Publications

Ghosh, A., Freda, P.J., Shahrestani, S., Orlenko, A., Scheer, J.K., Obafemi-Ajayi, T., Moore, J.H., Walker, C.T. 2026. Leveraging automated machine learning to benchmark, deconstruct, and compare frailty indices for predicting adverse spinal surgery outcomes. Scientific Reports. 16, 1849.

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.

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.

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.

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. 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.

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.

Poulsen, M.N., Freda, P.J., Troiani, V., Mowery, D.L. 2024. Developing a Framework to Infer Opioid Use Disorder Severity From Clinical Notes: Characterization Study. JMIR Mental Health. 11:e53366.

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.

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.

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 Using Natural Language Processing. AMIA Annu. Symp. Proc. 606–615.

Freda, P.J., Kranzler, H.R., Moore, J.H. 2022. Novel digital approaches to the assessment of problematic opioid use. BioData Mining.

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.

Poulsen, M.N., Freda, P.J., Troiani, V., Davoudi, A., Mowery, D.L. 2022. Classifying characteristics of opioid use disorder for hospital discharge summaries using natural language processing. Frontiers in Public Health.

Freda, P.J., Moore, J.H., Kranzler, H.R. 2021. The phenomics and genetics of addictive and affective comorbidity in opioid use disorder. Drug and Alcohol Dependence.

Freda, P.J., Ali, Z.M., Heter, N., Ragland, G.J., Morgan, T.J. 2019. Stage-specific genotype-by-environment interactions for cold and heat hardiness in Drosophila melanogaster. Heredity.

Everman, E.R, Freda, P.J., Brown, M., Schieferecke, A.J., Ragland, G.J., Morgan, T.J. 2018. Ovary development and cold tolerance of the invasive pest Drosophila suzukii (Matsumura) in the central plains. Environmental Entomology.

Freda, P.J., Alex, J.T., Morgan, T.J., 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).

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.

Orlenko, A., Freda, P.J., Ghosh, A., Choi, H., Matsumoto, N., Bright, T.J., Walker, C.T., Obafemi-Ajayi, T., Moore, J.H. 2024. Cluster Analysis reveals Socioeconomic Disparities among Elective Spine Surgery Patients. Pacific Symposium on Biocomputing, Kona, Hawaii.

Freda, P.J., Ali, Z., Heter, N., Morgan, T.J., Ragland, G.J. 2018. Phenotypic and Genetic Decoupling of Thermal Hardiness across Metamorphosis. Poster, 59th Annual Drosophila Research Conference, Philadelphia, PA, April 11-15.

Freda, P.J., Morgan, T.J., Ragland, G.J. 2017. Identifying mechanisms of cold hardiness across metamorphosis in Drosophila melanogaster. Oral presentation, 7th International Symposium of the Environmental Physiology of Ectotherms and Plants (ISEPEP7), Tartu, Estonia, August 1.

Brown, M., Freda, P.J., Everman, E.R., Morgan, T.J., Ragland, G.J. 2016. Phenotypic plasticity promotes persistence of an invasive pest. Poster, Manhattan, KS, April 21.

Freda, P.J., Morgan, T.J., Ragland, G.J. 2016. Decoupling of physiology across metamorphosis. Kansas State University Department of Entomology 3-minute thesis competition, April 6.

Freda, P.J., Morgan, T.J., Ragland, G.J. 2016. Decoupling of physiology across metamorphosis. Oral presentation, Society for Integrative and Comparative Biology (SICB) Conference, Portland, Oregon, January 4.

Freda, P.J., Morgan, T.J., Ragland, G.J. 2015. Decoupling of physiology across metamorphosis. Kansas State University Department of Entomology seminar series, November 30.

Freda, P.J., Morgan, T.J., Ragland, G.J. 2015. Evolution of complex life cycles: Is performance constrained across metamorphosis. Poster, 13th Annual Ecological Genomics Symposium, Manhattan, KS, November 6-8.

Freda, P.J., Morgan, T.J., Ragland, G.J. 2015. Ontogenetic constraint in the thermal physiology of Drosophila melanogaster. Poster, Ecological Genomics Summer Research Forum, Manhattan, KS, June 23.

Freda, P., DiMeglio, M., Braverman, J. 2015. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Poster, Arthropod Genomics Research Symposium, Kansas State University, June 18.

Freda, P., DiMeglio, M., Braverman, J. 2014. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Poster, Ecological Genomics Research Symposium, Kansas City, MO, October 31-November 2.

Freda, P., Braverman, J. 2014. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Saint Joseph's University Department of Biology, August 18.

Freda, P., Braverman, J. 2014. Temporal Variation at Microsatellite Loci in Wild-Caught Drosophila simulans. Sigma Xi Research Symposium Poster, Saint Joseph's University, April 12.

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., [et al.]. 2013. Estimating Phage Genome Sizes by Pulsed-Field Gel Electrophoresis. Fifth Annual SEA-PHAGES Symposium, Janelia Farm Research Campus, Ashburn, VA, June 7-9.

Castro, R., DiMeglio, M., Freda, P., Braverman, J. 2013. Drosophila Biodiversity on the Campus of Saint Joseph's University. Sigma Xi Research Symposium Poster, April 19.

Healy, B.E., Springer, C.J., Freda, P.J., 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 20-24.

Freda, P., Braverman, J. 2012. Drosophila Biodiversity on the Campus of Saint Joseph's University. Sigma Xi Research Symposium Poster, April 13.

Freda, P., Springer, C., Braverman, J. 2011. Computational Study of Flowering Time Genetics with QTL Cartographer. Sigma Xi Research Symposium Poster, Saint Joseph's University, April 8.