Peer reviewed publications

Trainor, P.J.*, DeFilippis, A.P.*, Thanassoulis, G., Brumback, L., Post, W., & Tsimikas, S. (2021). Accessing the Role of Atherothrombotic Factors in Atherosclerotic Cardiovascular Events–the Multi-Ethnic Study of Atherosclerosis. European Heart Journal, In Press.

Munasinghe-Arachchige, S.P., Sparks, K.M., Ahmed, A., Delanka-Pedige, H.M., Abeysiriwardana-Arachchige, I.S., Schaub, T., Trainor, P.J., & Nirmalakhandan, N. (2021). Algal-based wastewater treatment: Evaluation of nitrogenous byproducts in chlorinated effluent. Algal Research, 59(102443). doi: 10.1016/j.algal.2021.102443

Kulkarni, K. Pandey, A., Trainor, P.J., Carlisle, S.M., Chhillar, J.S., Yu, W., Moon, A. & Xu, J. (2021). Trained immunity in Anopheles gambiae: anti-bacterial immunity is enhanced by priming via sugar meal supplemented with a single bacterial strain. Frontiers in Microbiology, 12(649213). doi: 10.3389/fmicb.2021.649213

Ondo, A.L., Kerner, J.D., Kerner, J.V., Ondo, I.P., Trainor, P.J., Mings, S.M., & Shanler, S.D. (2021). Treatment of cutaneous Squamous Cell Carcinoma in situ with curettage followed by topical imiquimod 5% cream. Dermatologic Surgery, 47 (5). doi: 10.1097/DSS.0000000000002945

Singh, A.  Coulter, A.R., Trainor, P.J., Singam, N.S.V.,  Aladili, B.N., Amraotkar, A.R., Owolabi, U.S.,  & DeFilippis, A.P. (2021). Flow cytometric evaluation of platelet–leukocyte conjugate stability over time: methodological implications of sample handling and processing. Journal of Thrombosis and Thrombolysis, 51(1). doi: 10.1007/s11239-020-02186-5

Galbraith, N.J., Gardner, S.A, Walker, S.P., Trainor, P.J., Carter, J.V., Bishop, C., Sarojini, H., O’Brien, S.J., Bhatnagar, A., Polk, H.C., & Galandiuk, S. (2020). The role and function of IκKα/β in monocyte impairment. Scientific Reports, 10(12222). doi: 10.1038/s41598-020-68018-x

Carlisle, S.M., Trainor, P.J., Hong, K.U., Doll, M.A., & Hein, D.W. (2020). CRISPR/Cas9 knockout of human arylamine N-acetyltransferase 1 in MDA-MB-231 breast cancer cells suggests a role in cellular metabolism. Scientific Reports, 10(9804). doi: 10.1038/s41598-020-66863-4

Owolabi, U.S., Amraotkar, A.R., Coulter, A.R., Singam, N.S., Aladili, B.N., Singh, A., Trainor, P.J., Mitra, R., DeFilippis, A.P. (2020). Change in Matrix Metalloproteinase 2, 3, and 9 Levels at the Time of and After Acute Atherothrombotic Myocardial Infarction. Journal of Thrombosis and Thrombolysis, 49. doi: 10.1007/s11239-019-02004-7

Trainor, P.J., Yampolskiy, R.V., & DeFilippis, A.P. (2018). Wisdom of artificial crowds feature selection in untargeted metabolomics: An application to the development of a blood-based diagnostic test for thrombotic myocardial infarction. Journal of Biomedical Informatics, 81. doi: 10.1016/j.jbi.2018.03.007

Weirick, T., Trainor, P.J., Rouchka, E.C., DeFilippis, A.P., & Uchida, S. (2018). DRETools: A tool-suite for differential RNA editing detection. F1000 Research, 7(1366). doi: 10.12688/f1000research.16026.1

Carlisle, S.M., Trainor, P.J., Doll, M.A., Stepp, M.W., Klinge, C.M., & Hein, D.W. (2018). Knockout of human arylamine N-acetyltransferase 1 (NAT1) in MDA-MB-231 breast cancer cells leads to increased reserve capacity, maximum mitochondrial capacity, and glycolytic reserve capacity. Molecular Carcinogenesis, 57(11). doi: 10.1002/mc.22869

DeFilippis, A.P., Trainor, P.J. (2018). When given a lemon, make lemonade: Revising cardiovascular risk prediction scores. Annals of Internal Medicine, 169(1). doi: 10.7326/M18-1175

Khanal S., Shumway B.S., Zahin M., Redman R., Strickley, J.D., Trainor P.J., Rai S.N., Ghim S.J., Jenson A.B., & Joh J. (2018). Human Papillomavirus DNA integration, but not viral methylation, is associated with malignant progression of head and neck cancers. Oncotarget, 9(54). doi: 10.18632/oncotarget.25754

Trainor, P.J., DeFilippis, A.P., & Rai, S.N. (2017). Evaluaiton of classifier performance for multiclass phenotype discrimination in metabolomics. Metabolites, 7(2). doi: 10.3390/metabo7020030

Trainor, P.J., Hill, B.G., Carlisle, S.M., Rouchka, E.C., Bhatnagar, A., Rai, S.N., & DeFilippis, A.P. (2017). Systems characterization of differential plasma metabolome perturbations following thrombotic and non-thrombotic myocardial infarction Journal of Proteomics, 160. doi: 10.1016/j.jprot.2017.03.014

DeFilippis, A.P., Trainor, P.J., Hill, B.G., Amraotkar, A.R., Rai, S.N., Hirsch, G.A., Rouchka, E., & Bhatnagar, A. (2017). Identification of a plasma metabolomic signature of thrombotic myocardial infarction that is distinct from non-thrombotic myocardial infarction and stable coronary artery disease. PLoS One, 12(4). doi: 10.1371/journal.pone.0175591

