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Selected Journal Articles

  1. Karimnezhad, A. (2026). Constrained Binomial Mixture Modelling for Accurate Estimation of Microbial Strain Composition. Revised manuscript under review.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

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

  8. 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.

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

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

  11. 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

  12. 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.

  13. 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.

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

Software Packages

  1. Karimnezhad, A. (2026). StrainSolver: Python package for microbial strain mixture estimation. https://github.com/empiricalbayes/StrainSolver

    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/