Research

Software developed

• perfectphyloR: An R package to reconstruct a partition of sequences known as a perfect phylogeny at a user-given focal point on the genome, and to depict and test association in a genomic region based on the reconstructed partitions doi: 10.1101/674523
• SimRVSequences: An R package to simulate genetic sequence data for pedigrees, with functionality to simulate genetic heterogeneity among pedigrees doi: 10.1101/534552
• SimRVpedigree: An R package to simulate pedigrees ascertained on the basis of multiple affected members doi: 10.1101/234153. Note: Selected as one of the “Top 40”” new packages available on CRAN in Dec 2017 by R views. Profiled by the popular “R bloggers” site in Jan 2018 at https://www.r-bloggers.com/dec-2017-top-40-new-package-picks/ and by SFU Faculty of Science in Dec 2018
• trioGxE: An R package implementing a data-smoothing approach to explore and test gene-environment interaction in case-parent trio data, described in Shin et al. (2014).
• sampletrees and Rsampletrees: A C++ program and R package interface implementing the Markov chain Monte Carlo (MCMC) algorithm for sampling gene genealogies conditional on either phased or unphased SNP genotype data, described in Burkett et al. (2013a) and Burkett et al. (2013b). For a description of the software please see Burkett et al. (2016).
• CrypticIBDcheck: An R package to identify cryptic relatedness in genetic association studies. For a description of the features of the package and examples of its use, please see Nembot-Simo et al. (2013).
  
• rJPSGCS: An R interface to programs for fitting LD models and performing gene drops from Alun Thomas’ Java Programs for Statistical Genetics and Computational Statistics (JPSGCS).
• elrm: An R package implementing Exact Logistic Regression via MCMC, using the methods described in Zamar et al. (2007).
• luca: An R package implementing the methods described in Shin et al. (2007) for case-control inference of statistical interaction between genetic and nongenetic risk factors under covariate assumptions.
• LDheatmap: An R package implementing a graphical tool for exploring pairwise linkage disequilibria between Single Nucleotide Polymorphisms (SNPs). For a description of the features of the package and examples of its use, please see Shin et al. (2006) or the package’s homepage on GitHub
• hapassoc: The hapassoc R package implementing methods described in Burkett et al. (2004) for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm. For a description of the features of the package and examples of its use, please see Burkett et al. (2006).
• stepwise: R package and stand-alone C program implementing methods described in Graham et al. (2005) for stepwise detection of recombination breakpoints in sequence alignments

Recent Publications

2024

• Nieuwoudt C, Binte Farooq F, Brooks-Wilson A, Bureau A, Graham J (2024). Statistics to prioritize rare variants in family-based sequencing studies with disease subtypes. Genetic Epidemiology, 48(7): 324-343. DOI: 10.1002/gepi.22579.

2023

• Ratnasekera P, Graham J, McNeney B (2023). Inference of gene-environment interaction from heterogeneous case-parent trios. Front. Genet. - Statistical Genetics and Methodology DOI: 10.3389/fgene.2022.1065568.

2022

• Nickchi P, Karunarathna C, Graham J (2022). An exploration of linkage fine-mapping on sequences from case-control studies. Genetic Epidemiology, 47(1):1– 17. DOI: 10.1002/gepi.22502.
• Yu Y, Chen S, Jones SJ, Hoque R, Vishnyakova O, Brooks-Wilson A, McNeney B (2022) Penalized logistic regression analysis for genetic association studies of binary phenotypes Human Heredity DOI: 10.1159/000525650.
• Epasinghege Dona N and Graham J (2022). Datasets for a simulated family-based exome-sequencing study. Data in Brief 42: 108311. DOI: 10.1016/j.dib.2022.108311.

