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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    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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Obeid JS, Dahne J, Christensen S, Howard S, Crawford T, Frey LJ, Stecker T, Bunnell BE. Identifying and Predicting Intentional Self-Harm in Electronic Health Record Clinical Notes: Deep Learning Approach. JMIR Med Inform. 2020 Jul 30; 8(7):e17784. PMID: 32729840.
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    2. Frey LJ, Talbert DA. Artificial Intelligence Pipeline to Bridge the Gap between Bench Researchers and Clinical Researchers in Precision Medicine. Med One. 2020 Jan 10; 5. PMID: 33511289.
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    3. Obeid JS, Weeda ER, Matuskowitz AJ, Gagnon K, Crawford T, Carr CM, Frey LJ. Automated detection of altered mental status in emergency department clinical notes: a deep learning approach. BMC Med Inform Decis Mak. 2019 08 19; 19(1):164. PMID: 31426779.
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    4. Frey LJ. Artificial Intelligence and Integrated Genotype?Phenotype Identification. Genes (Basel). 2018 Dec 28; 10(1). PMID: 30597900.
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    5. Frey LJ. Data integration strategies for predictive analytics in precision medicine. Per Med. 2018 11; 15(6):543-551. PMID: 30387695.
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    6. 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.
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    7. Frey LJ, Bernstam EV, Denny JC. Precision medicine informatics. J Am Med Inform Assoc. 2016 07; 23(4):668-70. PMID: 27274018.
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    8. 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.
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    9. 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.
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    10. Frey LJ. Informatics tools to advance the biology of glycosaminoglycans and proteoglycans. Methods Mol Biol. 2015; 1229:271-87. PMID: 25325960.
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    11. 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.
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    12. 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.
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    13. Thibault JC, Frey L. Biomedical Terminology Mapper for UML projects. AMIA Jt Summits Transl Sci Proc. 2013; 2013:257-61. PMID: 24303278.
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    14. Piccolo SR, Frey LJ. Clinical and molecular models of glioblastoma multiforme survival. Int J Data Min Bioinform. 2013; 7(3):245-65. PMID: 23819258.
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    15. 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.
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    16. 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.
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    17. Kunz I, Lin MC, Frey L. Metadata mapping and reuse in caBIG. BMC Bioinformatics. 2009 Feb 05; 10 Suppl 2:S4. PMID: 19208192.
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    18. Piccolo SR, Frey LJ. Somatic mutation signatures of cancer. AMIA Annu Symp Proc. 2008 Nov 06; 202-6. PMID: 18999255.
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    19. 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.
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    20. 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.
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    21. 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.
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    22. 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.
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