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Lewis James Frey

Title
InstitutionMedical University of South Carolina
DepartmentPublic Health Sciences
AddressP.O. Box MSC 200
405K
Cannon Place - 135 Cannon St.
Phone843-792-4216
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    Collapse Overview 
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    Lewis Frey, PhD develops novel algorithms and information systems for the purpose of discovery and data integration applicable to precision medicine. He has extensive experience working with virtual machine deployments in networks and in big data technology deployed within Veterans Affairs (VA). In his research on Clinical Personalized Pragmatic Predictions of Outcomes (C3PO) he brings both of these areas together to create a quickly deployable system for building networks and sample size using the C3PO Big Data System he built for the VA. In addition to applying novel machine learning to medical data, his information systems approach combines the accumulated wealth of knowledge that exists in medical record systems with the vast amounts of molecular data being captured with high-throughput measurement technologies. The following are active areas of his research:

    Investigation of the utility of novel similarity measures to conduct predictive analytics
    ---The goal is to improve outcomes through utilizing similar patients to inform treatment approaches. Dr. Frey is interested in applying this approach to characterization of medical phenotypes of cancers and their interacting gene and protein pathways to improve outcomes.

    Development of a novel machine learning analysis technique
    ---For example, he used multiplicity measures of cancer gene networks to organize information in a clinically meaningful manner by integrating data from thousands of experiments testing for tumor somatic mutations. Using multiplicity measures of somatic mutations to organize cancers, he found that somatic mutations with high multiplicity scores correlated with known causal germline mutations.
    ---Extending techniques related to predicting glycan structure through gene expression data.

    Developing a novel data integration approach using ontological representations to combine data from multiple experiments
    ---The approach has been applied to characterize dendritic cell maturation relevant to cancer immunotherapy.


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    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. Frey LJ. Artificial Intelligence and Integrated Genotype?Phenotype Identification. Genes (Basel). 2018 Dec 28; 10(1). PMID: 30597900.
      View in: PubMed
    2. Frey LJ. Data integration strategies for predictive analytics in precision medicine. Per Med. 2018 11; 15(6):543-551. PMID: 30387695.
      View in: PubMed
    3. Liu G, Zhang J, Frey L, Gang X, Wu K, Liu Q, Lilly M, Wu J. Prostate-specific IL-6 transgene autonomously induce prostate neoplasm through amplifying inflammation in the prostate and peri-prostatic adipose tissue. J Hematol Oncol. 2017 01 11; 10(1):14. PMID: 28077171.
      View in: PubMed
    4. Frey LJ, Bernstam EV, Denny JC. Precision medicine informatics. J Am Med Inform Assoc. 2016 07; 23(4):668-70. PMID: 27274018.
      View in: PubMed
    5. Frey LJ, Sward KA, Newth CJ, Khemani RG, Cryer ME, Thelen JL, Enriquez R, Shaoyu S, Pollack MM, Harrison RE, Meert KL, Berg RA, Wessel DL, Shanley TP, Dalton H, Carcillo J, Jenkins TL, Dean JM. Virtualization of open-source secure web services to support data exchange in a pediatric critical care research network. J Am Med Inform Assoc. 2015 Nov; 22(6):1271-6. PMID: 25796596.
      View in: PubMed
    6. Luo G, Frey LJ. Efficient Execution Methods of Pivoting for Bulk Extraction of Entity-Attribute-Value-Modeled Data. IEEE J Biomed Health Inform. 2016 Mar; 20(2):644-54. PMID: 25608318.
      View in: PubMed
    7. Frey LJ. Informatics tools to advance the biology of glycosaminoglycans and proteoglycans. Methods Mol Biol. 2015; 1229:271-87. PMID: 25325960.
      View in: PubMed
    8. Frey LJ, Lenert L, Lopez-Campos G. EHR Big Data Deep Phenotyping. Contribution of the IMIA Genomic Medicine Working Group. Yearb Med Inform. 2014 Aug 15; 9:206-11. PMID: 25123744.
      View in: PubMed
    9. Guo JW, Sward K, Beck S, Wong B, Staggers N, Frey L. Using a content analysis to identify study eligibility criteria concepts in cancer nursing research. Comput Inform Nurs. 2014 Jul; 32(7):333-42. PMID: 24814997.
      View in: PubMed
    10. Thibault JC, Frey L. Biomedical Terminology Mapper for UML projects. AMIA Jt Summits Transl Sci Proc. 2013; 2013:257-61. PMID: 24303278.
      View in: PubMed
    11. Piccolo SR, Frey LJ. Clinical and molecular models of glioblastoma multiforme survival. Int J Data Min Bioinform. 2013; 7(3):245-65. PMID: 23819258.
      View in: PubMed
    12. Frey LJ, Piccolo SR, Edgerton ME. Multiplicity: an organizing principle for cancers and somatic mutations. BMC Med Genomics. 2011 Jun 29; 4:52. PMID: 21714919.
      View in: PubMed
    13. Cryer ME, Frey L. Agent-based modeling supporting the migration of registry systems to grid based architectures. Summit Transl Bioinform. 2009 Mar 01; 2009:26-30. PMID: 21347166.
      View in: PubMed
    14. Kunz I, Lin MC, Frey L. Metadata mapping and reuse in caBIG. BMC Bioinformatics. 2009 Feb 05; 10 Suppl 2:S4. PMID: 19208192.
      View in: PubMed
    15. Piccolo SR, Frey LJ. Somatic mutation signatures of cancer. AMIA Annu Symp Proc. 2008 Nov 06; 202-6. PMID: 18999255.
      View in: PubMed
    16. Piccolo SR, Camp N, Frey LJ. Polygenic model for predicting breast cancer risk via genome-wide polymorphisms. AMIA Annu Symp Proc. 2008 Nov 06; 1094. PMID: 18999159.
      View in: PubMed
    17. Edgerton ME, Fisher DH, Tang L, Frey LJ, Chen Z. Data mining for gene networks relevant to poor prognosis in lung cancer via backward-chaining rule induction. Cancer Inform. 2007 Feb 10; 3:93-114. PMID: 19455237.
      View in: PubMed
    18. Frey L, Edgerton M, Fisher D, Levy S. Ensemble stump classifiers and gene expression signatures in lung cancer. Stud Health Technol Inform. 2007; 129(Pt 2):1255-9. PMID: 17911916.
      View in: PubMed
    19. Frey L, Edgerton ME, Fisher DH, Tang L, Chen Z. Using prior knowledge and rule induction methods to discover molecular markers of prognosis in lung cancer. AMIA Annu Symp Proc. 2005; 256-60. PMID: 16779041.
      View in: PubMed
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