2021

• Gill E, Smith M, Gibson K, Morishita K, Lee A,, Falsafi R, Graham J, Foell D, Benseler S, Ross C, Luqmani R, Cabral D, Hancock R, Brown KL, the PedVas Initiative Investigators (2021). Different disease endotypes in phenotypically similar vasculitides affecting small-to-medium sized blood vessels. Frontiers in Immunology 12: 396.  DOI: 10.3389/fimmu.2021.638571
• Ratnasekera P and McNeney B (2021). Re-analysis of a genome-wide gene-by-environment interaction study of case-parent trios, adjusted for population stratification. Front. Genet. 11:600232. doi: 10.3389/fgene.2020.600232

2020

• Nieuwoudt C, Brooks-Wilson A and Graham J. SimRVsequences: an R package to simulate genetic sequence data for pedigrees. Bioinformatics, btz881, https://doi.org/10.1093/bioinformatics/btz881. 

2019

• CB Karunarathna and J Graham. perfectphyloR: An R package for reconstructing perfect phylogenies. BMC Bioinformatics 20, Article number: 729 (2019). DOI 10.1186/s12859-019-3313-4.
• Choi JC, Lu D, Beg MF, Graham J, and McNeney B for the Alzheimer's Disease Neuroimaging Initiative (2019). The Contribution Plot: Decomposition and Graphical Display of the RV Coefficient, with Application to Genetic and Brain Imaging Biomarkers of Alzheimer's Disease. Human Heredity, https://doi.org/10.1159/000501334.
• K Gibson, K Morishita, P Dancey, P Moorehead, B Drögemöller, X Xhan, J Graham, B Hancock, D Foell, S Benseler, R Luqmani, R Yeung, S Shenoi, M Bohm, A Rosenberg, C Ross, D Cabral, K Brown. Identification of novel Adenosine Deaminase 2 gene variants and varied clinical phenotype in pediatric vasculitis. Arthritis & Rheumatology  71: 1747-1755 DOI 10.1002/art.40913

2018

• Brown KL, Lubieniecki JM, Armaroli G, Kessel K, Gibson K, Graham J, Liu D, Hancock REW, Ross C, Benseler SM, Luqmani R, Cabral DA, Foell D and Kessel C on behalf of the ARChiVe Investigators Network within the PedVas Initiative (2018). S100A12 serum levels and PMN counts are elevated in childhood systemic vasculitides especially involving proteinase 3 specific anti-neutrophil cytoplasmic antibodies. Frontiers in Pediatrics, 23 November 2018, https://doi.org/10.3389/fped.2018.00341
• C Nieuwoudt, SJ Jones, A Brooks-Wilson, J Graham (2018). Simulating pedigrees ascertained for multiple disease-affected relatives. Source Code for Biology and Medicine, 13:2. https://doi.org/10.1186/s13029-018-0069-6
• Graham J, McNeney B, Platt RW (2018). Small sample methods. In N. Breslow, O. Borgan, N. Chatterjee, M. H. Gail, A. Scott, and C. J. Wild, editors, Handbook of Statistical Methods for Case-Control Studies, Chapman & Hall/CRC Handbooks of Modern Statistical Methods, chapter 9, pages 134–162. Chapman & Hall/CRC Press, Boca Raton, Florida.
• Liu D, Graham J (2018). Simple measures of individual cluster-membership certainty for hard-partitional clustering.  The American Statistician DOI https://doi.org/10.1080/00031305.2018.1459315. Published online June 5, 2018.
  
• Karanurathna C, Graham J (2018).  Using gene genealogies to localize rare variants associated with complex traits in diploid populations. Hum Hered 2017–18;83:30–39. DOI https://doi.org/10.1159/000486854. Published online May 15, 2018.

2017

• Szefer E, Lu D, Nathoo FS, Beg MF, Graham J for the Alzheimer's Disease Neuroimaging Initiative. Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation. Statistical Applications in Genetics and Molecular Biology. 16: 349-366. DOI: https://doi.org/10.1515/sagmb-2016-0077
• Jones SJ, Voong J, Thomas R, English A, Schuetz J, Slack GW, Graham J, Connors JM and Brooks-Wilson A. Non-random occurrence of lymphoid cancer types in 140 families. Leukemia and Lymphoma 57(9):2134-2143. DOI: 10.1080/10428194.2017.1281412

2016

• Greenlaw K, Szefer E, Graham J, Lesperance ML, Nathoo FS (2017). A Bayesian group sparse multi-task regression model for imaging genetics. Bioinformatics, DOI: 10.1093/bioinformatics/btx215.
• Burkett KM, McNeney B and Graham J. sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data. Bioinformatics 2016;  doi: 10.1093/bioinformatics/btv763.  Published online January 2016. Published online January 2016.

