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Research & Software

Interests

Data Science in Medicine, Big Data, Deep Learning, Computational Biology, Statistical Computing and Graphics.

R Software

  • datanugget R package: This is a data compression algorithm that replaces a big dataset by a few thousand nuggets preserving the structure of the data that maybe lost by using random sampling. The compressed datasets can be used for functions in the WCluster and PPbigdata.  Please get it directly from CRAN
  • WCluster R package: This package Please get it directly from CRAN
  • PPbigdata R package: Please get it directly from CRAN
  • DNAMR R Package: DNAMR1.3   This is the latest version of the DNAMR package. It has updates of functions: second_der, cnormalize, transAI, transatan, transgap, and transasinh
  • Older versions of DNAMR:       DNAMR1.2 (under R 4.0) and DNAMR (under R 3.0) R Package with code from 2014 book It includes quantile normlization, conditional T and many other functions.
  • ARF R package , includes ARF  MARF and MPART
  • fdaRNA package:  Includes Functional Data Normalization, Quantile normalization, Fisher-Yates Normalization,   functional RMA M-estimator Funtional RMA(more statistically efficient than regular RMA).
  • ERF Enriched Random Forest R package.  This version has some bugs. A new better version will be uploaded in one week
  • LoST  and JLE.   An R package called LoST containing the function JLE  will be available here shortly after it passes approval. The R package will also be available at CRAN shortly.

