Chengpeng Bi, Mara Becker, Steve Leeder. Derivation of minimum best sample size from microarray data sets: A Monte Carlo approach. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2011 IEEE Symposium on. 2011; 1-6.
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    19. Chengpeng Bi. Tackling the challenging motif problem through hybrid particle swarm optimized alignment clustering. 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). 2011; 1-8.
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    20. Chengpeng Bi, Carrie Vyhlidal, Steve Leeder. Supervised learning of maternal cigarette-smoking signatures from placental gene expression data: A case study. 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2010; 1-6.
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    21. Saunders CJ, Friez MJ, Patterson M, Nzabi M, Zhao W, Bi C. 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. Genet Test Mol Biomarkers. 2010 Apr; 14(2):241-7. PMID: 20384458.
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    22. Chengpeng Bi. Deterministic local alignment methods improved by a simple genetic algorithm. Neurocomputing. 2010; 8(1).
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    23. Chengpeng Bi. Comparison of optimization techniques for sequence pattern discovery by maximum-likelihood. Pattern recognition letters. 2010; 31(14).
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    24. Bi C. A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences. IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep; 6(3):370-86. PMID: 19644166.
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    25. Bi C. DNA motif alignment by evolving a population of Markov chains. BMC Bioinformatics. 2009 Jan 30; 10 Suppl 1:S13. PMID: 19208112.
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    26. Chengpeng Bi . A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences. IEEE/ACM Trans Comput Biol Bioinform . 2009; 6(3).
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    27. Chengpeng Bi. Evolutionary Metropolis sampling in sequence alignment space. 2008 IEEE Congress on Evolutionary Computation (IEEE World Congress on Computational Intelligence). 2008; 6(1).
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    28. Bi C. Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study. J Proteome Res. 2008 Jan; 7(1):192-201. PMID: 18081244.
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    29. Bi C, Leeder JS, Vyhlidal CA. A comparative study on computational two-block motif detection: algorithms and applications. Mol Pharm. 2008 Jan-Feb; 5(1):3-16. PMID: 18076137.
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    30. Chengpeng Bi. Multiple sequence local alignment using Monte Carlo EM algorithm. International Symposium on Bioinformatics Research and Applications. 2007; 465-476.
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    31. Bi C. SEAM: a Stochastic EM-type Algorithm for Motif-finding in biopolymer sequences. J Bioinform Comput Biol. 2007 Feb; 5(1):47-77. PMID: 17477491.
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    32. Chengpeng Bi. A genetic-based EM motif-finding algorithm for biological sequence analysis. 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology. 2007; 4(1).
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    33. Bi C, Rogan PK. BIPAD: a web server for modeling bipartite sequence elements. BMC Bioinformatics. 2006 Feb 17; 7:76. PMID: 16503993.
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    34. Bode J, Winkelmann S, G?tze S, Spiker S, Tsutsui K, Bi C, A K P, Benham C. Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy. J Mol Biol. 2006 Apr 28; 358(2):597-613. PMID: 16516920.
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    35. Bi C, Rogan PK. Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Res. 2004; 32(17):4979-91. PMID: 15388800.
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    36. Bi C, Benham CJ. WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA. Bioinformatics. 2004 Jun 12; 20(9):1477-9. PMID: 15130924.
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    37. Benham CJ, Bi C. The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J Comput Biol. 2004; 11(4):519-43. PMID: 15579230.
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    38. Chengpeng Bi, Craig J Benham . The Approximate Algorithm for Analysis of the Strand Separation Transition in Super helical DNA Using Nearest Neighbor Energetics. CSB. 2003; 460-461.
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