2014

• Burkett KM, McNeney B, Graham J and Greenwood CMT. Using gene genealogies to detect rare variants associated with complex traits. Hum Hered 2014;78:117-130, DOI: 10.1159/000363443. Published online Aug. 15, 2014.
• Bull SB, Graham J and Greenwood CMT. Statistical Genetic Modeling and Analysis of Complex Traits. In JF Lawless ed. Statistics in Action: A Canadian Perspective. Chapman & Hall/CRC 2014, 125-146, URL: http://ssc.ca/en/statistics-in-action.
• Shin J-H, Infante-Rivard C, McNeney B and Graham J. A data-smoothing approach to explore and test gene-environment interaction in case-parent trios. Statistical Applications in Genetics and Molecular Biology. Volume 13, Issue 2, Pages 159–171, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: 10.1515/sagmb-2013-0023, January 2014

2013

• Burkett KM, Greenwood CMT, McNeney B and Graham J. Gene genealogies for genetic association mapping, with application to Crohn's disease.  Frontiers in Statistical Genetics and Methodology  4:260. doi: 10.3389/fgene.2013.00260, November 2013.
  
• Lubieniecka JM, Graham J, Heffner D, Mottus R, Reid R, Hogge D, Grigliatti TA and Riggs WK. A discovery study of daunorubicin induced cardiotoxicity in a sample of acute myeloid leukemia patients prioritizes P450 oxidoreductase polymorphisms as a potential risk factor. Frontiers in in Pharmacogenetics and Pharmacogenomics. 4:231. doi: 10.3389/fgene.2013.00231, November 2013.
  
• Burkett K, 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. Volume 12, Issue 5, Pages 559–581, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: 10.1515/sagmb-2012-0011, August 2013.
• Yazdanpanah M, Chen C, Graham J. Secondary analysis of publicly-available data reveals superoxide and oxygen radical pathways are enriched for associations between type 2 diabetes and low-frequency variants. Annals of Human Genetics. Volumne 77, Issue 6, pages 472-481. 14 AUG 2013 | DOI: 10.1111/ahg.12035
  
• JM Lubieniecka, J Liu, J Graham, D Heffner,R Reid, D Hogge, WK Riggs and TA Grigliatti. Single nucleotide polymorphisms in reductase genes are not associated with response to daunorubicin based remission induction. Cancer Epidemiology Biomarkers and Prevention, 22:1918-1920. October 2013. doi: 10.1158/1055-9965.EPI-13-0671
• Burkett K, McNeney B, Graham J. A Markov-chain Monte Carlo sampler for gene genealogies conditional on haplotype data. In Y.P. Chaubey ed. Some Recent Advances in Mathematics and Statistics, Proceedings of Statistics 2011 Canada/IMST 2011-FIM XX, Montreal, July 2011. Singapore: World Scientific 2013, 29-44. [PDF].
• Nembot-Simo A, Graham J and McNeney B. CrypticIBDcheck: An R package for checking relatedness in nominally unrelated subjects. Source Code for Biology and Medicine  2013, 8:5. doi:10.1186/1751-0473-8-5
  

