Peer-Reviewed Articles & Reviews
Ghosh, A., Freda, P.J., Shahrestani, S., Boyke, A.E., Orlenko, A., Choi, H., Matsumoto, N., Obafemi-Ajayi, T., Moore, J.H., Walker, C.T. 2025. Preoperative anemia is an unsuspecting driver of machine learning prediction of adverse outcomes after lumbar spinal fusion. The Spine Journal. 25, 8. 1596-1607. https://doi.org/10.1016/j.spinee.2025.01.031
Sha, Z., Freda, P.J., Bhandary, P., Ghosh, A., Matsumoto, N., Moore, J.H., Hu, T. 2024. Distinct network patterns emerge from Cartesian and XOR epistasis models: a comparative network science analysis. BioData Mining. 17, 61. https://doi.org/10.1186/s13040-024-00413-w
Freda, P.J., Ghosh, A., Bhandary, P., Matsumoto, N., Chitre, A.S., Zhou, J., Hall, M.A., Palmer, A.A., Obafemi-Ajayi, T., Moore, J.H. 2024. PAGER: A novel genotype encoding strategy for modeling deviations from additivity in complex trait association studies. BioData Mining. 17, 41. https://doi.org/10.1186/s13040-024-00393-x
Li, C. Mowery, D.L., Ma, X., Yang, R., Vurgun, U., Hwang, S., Donnelly, H.K., Bandhey, H., Senathirajah, Y., Visweswaran, S., Sadhu, E.M., Akhtar, Z., Getzen, E., Freda, P.J., Long, Q., Becich, M.J. 2024. Realizing the potential of social determinants data in EHR systems: A scoping review of approaches for screening, linkage, extraction, analysis, and interventions. Journal of Clinical and Translational Science. 8, 1. e147
Freda, P.J., Ye, S., Zhang, R., Moore, J.H., Urbanowicz, R.J. 2024. Assessing the limitations of relief-based algorithms in detecting higher-order interactions. BioData Mining. 17, 37. https://doi.org/10.1186/s13040-024-00390-0
Batista, S., Madar, V., Freda, P.J., Bhandary, P., Ghosh, A., Matsumoto, N., Chitre, A.S., Palmer, A.A., Moore, J.H. 2024. Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis. BioData Mining. 17, 7. https://doi.org/10.1186/s13040-024-00358-0
Poulsen, M.N., Freda, P.J., Troiani, V., Mowery, D.L. 2024. Developing a Framework to Infer Opioid Use Disorder Severity From Clinical Notes to Inform Natural Language Processing Methods: Characterization Study. JMIR Mental Health. 11:e53366. doi:10.2196/53366
Orlenko, A., Freda, P.J., Ghosh, A., Choi, H., Matsumoto, N., Bright, T.J., Walker, C.T., Obafemi-Ajayi, T., Moore, J.H. 2023. Cluster Analysis reveals Socioeconomic Disparities among Elective Spine Surgery Patients. Biocomputing 2024. pp. 359-373. https://doi.org/10.1142/9789811286421_0028
Freda, P.J., Ghosh, A., Zhang, E., Luo, T., Chitre, A.S., Polesskaya, O., St. Pierre, C.L., Gao, J., Martin, C.D., Chen, H., Garcia-Martinez, A.G., Wang, T., Han, W., Ishiwari, K., Meyer, P., Lamparelli, A., King. C.P., Palmer, A.A., Li, R., Moore, J.H. 2023. Automated quantitative trait locus analysis (AutoQTL). BioData Mining. https://doi.org/10.1101/2023.01.12.523835
Kennedy, E.E., Davoudi, A., Hwang, S., Freda, P.J., Urbanowicz, R., Bowles, K.H., Mowery, D.L. 2022. Identifying Barriers to Post-Acute Care Referral and Characterizing Negative Patient Preferences Among Hospitalized Older Adults Using Natural Language Processing. AMIA Annu. Symp. Proc. 606–615. PMC10148308. PMID: 37128417.
