Publications

Refereed publications

2025 (published/submitted/preprint)

  • Zhao K, Yang A, Oualkacha K, Yixiao Z, Klein K, Hudson M, Colmegna I, Bernatsky S, Greenwood CMT. (2024). A novel high-dimensional model for identifying regional DNA methylation QTLs.
    Revision Requested. 
  • St-Pierre J, Bhatnagar S, Orri M, Boivin M, Dupuis J, Oualkacha K. Penalized generalized linear mixed models for longitudinal outcomes in genetic association studies. preprint https://arxiv.org/abs/2501.11083
  • Doukali M, Bouezmarni T, Oualkacha K. Copula-Based Expectile Regression: estimation and inference. Econometric Reviews. 00: 1-35. Revision Requested.
  • St-Pierre J, Oualkacha K, Bhatnagar S. Hierarchical selection of genetic and gene by environment interaction effects in high-dimensional mixed models. Statistical Methods in Medical Research. 34(1): 180-198. Lien preprint: https://arxiv.org/pdf/2312.13460.pdf

2024  

  • Ribaud M, Labbe A, Fouda K, Oualkacha K. Fast matrix completion in epigenetic methylation studies with informative Covariates. Biostatistics. 25(4): 1062-1078. Lien
  • Zhao K, Oualkacha K, Lakhal-Chaieb L, Labbe A, Klein K, Shao X, Bernatsky S, Hudson M, Colmegna I, Pastinen T, Zhang T, Daley D,  Greenwood CMT. Addressing dispersion in mis-measured multivariate binary outcomes:  A novel statistical approach for detecting differentially methylated regions in bisulfite sequencing data. Statistics in Medicine.  43(20): 3899-3920. Lien ; preprint: https://arxiv.org/abs/2101.07374
  •  Ouhourane M, Yang Y, Oualkacha K. Group Penalized Expectile Regression. Statistical Methods & Applications. 33: 1251-1313. Lien 
  •  Kharoubi R, Oualkacha K, Mkhadri A. High-Dimensional Penalized Bernstein Support Vector Classifier. Computational Statistics. 39: 1909-1936. Lien. preprint: https://doi.org/10.48550/arXiv.2303.09066

2023 

  • DOSSA HRG, Bureau A, Maziade M, Lakhal-Chaieb L, Oualkacha K. A Novel Rare Variants Association Test for Binary Traits in Family-Based Designs via Copulas. Statistical Methods in Medical Research. 1-27.  PDF
  • Anzarmou Y, Mkhadri A,  Oualkacha K. Sparse overlapped linear discriminant analysis. TEST. 32: 388–417. https://doi.org/10.1007/s11749-022-00839-6
  • St-Pierre J, Oualkacha K, Bhatnagar SR. Efficient penalized generalized linear mixed models for variable selection and genetic risk prediction in high-dimensional data. Bioinformatics. 39(2): 1367-4811.  PDF
  • Barry AD, Oualkacha K, Charpentier A. Alternative fixed-effects panel model using weighted asymmetric least squares regression. Statistical Methods & Applications. https://doi.org/10.1007/s10260-023-00692-3
  • Anzarmou Y, Mkhadri A, Oualkacha K. The Kendall interaction filter for variable interaction screening in high dimensional classification problems, Journal of Applied Statistics. 50(7): 1496-1514. 10.1080/02664763.2022.2031125

2022  

  • St-Pierre J, Oualkacha K. A copula-based set-variant association test for bivariate continuous, binary or mixed phenotypes. The International Journal of Biostatistics. doi:10.1515/ijb-2022-0010
  • Ouhourane M, Yang Y, Benedet AL, Oualkacha K. Group Penalized Smooth Quantile Regression.  Statistical Methods & Applications. 31, pages 495–529. https://doi.org/10.1007/s10260-021-00580-8
  • Barry AD, Oualkacha K, Charpentier A. A new GEE method to account for heteroscedasticity, using asymmetric least-square regressions. Journal of Applied Statistics. 49(14): pages 3564-3590. https://doi.org/10.1080/02664763.2021.1957789

2021  

  • Escribe C, Lu T, Keller-Baruch J, Forgetta V, Xiao B, Richards JB, Bhatnagar S,  Oualkacha K, Greenwood C. Block coordinate descent algorithm improves variable selection and estimation in error-in-variables regression. Genetic Epidemiology. 45(8): 874–890. http://10.1002/gepi.22430
  • Anzarmou Y, Mkhadri A, Oualkacha K (2021). The Kendall Interaction Filter for Variable Interaction Screening in Ultra High Dimensional Classification Problems. preprint: https://arxiv.org/abs/2010.06688
  • Catherine Schramm, Sébastien Jacquemont, Karim Oualkacha, Aurélie Labbe, Celia MT Greenwood (2021). KSPM: A Package For Kernel Semi-Parametric Models. The R Journal. in press. pdf
  • Mohammadhasanzadeh H, Oualkacha K, Zhang W, et al. On path to informing hierarchy of eplet-mismatches as determinants of kidney transplant loss. Kidney International Reports. 6:1567-1579.