2012

• Lubieniecka JM, Liu J, Graham J, Reid R, Hogge D, Grigliatti TA, Riggs WK,. Non-synonymous single nucleotide polymorphisms (nsSNPs) in aldo-keto and carbonyl reductase genes are not associated with acute cardiotoxicity after daunorubicin based chemotherapy.  Cancer Epidemiology, Biomarkers & Prevention November 2012 21:2118-2120 doi:10.1158/1055-9965.EPI-12-1037 .
• Gyllenberg A, Asad S, Piehl F, Swanberg M, Padyukov L, Van Yserloo B, Rutledge EA, McNeney B, Graham J, Orho-Melander M, Lindholm E, Graff C, Forsell C, Åkesson K, Landin-Olsson M, Carlsson A, Lindblad B, Forsander G, Ludvigsson J, Marcus C, Ivarsson S, Lernmark A, Alfredsson L, Åkesson K, Olsson T, Kockum I. Age dependent variation of genotypes in Major Histocompatibility Complex Class II Transactivator in controls and association to type 1 diabetes. Genes and Immunity October 2012 13: 632-640 doi:10.1038/gene.2012.44.
• Schuetz JM, Daley D, Graham J, Berry BR, Gallagher RP, Connors JM, Gascoyne RD, Spinelli JJ, Brooks-Wilson AR. Genetic variation in cell death genes and risk of non-Hodgkin lymphoma. PLoS ONE 2012 7(2): e31560. doi:10.1371/journal.pone.0031560
• Shin J-H, Infante-Rivard C, Graham J and McNeney B. Adjusting for spurious gene-by-environment interaction using case-parent triads. Statistical Applications in Genetics and Molecular Biology 2012, Volume 11, Issue 2, Pages 1–21. DOI: 10.2202/1544-6115.1714

2011

• C Qu, JM Schuetz, JE Min, S Leach, D Daley, JJ Spinelli, A Brooks-Wilson and J Graham. Cost-effective prediction of gender-labeling errors and estimation of gender-labeling error rates in candidate-gene association studies. Frontiers in Statistical Genetics and Methodology. 2011 2:31. doi: 10.3389/fgene.2011.00031.
• Min JE, Whiteside M, Brinkman F, McNeney B and Graham J. A statistical approach to high-throughput screening of predicted orthologs. Computational Statistics and Data Analysis 2011 55:935-943. doi:10.1016/j.csda.2010.08.002.

2010

• Shin J-H, McNeney B and Graham J. On the use of allelic transmission rates for assessing gene-by-environment interaction in case-parent trios. Annals of Human Genetics 2010 Sep 1;74(5):439-51. PubMed ID: 20649530
• Saferali A, Grundberg E, Berlivet S, Beauchemin H, Morcos L, Polychronakos C, Pastinen T, Graham J, McNeney B and Naumova AK. Cell culture-induced aberrant methylation of the imprinted IG DMR in human lymphoblastoid cell lines. Epigenetics 2010 5(1):5-16. Abstract. PubMed ID: 20026906

2008

NB: In 2008-09, McNeney was on sabbatical leave and Graham was on parental leave.

• Wallace AM, Sandford AJ, English JC, Burkett KM, Li H, Finley RJ, Muller NL, Coxson HO, Pare PD, Abboud RT. Matrix metalloproteinase expression by human alveolar macrophages in relation to emphysema. COPD 2008. 5:13-23. PubMed ID: 18259971

2007

• Zamar D, McNeney B and Graham J. elrm: Software Implementing Exact-Like Inference for Logistic Regression Models. Journal of Statistical Software 2007, 21(3). Available at http://www.jstatsoft.org/v21/i03
• Shin J-H, Janer M, McNeney B, Blay S, Deutsch K, Sanjeevi CB, Kockum I, Lernmark Å and Graham J for the Swedish Childhood Diabetes Study Group and the Diabetes Incidence in Sweden Study Group. IA-2 autoantibodies in incident type I diabetes patients are associated with a polyadenylation signal polymorphism in GIMAP5. Genes and Immunity 2007 Sept;8(6):503–512. PubMed ID: 17641683
• Bekris LM, Shephard C, Janer M, Graham J, McNeney B, Shin J-H, Zarghami M, Griffith W, Farin F, Kavanagh TJ, Lernmark A. Glutamate cysteine ligase catalytic subunit promoter polymorphisms and associations with type 1 diabetes age-at-onset and GAD65 autoantibody Levels. Exp Clin Endocrinol Diabetes 2007 Apr;115(4):221-8. PubMed ID: 17479437
• Shin J-H, McNeney B, Graham J. Case-control inference of interaction between genetic and nongenetic risk factors under assumptions on their distribution. Statistical Applications in Genetics and Molecular Biology 2007 Apr; 6(1), Article 13. Available at: http://www.bepress.com/sagmb/vol6/iss1/art13
• Tanaka G, Sandford AJ, Burkett K, Connett JE, Anthonisen NR, Pare PD, He JQ. Tumour necrosis factor and lymphotoxin A polymorphisms and lung function in smokers. Eur Respir J 2007 Jan; 29(1):34-41. PubMed ID: 16971410