Freda, P.J., Kranzler, H.R., and Moore, J.H. 2022. Novel digital approaches to the assessment of problematic opioid use. BioData Mining. https://doi.org/10.1186/s13040-022-00301-1
Freda, P.J., Toxopeus, J., Dowle, E.J., Ali, Z.A., Heter, N., Collier, R.L., Sower, I., Tucker, J.C., Morgan, T.J., Ragland, G.J. 2022. Transcriptomic and functional genetic evidence for distinct ecophysiological responses across complex life cycle stages. Journal of Experimental Biology. https://doi.org/10.1242/jeb.244063.
Poulsen, M.N., Freda, P.J., Troiani, V., Davoudi, A., and Mowery, D.L. 2022. Classifying characteristics of opioid use disorder for hospital discharge summaries using natural language processing. Frontiers in Public Health, https://www.frontiersin.org/articles/10.3389/fpubh.2022.850619/full
Freda, P.J., Moore, J.H., and Kranzler, H.R. 2021. The phenomics and genetics of addictive and affective comorbidity in opioid use disorder. Drug and Alcohol Dependence, https://doi.org/10.1016/j.drugalcdep.2021.108602.
Freda, P.J., Ali, Z.M., Heter, N., Ragland, G.J., and Morgan, T.J. 2019. Stage-specific genotype-by-environment interactions for cold and heat hardiness in Drosophila melanogaster. Heredity, https://doi.org/10.1038/s41437-019-0236-9.
Everman, E.R, Freda, P.J., Brown, M., Schieferecke, A.J., Ragland, G.J., and Morgan, T.J. 2018. Ovary development and cold tolerance of the invasive pest Drosophila suzukii (Matsumura) in the central plains. Environmental Entomology, doi: 10.1093/ee/nvy074.
Freda, P.J., Alex, J.T., Morgan, T.J., and Ragland, G.J. 2017. Genetic Decoupling of Thermal Hardiness across Metamorphosis in Drosophila melanogaster. Integrative and Comparative Biology, 57(5), 999-1009.
Leung, W., Shaffer, C.D., Reed, L.K., […], Freda, P.J., […], Elgin, S.C.R. 2015. Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution. G3-Genes Genomes Genetics, 5(5), doi:10.1534/g3.114.015966.
Freda, P.J., Braverman, J. 2013. Drosophila suzukii, or Spotted Wing Drosophila, Recorded in Southeastern Pennsylvania, U.S.A. Entomological News, 123(1), 71-75.
Freda, P.J., Braverman, J. 2013. An Efficient, Practical, and Reliable Drosophila Trap. Drosophila Information Service, 96, 199-201.
Abstracts & Presentations
Orlenko, A., Freda, P.J., Ghosh, A., Choi, H., Matsumoto, N., Bright, T.J., Walker, C.T., Obafemi-Ajayi, T., Moore, J.H. 2023. Cluster Analysis reveals Socioeconomic Disparities among Elective Spine Surgery Patients. Kona, Hawaii, 2024.
Freda, P.J., Ali, Z., Heter, N., Morgan, T.J., and Ragland, G.J. 2018. Phenotypic and Genetic Decoupling of Thermal Hardiness across Metamorphosis. 59th Annual Drosophila Research Conference, Philadelphia, PA, April 11th-15th, 2018.
Freda, P.J., Morgan, T.J., and Ragland, G.J. 2017. Identifying mechanisms of cold hardiness across metamorphosis in Drosophila melanogaster. 7th International Symposium of the Environmental Physiology of Ectotherms and Plants (ISEPEP7), Tartu, Estonia, August 1st, 2017.
Brown, M., Freda, P.J., Everman, E.R., Morgan, T.J., and Ragland, G.J. 2016. Phenotypic plasticity promotes persistence of an invasive pest following environmental stress. Poster presented at undergraduate research forum by Brown, M. Manhattan, KS, April 21, 2016.
