Research

Software

[3] SMLE: Joint Feature Screening via Sparse MLE (R package; available at CRAN)

[2] sampletrees and Rsampletrees: A Markov chain Monte Carlo algorithm for sampling gene genealogies conditional on unphased SNP genotype data. The algorithm has been implemented in C++. The R program Rsampletrees, available at CRAN, can be used for pre- and post-processing of sampletrees files. (https://sfustatgen.github.io/research/sampletrees.html)

[1] hapassoc: Inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm (R package). (https://sfustatgen.github.io/research/hapassoc.html)

Publications and Preprints

- My students/trainees are in bold

[26] Rakesh M,  Vézina H, Laprise C, Freeman EF, Burkett KM, Roy-Gagnon M-H. GENLIB: new function to simulate haplotype transmission in large complex genealogies. Bioinformatics, btad136, 2023. https://doi.org/10.1093/bioinformatics/btad136

[25] Zang Q,  Xu C, Burkett KM. SMLE: An R Package for Joint Feature Screening in Ultrahigh-dimensional GLMs (submitted); https://arxiv.org/abs/2201.03512

[24] Onifade MY, Roy-Gagnon MH, Parent ME, Burkett KM. Comparison of mixed model based approaches for correcting for population substructure with application to extreme phenotype sampling. BMC Genomics, 23, Article number: 98, 2022. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08297-y

[23] Burkett K, Rakesh M, Morris P, Vézina H, Laprise C, Freeman E, Roy-Gagnon, M-H. Correspondence between genomic- and genealogical/coalescent-based inference of homozygosity by descent in large French Canadian genealogies. Frontiers in Genetics, Statistical Genetics and Methodology. 12:808829, 2022. https://doi.org/10.3389/fgene.2021.808829

[22] Emlaw JR, Tessier JG, McCluskey GD, McNulty MS, Sheikh Y, Burkett KM, Musgaard M,daCosta CJB. A single historical substitution drives an increase in acetylcholine receptor complexity. PNAS: 118 (7) e2018731118, 2021.

[21] Liu R, Burkett K, Rapinski M, Arnason JT, Johnson F, Hintz P, Baker J, Harris CS. Biochemometric Analysis of Fatty Acid Amide Hydrolase Inhibition by Echinacea Root Extracts. Planta Med. 87:294-304, 2021. doi: 10.1055/a-1289-9569. 

[20] Emlaw JR, Burkett KM, daCosta CJB. Contingency between Historical Substitutions in the Acetylcholine Receptor Pore. ACS Chemical Neuroscience, 11: 2861-2868, 2020.

[19] Panarella M, Burkett KM. A cautionary note on the effects of population stratification under an extreme phenotype sampling design. Frontiers in Genetics Frontiers in Genetics, 10: 398, 2019. https://doi.org/10.3389/fgene.2019.00398

[18] Wang C, Roy-Gagnon MH, Lefebvre JF, Burkett* KM and Dubois* L. Modeling gene-environment interactions in longitudinal family studies: a comparison of methods and their application to the association between the IGF pathway and childhood obesity. BMC Medical Genetics. 20: 9, 2019.* Co-last authors doi: 10.1186/s12881-018-0739-x

[17] Burkett KM, McNeney B, Graham J. Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. Bioinformatics. 32:1580-2, 2016.

[16] Burkett KM, Roy-Gagnon MH, Lefebvre JF, Wang C, Fontaine-Bisson B, Dubois L. A comparison of statistical methods for the discovery of genetic risk factors using longitudinal family study designs. Frontiers in Immunology, 6:589, 2015. https://doi.org/10.3389/fimmu.2015.00589

[15] Burkett KM, McNeney B, Graham J, Greenwood CMT. Using gene genealogies to detect rare variants associated with complex traits. Human Heredity, 78:117-130, 2014.

[14] Burkett KM, Greenwood CMT, McNeney B, Graham J. Gene genealogies for genetic association mapping, with application to Crohn's disease. Frontiers in Statistical Genetics and Methodology, 4: article 260, 2013.

[13] Burkett KM, McNeney B, Graham, J. Markov chain Monte Carlo sampling of gene genealogies conditional on unphased SNP genotype data. Statistical Applications in Genetics and Molecular Biology, 12: 559-581, 2013.

[12] Burkett KM, Greenwood CMT. A sequence of methodological changes due to sequencing. Current Opinion in Allergy & Clinical Immunology, 13: 470-477, 2013.

[11] Burkett KM, McNeney B, Graham J. A Markov chain Monte Carlo sampler for gene genealogies conditional on haplotype data. In Chaubney, Y., editor, Some Recent Advances in Mathematics and Statistics, Proceedings of Statistics 2011 Canada/IMST 2011-FIM XX, Montreal, July 2011. Singapore, World Scientific Publishing, 2013, 29-44.

[10] Wallace AM, Sandford AJ, English JC, Burkett K, Li H, Finley RJ, Müller NL, Coxson HO, Paré PD, Abboud RT. Matrix metalloproteinase expression by human alveolar macrophages in relation to emphysema. COPD, 5: 13-23, 2008.

[9] Tanaka G, Sandford AJ, Burkett K, Connett JE, Anthonisen NR, Paré PD, He JQ. Tumour necrosis factor and lymphotoxin A polymorphisms and lung function in smokers. European Respiratory Journal, 29: 34-41, 2007.

[8] Wallace AM, He JQ, Burkett K, Ruan J, Connett JE, Anthonisen NR, Paré PD, Sandford AJ. Contribution of alpha- and beta-defensins to lung function decline and infection in smokers: an association study. Respiratory Research, 7: 76, 2006.

[7] Burkett K, McNeney B, Graham J. hapassoc: software for likelihood inference of trait associations with SNP haplotypes and other attributes. Journal of Statistical Software, 16 (2): 1-19, 2006.

[6] He JQ, Burkett K, Connett JE, Anthonisen NR, Paré PD, Sandford AJ. Interferon gamma gene and its interaction with smoking are associated with lung function in smokers. Human Genetics, 119: 365-375, 2006.

[5] Bergwitz C, Roslin NR, Tieder M, Loredo-Osti JC, Bastepe M, Abu-Zahra H, Frappier D, Burkett K, Carpenter TO, Anderson D, Garabàdian M, Sermet I, Fujiwara TM, Morgan K, Tenenhouse HS, Jüppner H. SLC34A3 mutations in patients with hereditary hypophosphatemic rickets with hypercal- ciuria (HHRH) predict a key role for the sodium-phosphate co-transporter NaPi-IIc in maintaining phosphate homeostasis. American Journal of Human Genetics, 78: 179-192, 2006.

[4] Burkett K, Ghadessi M, McNeney B, Graham J, and Daley D. A Comparison of Three Methods for Selecting Tagging Single Nucleotide Polymorphisms. BMC Genetics, 6(Suppl) S71, 2005.

[3] Daley D and Burkett K. Approaches to study inflammatory gene haplotypes and susceptibility to cardiac, vascular and pulmonary diseases. Current Opinion in Molecular Therapeutics, 7: 226-233, 2005.

[2] Burkett K, McNeney B, Graham J. A Note on Inference of Trait Associations with SNP Haplotypes and Other Attributes in Generalized Linear Models. Human Heredity, 57: 200-206, 2004.

[1] Tebbutt SJ, He JQ, Burkett K, Ruan J, Opushnyev IV, Tripp BW, Zeznik JA, Abara CO, Nelson CC, Wal- ley KR. Microarray genotyping resource to determine population stratification in genetic association studies of complex disease. BioTechniques, 37: 977-985, 2004.