2020

  • Zhao K, Oualkacha K, Lakhal‐Chaieb L, Labbe A, Klein K, Ciampi A, Hudson M, Colmegna I, Pastinen T, Zhang T, Daley D, Greenwood CMT (2020), A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation. Biometrics. doi:10.1111/biom.13307. pdf
  • Bhatnagar SR, Yi Y, Lu T, Schurr E, Loredo-Osti JC, Forest M, Oualkacha K, Greenwood CMT (2020). Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models. Plos Genetics. 16(5): e1008766. pdf

2019 

  • Fodé Tounkara, Geneviève Lefebvre, Celia MT Greenwood and Karim Oualkacha (2019). A flexible copula-based approach for the analysis of secondary phenotypes in ascertained samples. Statistics in Medicine. 39: 517-543. https://doi.org/10.1002/sim.8416
  • Rachid Kharoubi, Karim Oualkacha, Abdallah Mkhadri (2019). The Cluster Correlation-Network Support Vector Machine for High-dimensional Binary Classification. Journal of Statistical Computation and Simulation. 89:6, 1020-1043, http://DOI: 10.1080/00949655.2019.1575382
  • Lai Jiang, Karim Oualkacha, Vanessa Didelez, Antonio Ciampi, Pedro Rosa, Andréa L. Benedet, Sulantha Mathotaarachchi, J. Brent Richards, and Celia M.T. Greenwood (2019). Constrained Instruments and their Application to Mendelian Randomization with Pleiotropy. Genetic Epidemiology. https://doi.org/10.1002/gepi.22184

2018

  • Sun J, Oualkacha K, Greenwood CMT, Lakhal-Chaieb L (2018). Multivariate association test for rare variants controlling for cryptic and family relatedness. Canadian Journal of Statistics. 47: 90-107. https://doi.org/10.1002/cjs.11475
  • D’Souza Y, Ferradji A, Saw CL, Oualkacha K, Richard L, Popradi G and Sapir-Pichhadze R. (2018). Inaccuracies in epitope repertoire estimations when using multilocus allele-level HLA genotype imputation tools. HLA: Immune Response Genetics. https://doi.org/10.1111/tan.13307.
  • Sun J, Oualkacha K, Forgetta V, Zheng HF, Richards B, Orwoll E,  Evans D, Greenwood CMT, (2018). Exome-wide rare variant analyses of two bone mineral density phenotypes: the challenges of analyzing rare genetic variation. Scientific Reports, Volume 8, Issue 1: 220.
  • Auerbach J, Howey R, Jiang L, Justice A, Li L, Oualkacha K, Sayols-Baixeras S, Aslibekyan SW (2018). Causal modeling in a multi-omics setting: insights from Genetic Analysis Workshop 20. BMC Genetics. 19 (Suppl 1) :74. https://doi.org/10.1186/s12863-018-0645-4
  • Zhao K, Jiang L, Klein K, Greenwood CMT, Oualkacha K. (2018). CpG-set association assessment of lipid concentration changes and DNA methylation on chromosome 11. BMC Proceeding. 12 (Suppl 9) :30. https://doi.org/10.1186/s12919-018-0127-8
  • Jiang L, Zhao K, Klein K, Canty AJ, Oualkacha K, Greenwood CMT. (2018). Investigating potential causal relationships between SNPs, DNA methylation and HDL. BMC Proceeding.  12 (Suppl 9) :20. https://doi.org/10.1186/s12919-018-0117-x