2006

• Gupta M, Graham J, McNeney B, Zarghami M, Landin-Olsson M, Hagopian WA, Palmer J, Lernmark Å and Sanjeevi CB. MHC class I chain-related gene-A is associated with IA2 and IAA but not GAD in Swedish type 1 diabetes mellitus Ann N Y Acad Sci 2006 Oct; 1079: 229–239. PubMed ID: 17130560
• Bergwitz C, Roslin NM, Tieder M, Loredo-Osti JC, Bastepe M, Abu-Zahra H, Frappier D, Burkett K, Carpenter TO, Anderson D, Garabédian M, Sermet I, Fujiwara TM, Morgan K, Tenenhouse HS, and Jüppner H. SLC34A3 mutations in patients with hereditary hypophosphatemic rickets with hypercalciuria predict a key role for the sodium-phosphate cotransporter NaPi-IIc in maintaining phosphate homeostasis. Am J Hum Genet 2006 Feb; 78(2): 179–192. PubMed ID: 16358214
• Shin J-H, Blay S, McNeney B, Graham J. LDheatmap: An R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. Journal of Statistical Software 2006, 16 Code Snippet 3. Available at www.jstatsoft.org/v16/c03
• Wallace AM, He JQ, Burkett KM, Ruan J, Connett JE, Anthonisen NR, Pare PD and Sandford AJ. Contribution of alpha- and beta-defensins to lung function decline and infection in smokers: an association study. Respir Res 2006 May 15;7:76. PubMed ID: 16700921
• Burkett K, Graham J and McNeney B. hapassoc: software for likelihood inference of trait associations with SNP haplotypes and other attributes. Journal of Statistical Software 2006, 16(2). Available at www.jstatsoft.org/v16/i02
• He JQ, Burkett K, Connett JE, Anthonisen NR, Pare PD, Sandford AJ. Interferon gamma polymorphisms and their interaction with smoking are associated with lung function. Hum Genet 2006 May;119(4):365-375. PubMed ID: 16474934

2004 and 2005

• Burkett KM, Ghadessi M, McNeney B, Graham J, Daley D. A comparison of five methods for selecting tagging single-nucleotide polymorphisms. BMC Genet 2005 Dec 30;6 Suppl 1:S71. PubMed ID: 16451685
• Valdes AM, Thomson G, Graham J, Zarghami M, McNeney B, Kockum I, Smith A, Lathrop M, Steenkiste AR, Dorman JS, Noble JA, Hansen JA, Pugliese A, Lernmark A; Swedish Childhood Study Group; Diabetes Incidence in Sweden Study Group; Type 1 Diabetes Component of the 13th International Histocompatibility Working Group. D6S265*15 marks a DRB1*15, DQB1*0602 haplotype associated with attenuated protection from type 1 diabetes mellitus. Diabetologia 2005 Dec;48(12):2540-3. PubMed ID: 16320082
• Daley D and Burkett K. Approaches to the study of inflammatory gene haplotypes and susceptibility to cardiac, vascular and pulmonary diseases. Curr Opin Mol Ther 2005 Jun;7(3):226-33. PubMed ID: 15977419
• Graham J, McNeney B, Seillier-Moiseiwitsch F. Stepwise detection of recombination breakpoints in sequence alignments. Bioinformatics 2005 Mar 1;21(5):589-95. PubMed ID: 15388518
• Burkett K, McNeney B, Graham J. A note on inference of trait associations with SNP haplotypes and other attributes in generalized linear models. Hum Hered 2004;57(4):200-6. PubMed ID: 15583426
• Tebbutt SJ, He JQ, Burkett KM , Ruan J, Opushnyev IV, Tripp BW, Zeznik JA, Abara CO, Nelson CC, Walley KR. Microarray genotyping resource to determine population stratification in genetic association studies of complex disease. Biotechniques 2004; 37(6):977-85.PMID: 15597547

Posters

Our poster presentations can be found here.