Freda, P.J., Morgan, T.J., and Ragland, G.J. 2016. Decoupling of physiology across metamorphosis. Kansas State University, Department of Entomology 3-minute thesis competition, April 6th, 2016.
Freda, P.J., Morgan, T.J., and Ragland, G.J. 2016. Decoupling of physiology across metamorphosis. Society for Integrative and Comparative Biology (SICB) Conference, Portland, Oregon, January 4th, 2016.
Freda, P.J., Morgan, T.J., and Ragland, G.J. 2015. Decoupling of physiology across metamorphosis. Kansas State University, Department of Entomology seminar series, November 30th, 2015.
Freda, P.J., Morgan, T.J., and Ragland, G.J. 2015. Evolution of complex life cycles: Is performance constrained across metamorphosis. 13th Annual Ecological Genomics Symposium. Poster Presentation, Manhattan, KS. November 6-8, 2015.
Freda, P.J., Morgan, T.J., and Ragland, G.J. 2015. Ontogenetic constraint in the thermal physiology of Drosophila melanogaster: A genomic assessment of the adaptive decoupling hypothesis. Ecological Genomics Summer Research Forum, Manhattan, KS, June 23rd, 2015.
Freda, P., DiMeglio, M., and Braverman, J. 2015. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Poster Presentation, Arthropod Genomics Research Symposium, Kansas State University, June 18th, 2015.
Freda, P., DiMeglio, M., and Braverman, J. 2014. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Poster Presentation, Ecological Genomics Research Symposium, Kansas City, MO, October 31st – November 2nd, 2014.
Freda, P. and Braverman, J. 2014. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Thesis defense presentation. Saint Joseph’s University, Department of Biology seminar series, Philadelphia, PA, August 18th, 2014.
Freda, P. and Braverman, J. 2014. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Sigma Xi Research Symposium Poster, Saint Joseph’s University, April 12th, 2014.
Meghan M. M., London, S. C., Angelucci, V. C., Burke, S. M., Del Buono, M., Dell’Arciprete, A. M., Eastman, J. M., Freda, P. J., Giacobbo, A. J., Harrison, J. N., Leconey, B. A., Martino, V. L., Mengel, T. A., Patel, C. V., Puetz, W. J., Robinson, L. M., Senss, A. M., Southwell, M. J., Thelmo, F. L., Turro, K. N., Vilbert, A. C., Weiss, W., King-Smith, C., Braverman, J. and Lee-Soety, J. Y. Estimating Phage Genome Sizes by Pulsed-Field Gel Electrophoresis for Preliminary Cluster Identification. Poster presentation. Fifth Annual SEA-PHAGES Symposium. Janelia Farm Research Campus, Ashburn, VA. June 7-9, 2013.
Castro, R., DiMeglio, M., Freda, P. and Braverman, J. 2013. Drosophila Biodiversity on the Campus of Saint Joseph’s University. Sigma Xi Research Symposium Poster, Saint Joseph’s University, April 19th, 2013.
Healy, B.E., Springer, C.J., Freda, P.J., and Braverman, J.M. 2012. Genomic regions responsible for altered reproductive characteristics of Arabidopsis thaliana grown at elevated [CO2]. ASPB Plant Biology Meeting, Austin, Texas, July 20th – 24th, 2012.
Freda, P. and Braverman, J. 2012. Drosophila Biodiversity on the Campus of Saint Joseph’s University. Sigma Xi Research Symposium Poster, Saint Joseph’s University, April 13th, 2012.
Freda, P., Springer, C. and Braverman, J. 2011. Computational Study of Flowering Time Genetics with QTL Cartographer. Sigma Xi Research Symposium Poster, Saint Joseph’s University, April 8th, 2011.
Philip J. Freda, Jr., Ph.D. 