2017

  • Lakhal-Chaieb L, Greenwood CMT, Ouhourane M, Zhao K, Abdous B,  Oualkacha K. (2017). A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type. Statistical Applications in Genetics and Molecular Biology. 16(5-6):333-347. doi: 10.1515/sagmb-2016-0062. https://doi.org/10.1515/sagmb-2016-0062
  • Ferradji A, D’Souza Y, Saw CL, Oualkacha K, Richard L, Sapir-Pichhadze R. (2017). Performance of an allele-level multi-locus HLA genotype imputation tool in hematopoietic stem cell donors from Quebec. Immun Inflamm Dis., doi: 10.1002/iid3.185
  • Lajoie M, Drouin S, Caron M, St-Onge P, Ouimet M, Gioia R, Lafond MH, Vidal R, Richer C, Oualkacha K, Droit A, Sinnett D. (2017). Specific expression of novel long non-coding RNAs in high-hyperdiploid childhood acute lymphoblastic leukemia. PLoS One. 12(3):e0174124. doi: 10.1371/journal.pone.0174124

2016

  • Turgeon M, Oualkacha K, Ciampi A, Miftah H, Dehghan G, Zanke BW, Benedet AL, Rosa-Neto P, Greenwood CM, Labbe A; Alzheimer’s Disease Neuroimaging Initiative (2016). Principal component of explained variance: An efficient and optimal data dimension reduction framework for association studies. Statistical Methods in Medical Research, doi:10.1177/0962280216660128.
  • Mkhadri A., Ouhourane, M., Oualkacha, K. (2016). A coordinate descent algorithm for computing penalized smooth quantile regression.  Statistics and Computing, doi:10.1007/s11222-016-9659-9.
  • Sun, J., Oualkacha, K., Forgetta, V., Zheng, H.-F., Richards, J.B., Ciampi, A., Greenwood, C.M.T., UK10K Consortium (2016). A method for analyzing multiple continuous phenotypes in rare variant association studies allowing for flexible correlations in variant effects. European Journal of Human Genetics, doi: 10.1038/ejhg.2016.8.
  • Oualkacha, K., Lakhal-Chaieb, L, Greenwood, C.M.T. (2016). RVPedigree: a suite of family-based rare variant association tests for normally and non-normally distributed quantitative traits.  International Journal of Epidemiology, doi: 10.1093/ije/dyw047.
  • Kathleen Oros Klein, Karim Oualkacha, Marie-Hélène Lafond, Sahir Bhatnagar, Patricia N. Tonin and Celia M.T. Greenwood (2016). Gene Coexpression Analyses Differentiate Networks Associated with Diverse Cancers Harboring TP53 Missense or Null Mutations. Frontiers in Genetics-Statistical Genetics and Methodology, doi: 10.3389/fgene.2016.00137.
  • Sun, J., Bhatnagar, S., Oualkacha, K., Ciampi, A., Greenwood, C.M.T. (2015). Joint analysis of multiple blood pressure phenotypes in GAW19 data by using a multivariate rare-variant association test. BMC Proceedings. 10(Suppl 7):309-313.

2015

  • Lakhal-Chaieb L., Oualkacha, K., Richard, B.J., Greenwood, C.M.T. A rare variant association test in family-based designs and non-normal quantitative traits. Statistics in Medicine, 35 (6).
  • The UK10K Consortium (including Oualkacha, K.) (2015). The UK10K project identifies rare variants in health and disease. Nature, 526, 82-90.
  • Sun, J., Oualkacha, K., Greenwood, C.M.T. (2015). Multivariate association test for rare variants controlling for cryptic and family relatedness. Annual Meeting of the International-Genetic-Epidemiology-Society (IGES), Volume: 39.

2013

  • Oualkacha, K., Cingolani, P., Dastani, Z., Li, R., Spector, T. D., Hammond, C. J., Richards, J. B., Ciampi, A. and Greenwood, C. (2013). Adjusted Sequence Kernel Association Test for Rare Variants Controlling for Cryptic and Family Relatedness. Genetic Epidemiology, Volume 37, Issue 4, pages 366–376.
  • Dufresne, L., Oualkacha, K., Forgetta. V., Greenwood. CMT. (2013). Pathway Analysis for Genetic Association Studies: To Do, or Not To Do? That is the Question. BMC proceedings.

2012

  • Oualkacha, K. and Rivest, L. P. (2012). On the estimation of the mean displacement in SE(p). Biometrika,  14 pages, doi: 10.1093/biomet/ass020.
  • Oualkacha, K., Labbe, A., Ciampi, A., Roy, M.A. and Maziade, M. (2012). Principal components of heritability for high dimension quantitative traits and general pedigrees. Journal of Statistical Applications in Genetics and Molecular Biology, Volume 11. Issue 2, Article 4.

2009

  • Oualkacha, K. and Rivest, L. P. (2009). A new statistical model for random unit vectors. Journal of Multivariate Analysis. 100, 70-80.