logo-dark

Selected Journal Articles

  1. Karimnezhad, A. and Perkins, T. J. (2024). Empirical Bayes single nucleotide variant- calling for next-generation sequencing data. Scientific Reports 14, 1550, https://doi.org/10.1038/s41598-024-51958-z

  2. Karimnezhad, A. (2022). More accurate estimation of cell composition in bulk expres- sion through robust integration of single-cell information. Bioinformatics Advances, 2(1), https://doi.org/10.1093/bioadv/vbac049.

  3. Karimnezhad, A. (2022). A Simple Yet Efficient Method of Local False Discovery Rate Estimation Designed for Genome-Wide Association Data Analysis. Statistical Methods and Applications, 31, 159-180.

  4. Karimnezhad, A., Palidwor, A. P., Thavorn, K., Campbell, P., Lo, B., Stewart, D. J. and Perkins, T. J. (2020). Accuracy and Reproducibility of Somatic Point Mutation Calling in Clinical-type Targeted Sequencing Data. BMC Medical Genomics. 13, 156.

  5. Karimnezhad, A. and Bickel, D. R. (2020). Incorporating Prior Knowledge about Genetic Variants into the Analysis of Genetic Association Data: An Empirical Bayes Approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 17(2), 635-646.

  6. Karimnezhad, A. and Zarepour, M. (2020). A General Guide in Bayesian and Robust Bayesian Estimation Using Dirichlet Processes. Metrika. 83, 321-346.

  7. Karimnezhad, A. and Parsian, A. (2019). Bayes and Robust Bayes Inference in a General Setting. Communications in Statistics - Theory and Methods. 48(15), 3899-3920.

  8. Karimnezhad, A. and Moradi, F. (2018). Allelic Frequency Estimation in Presence of Uncertain Priors. Journal of Theoretical Biology 459, 119-129.

  9. Karimnezhad, A. and Parsian, A. (2018). Most Stable Sample Size Determination in Clinical Trials. Statistical Methods and Application 27(3), 437-454.

  10. Trafimow, D., Amrhein, V. and 52 others including Karimnezhad, A. (2018). Manipu- lating the alpha level cannot cure significance testing. Frontiers in Psychology 9-690. doi: 10.3389/fpsyg.2018.00699

  11. Karimnezhad, A., Lucas, P. J. and Parsian, A. (2017). Constrained Parameter Estimation with Uncertain Priors for Bayesian Networks. Electronic Journal of Statistics, 11(2), 4000- 4032.

  12. Mei, S., Karimnezhad, A., Forest, M., Bickel, D. R., Greenwood, C. (2017). The Per- formance of a New Local False Discovery Rate Method on Tests of Association between Coronary Artery Disease (CAD) and Genome-wide Genetic Variants. PLoS ONE, 12(9): e0185174.

  13. Karimnezhad, A. and Moradi, F. (2016). Bayesian Parameter Learning with an Applica- tion, Metron, 74(1), 61-74.

Software Packages

  1. Karimnezhad, A. (2024). SNVLFDR: LFDR-based Variant Calling . R package, version 1.0.1. https://cran.r-project.org/web/packages/SNVLFDR

  2. Karimnezhad, A. (2024). CSCDRNA: Covariance Based Decomposition of Bulk Expression with Single-Cell Sequencing. R package, version 2.0.1. https://github.com/empiricalbayes/CSCDRNA

  3. Karimnezhad, A. (2020). LFDR.MME: Estimating Local False Discovery Rates Using the Method of Moments. R package, version 1.0.1 https://cran.r-project.org/web/packages/LFDR.MME

  4. Karimnezhad, A., Kim, J., Akpawu, A., Chitpin, J. and Bickel, D. R. (2017). LFDR.Empirical- Bayes: Estimating Local False Discovery Rates Using Empirical Bayes Methods. R package, version 1.0. https://cran.r-project.org/web/packages/LFDREmpiricalBayes

  5. Karimnezhad, A., Kim, J. and Bickel, D. R. (2017). LFDR.EmpiricalBayes. Shiny App. https://empiricalbayes.shinyapps.io/lfdrempiricalbayesapp/