Recent Papers

  1. (2025) Nguyen T.H., Hamad I., Kleinewietfeld M., Amaratunga D., Cabrera J., Sargsyan D., Sengupta R., Owokotomo O., Katehakis M., Shkedy Z. Development of multiple microbiome biomarkers using penalized regression methods. Journal of Applied Microbiology 136 (10),
  2. (2025) D Amaratunga, J Cabrera, N Diaz-Tena, MN Katehakis, CP Lin, J Wang. Novel methods for adaptive time-series forecasting and prediction-interval constructionAnnals of Operations Research, 1-19
  3. (2025) M Yuan, A Wassef, D Sargsyan, V Nersisyan, J Cabrera, RG Nahass, Genetic and Inflammatory Signatures Associated With Worse Prognosis in Hospitalized Patients With Severe SARS‐CoV‐2 Infection With and Without DiabetesJournal of Medical Virology 97 (6),
  4. (2025) S Weigle, D Sargsyan, J Cabrera, L Diya, J Sendecki, M Lubomirski. Randomization in Pre‐Clinical Studies: When Evolution Theory Meets Statistics Pharmaceutical Statistics 24 (3)
  5. (2025) M Dastgiri, J Cabrera, Y Duan, D Sargsyan, CW Gambogi, A Adokwei Novel machine learning approach to differential cell flow cytometry analysis based on projection pursuit. Journal of Biopharmaceutical Statistics, 1-13
  6. (2025)Y Duan, J Cabrera,  A New Projection Pursuit Index for Big Data Journal of Computational and Graphical Statistics, 1-12
  7. (2025) K Tatikola, J Cabrera, CP Lin, H Geys, F Tekle, J Sendecki, S Altan. Quasi-Empirical Bayes methods for parameter estimation involving many small sampleJournal of Biopharmaceutical Statistics, 1-10
  8. (2025) Dey R, Duan Y, J Cabrera J.,Cheng G., R Package ‘WCluster’
  9. (2025) J Wang, J Cabrera, D Sargsyan, K Tatikola, KL Tsui Analysis of continuous monitoring device data. Journal of Biopharmaceutical Statistics, 1-9
  10. (2025) Principal phrase mining: an automated method for extracting meaningful phrases from text. E Small, J Cabrera. International Journal of Computers and Applications 47 (1), 84-92
  11. (2025) Data nuggets: A method for reducing big data while preserving data structure TE Beavers, G Cheng, Y Duan, J Cabrera, M Lubomirski, D Amaratunga, Journal of Computational and Graphical Statistics 34 (1), 330-342     7
  12. (2025) K Tatikola, J Cabrera. Estimating the Strength of Binding Affinity via Delta–Delta‐G for Hit Screening After a Deming Regression Calibration Pharmaceutical Statistics 24 (1).
  13. (2024) J Cabrera, B Emir, G Cheng, Y Duan, D Alemayehu, Y Cherka. An enriched approach to combining high-dimensional genomic and low-dimensional phenotypic data. Journal of Biopharmaceutical Statistics 34 (6), 1026-1032
  14. (2024) CP Lin, Y Duan, D Sargsyan, H Geys, J Sendecki, K Tatikola, S Mohanty, J Cabrera. Improved automated spot counting and modeling with bias correction. Journal of Biopharmaceutical Statistics, 1-7
  15. (2024) Y Duan, J Cabrera, D Sargsyan A novel two-stage deming regression framework with applications to association analysis between clinical risks. arXiv preprint arXiv:2405.20992
  16. (2024) CV Ananth, R Lee, L Valeri, Z Ross, HL Graham, SP Khan, J Cabrera. Placental Abruption and Cardiovascular Event Risk (PACER): Design, data linkage, and preliminary findings. Paediatric and perinatal epidemiology 38 (3), 271-2863
  17. (2024) AE Moreyra, C Mehta, NM Cosgrove, S Zinonos, D Sargsyan, A Gold, Factors influencing the indication of coronary angiography in patients presenting with chest pain unspecified: an analysis of two decades (1994–2014) International Journal for Quality in Health Care 36 (1), mzae012
  18. (2003) Altan S, Amaratunga D, Cabrera J, Geiss H, Lubomiski M, J Kolassa Novick S. Tan, C.    Survey and Recommendations on the use of P-values driving decisions in Nonclinical Pharmaceutical Applications. Stat in Biopharma Research 15-2 pp 343-358.
  19. (2025) Y Duan, J Cabrera, B Emir. A New Projection Pursuit Index for Big Data. arXiv:2312.06465
  20. (2023) Automated Spot Counting in Microbiology. CP Lin, Y Duan, D Sargsyan, J Cabrera, CM Livingston, R Vogel. IEEE/ACM Transactions on Computational Biology and Bioinformatics
  21. (2023) N Bhatia, D Vakil, S Zinonos, J Cabrera, NM Cosgrove, M Dastgiri. US Initiative to Eliminate Racial and Ethnic Disparities in Health: The Impact on the Outcomes of ST‐Segment–Elevation Myocardial Infarction in New Jersey. Journal of the American Heart Association 12 (9)
  22. (2023) RC Camacho, D Polidori, T Chen, B Chen, HH Hsu, B Gao, M Marella, J Cabrera. Validation of a diet‐induced Macaca fascicularis model of non‐alcoholic steatohepatitis with dietary and pioglitazone interventions. Diabetes, Obesity and Metabolism 25 (4), 1068-1079
  23. (2022) KE Cherasia, J Cabrera, LT Fernholz, R Fernholz. Data Nuggets in Supervised Learning. Robust and Multivariate Statistical Methods: Festschrift in Honor of David E …
  24. (2022) Socio-economic impact on COVID-19 cases and deaths and its evolution in New JerseyD Amaratunga, J Cabrera, D Ghosh, MN. Katehakis, J Wang, W Wang. Annals of Operations Research 317:5–18
  25. (2022) Duan, Y., Lin, C. P., Sargsyan, D., Cabrera, J., Livingston, C., Vogel, R., Sendecki, J., Talloen, W., Geys, H., & Mohanty, S. Particle count estimation in dilution series experiments. Naval Research Logistics.
  26. (2022) Tresadern G, Tatikola K, Cabrera J, Wang L, Abel A, Vlijmen H, Geys H. The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions. ournal of Chemical Information and Modeling. Jan 21.
  27. (2022) Cuccurullo SJ, Fleming TK, Kostis JB, Greiss C, Gizzi MS, Eckert A, Ray AR, Scarpati R, Cosgrove NM, Beavers T, Cabrera J, Sargsyan D, Kostis W. Impact of Modified Cardiac Rehabilitation Within a Stroke Recovery Program on All-Cause Hospital Readmissions. Am J Phys Med Rehabil. Jan 1, 2022.
  28. (2022) Beavers T, Cabrera J, Lubomirski M, Amaratunga J, Teigler J Data Nuggets: A Method for Reducing Large Datasets While Maintaining Data Structure (under review)
  29. (2021) Cislo P., Emir B., Cabrera J., Li B., Alemayehu D. Finite Mixture Models, a Flexible Alternative to Standard Modeling Techniques for Extrapolated Mean Survival Times Needed for Cost-Effectiveness Analyses. Value in Health 24-11, pp 1643-1650
  30. (2021) Ghosh D, Cabrera J. Enriched Random Forest for High Dimensional Genomic Data. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jun 15
  31. (2021) Dickson, KM Cabrera J, Egan S, Balica A. Long Term Outcomes of Sonographically Guided Intrauterine Device Placement. Accepted for publication.
  32. (2021) Cabrera J Amaratunga, Kostis W, Kostis J., Personalized Disease Networks (Accepted for publication), International Journal of Cardiology Cardiovascular Risk and Prevention.
  33. (2021) Kostis, J. B., Lin, C. P., Dobrzynski, J. M., Kostis, W. J., Ambrosio, M., & Cabrera, J. Prediction of stroke using an algorithm to estimate arterial stiffness. International Journal of Cardiology Cardiovascular Risk and Prevention, 11, 2021.
  34. (2021) Lin, C.P., Ling, M. H., Cabrera, J., Yang, F., Yu, D. Y. W., & Tsui, K. L. . Prognostics for lithium-ion batteries using a two-phase gamma degradation process model. Reliability Engineering & System Safety, 107797.
  35. (2021) Kostis, J. B., Cabrera, J., Lin, C. P., Dobrzynski, J. M., Giakoumis, M., & Kostis, W. J. A novel noninvasive method of estimating vascular age compared to chronological age. Journal of the American College of Cardiology, 77(18_Supplement_1), 1550-1550.
  36. (2021) Christina M Ackerman, Jennifer L Nguyen, Swapna Ambati, Maya Reimbaeva, Birol Emir, Javier Cabrera, Michael Benigno, Deepa Malhotra, Jennifer Hammond, Mert Ozan Bahtiyar, Clinical and Pregnancy Outcomes of COVID-19 Among Hospitalized Pregnant Women in the United States, Open Forum Infectious Diseases, 3;9(2).
  37. (2021) Amaratunga, J. Cabrera, Debopriya Ghosh, M. Katehakis, J Wang, W Wang. Socio-economic impact on COVID-19 cases and deaths and its evolution in New Jersey. Annals of Operations Research, Feb 2021,1-14
  38. (2021) Moreyra, A, Cosgrove N, Zinonos S, YanY., Cabrera J, Kostis JB, Constrictive Pericarditis after Open Heart Surgery: A 20-Year Case Controlled Study. International Journal of Cardiology Cardiovascular Risk and Prevention, v329, p63-66.
  39. (2021) Hitner E, Zinonos S, Kostis JB, Cabrera J, Moreyra, A , Kostis, WJ, A Twenty-Year Analysis of Demographics, Surgical Management, and Outcomes of Aortic Stenosis in New Jersey Am J Cardiol. 150:82-88.

For a full list please go to Google Scholar