Gibb, A.A., Epstein, P.N., Uchida, S., McNally, L.A., Obal, D., Katragadda, K., Trainor, P.J., Conklin, D.J., Brittian, K.R., Tseng, M.T., Wang J., Jones, S.P., Bhatnagar, A., & Hill, B.G. (2017). Exercise-induced changes in glucose metabolism promote physiologic cardiac growth. Circulation, 136(21). doi: 10.1161/CIRCULATIONAHA.117.028274

Khanal, S., Trainor, P.J., Zahin, M., Ghim, S.J., Joh, J., Rai, S.N., Jenson, A.B., & Shumway, B.S. (2017). Histologic variation in high grade oral epithelial dysplasia when associated with high-risk human papillomavirus. Oral Surgery, Oral Medicine, Oral Pathology, and Oral Radiology, 123(5). doi: 10.1016/j.oooo.2017.01.008

Sultan, A., Zheng, Y., Trainor, P.J., Yong, S., Amraotkar, A.R., Hill, B.G., & DeFilippis, A.P. (2017). Circulating prolidase activity in patients with myocardial infarction. Frontiers in Cardiovascular Medicine, 4(50). doi: 10.3389/fcvm.2017.00050

Amraotkar, A.R., Ghafghazi, S., Trainor, P.J., Hargis C.W., Irfan A.B., Rai S.N., Bhatnagar A., & DeFilippis A.P. (2017). Presence of multiple coronary angiographic characteristics for the diagnosis of acute coronary thrombus. Cardiology Journal, 24(1). doi: 10.5603/CJ.a2017.0004

Khosravi, F., Trainor, P.J., Lambert, C., Kloecker, G., Wickstrom, E., Rai, S.N., & Panchapakesan, B. (2016). Static micro-array isolation, dynamic time series classification, capture and enumeration of spiked breast cancer cells in blood: the nanotube–CTC chip. Nanotechnology, 27(44). doi: 10.1088/0957-4484/27/44/44LT03

Carlisle, S.M., Trainor, P.J., Yin, X., Doll, M.A., Stepp, M.W., States, J.C., Zhang, X., & Hein, D.W. (2016). Untargeted polar metabolomics of transformed MDA-MB-231 breast cancer cells expressing varying levels of human arylamine N-acetyltransferase 1. Metabolomics, 12(7). doi: 10.1007/s11306-016-1056-z

Amraotkar, A.R., Song, D.D., Trainor, P.J., Ismail, I., Kothari, K., Sing, A., Moore, J.B., Rai, S.N., Bhatnagar, A., & DeFilippis, A.P. (2016). Platelet count and mean platelet volume at the time of and after acute myocardial infarction. Clinical and Applied Thrombosis/Haemostasis, 23(8). doi: 10.1177/1076029616683804

DeFilippis, A.P., Chernyavskiy, I., Amraotkar, A.R., Trainor, P.J., Kothari, S., Ismail, I., Hargis, C.W., Korley, F.K., Tsimikas, S., Rai, S.N., & Bhatnagar, A. (2016). Circulating levels of plasminogen and oxidized phospholipids bound to plasminogen distinguish between atherothrombotic and non-atherothrombotic myocardial infarction. Journal of Thrombosis and Thrombolysis, 42(1). doi: 10.1007/s11239-015-1292-5

Egan, J.M., Sloughter, J.M., Cardoso, T., Trainor, P.J., Wu, K., Safford, H., & Fournier, D. (2016). Multi-temporal ecological analysis of Jeffrey pine beetle outbreak dynamics within the Lake Tahoe Basin. Population Ecology, 58(3). doi: 10.1007/s10144-016-0545-2

Trainor, P.J., Rai, S.N., Khosravi, F., & Panchapakesan, B. (2016). Classification of biosensor time series using dynamic time warping: applications in screening cancer cells with characteristic biomarkers. Open Access Medical Statistics, 6. doi: 10.2147/OAMS.S104731

Khosravi, F., Trainor, P.J., Rai, S.N., Kloecker, G., Wickstrom, E. & Panchapakesan, B. (2016). Label-free capture of breast cancer cells spiked in buffy coats using carbon nanotube antibody micro-arrays. Nanotechnology, 27(13). doi: 10.1088/0957-4484/27/13/13LT02

Khanal, S., Cole, ET., Joh, J., Ghim, S.J., Jenson, A.B., Rai, S.N., Trainor, P.J., & Shumway, B.S. (2015). Human papillomavirus detection in histologic samples of multifocal epithelial hyperplasia: a novel demographic presentation. Oral Surgery, Oral Medicine, Oral Pathology, and Oral Radiology, 120(6). doi: 10.1016/j.oooo.2015.07.035

Published software

Trainor, P.J. BayesianGLasso: Bayesian Graphical Lasso. Available from

Publications in preprint

Kulkarni, A., Pandey, A., Trainor, P.J., Carlisle, S.M., Yu, W., Kukutla, P., & Xu, J. (2020). Transcription factors Aryl hydrocarbon receptor and TGF-inducible early gene are involved in an axis modulating immune response in mosquitoes. bioRxiv, doi: 10.1101/2020.11.05.368985

Trainor, P.J., Mitchell, J.M., Carlisle, S.M., Moseley, H.N.B., Rai, S.N., & DeFilippis, A.P. (2018). Inferring metabolite interactomes via Bayesian graphical model selection utilizing molecular structure informative priors. bioRxiv, doi: 10.1101/386409

Publications under review

Sharma, M., Trainor, P.J., Amraotkar, A.R., & DeFilippis, A.P. (2019). The economic and educational impact upon general health literacy.