Research Topics
Species | Alun ThomasSummaryAffiliation: University of Utah Country: USA Publications
Research Grants
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Detail Information
Publications
Case-control association testing by graphical modeling for the Genetic Analysis Workshop 17 mini-exome sequence dataHaley J Abel
Division of Genetic Epidemiology, University of Utah, 391 Chipeta Way, Salt Lake City, UT 84105, USA
BMC Proc 5:S62. 2011..We found that our approach was able to describe the relationships between the outcomes and covariates and that it could correctly detect associations of disease with several loci and with a reasonable false-positive detection rate...- Graphical modeling of the joint distribution of alleles at associated lociAlun Thomas
Department of Medical Informatics, University of Utah, Salt Lake City, UT 84108, USA
Am J Hum Genet 74:1088-101. 2004..Graphical models provide more flexibility to express these features of the joint distribution of alleles than do monotonic functions connecting physical and genetic maps... 
Towards linkage analysis with markers in linkage disequilibrium by graphical modellingAlun Thomas
Department of Biomedical Informatics, Genetic Epidemiology, University of Utah, Salt Lake City, Utah 84108, USA
Hum Hered 64:16-26. 2007..We conclude with a discussion of how this still experimental approach might be further developed...- GMCheck: Bayesian error checking for pedigree genotypes and phenotypesAlun Thomas
Department of Medical Informatics and Center for High Performance Computing, University of Utah 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA
Bioinformatics 21:3187-8. 2005..GMCheck uses graphical modeling to find the posterior probabilities of data errors given genotypes or phenotypes in a specified pedigree structure... - Characterizing allelic associations from unphased diploid data by graphical modelingAlun Thomas
Department of Medical Informatics and Center for High Performance Computing, University of Utah, Salt Lake City, Utah 84108, USA
Genet Epidemiol 29:23-35. 2005..The graphical model approach is shown to have some advantages in terms of tractability and can be used to select informative subsets of loci and to map loci influencing phenotypes... - The conditional independences between variables derived from two independent identically distributed Markov random fields when pairwise order is ignoredAlun Thomas
Genetic Epidemiology, University of Utah, Salt Lake City, UT 84108, USA
Math Med Biol 27:283-8. 2010..It explains why, in terms of the conditional independence structure, it sometimes does not matter whether you consider haplotypes or genotypes... - Shared genomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assaysA Thomas
Department of Biomedical Informatics, University of Utah, 391 Chipeta Way, Salt Lake City, UT 84108, USA
Ann Hum Genet 72:279-87. 2008.... - Assessment of SNP streak statistics using gene drop simulation with linkage disequilibriumAlun Thomas
Department of Biomedical Informatics, University of Utah, USA
Genet Epidemiol 34:119-24. 2010..This is illustrated by reanalysis of a previously reported linkage of prostate cancer to chromosome 1p23... - Simulating realistic zero loop pedigrees using a bipartite Prufer code and graphical modellingAlun Thomas
Department of Medical Informatics and Center for High Performance Computing, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA
Math Med Biol 21:335-45. 2004..Summary statistics from pedigrees generated in this way can be used to check real pedigrees for anomalies due to biased sampling or phenotypic effects on the pedigree structure... - A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulationAlun Thomas
Department of Biomedical Informatics, Division of Genetic Epidemiology, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA
Bioinformatics 25:1287-92. 2009..Efficient models for genetic linkage disequilibrium (LD) are needed to enable appropriate statistical analysis of the dense, genome-wide single nucleotide polymorphism assays currently available... - Effect of linkage disequilibrium on the identification of functional variantsAlun Thomas
Division of Genetic Epidemiology, University of Utah, Salt Lake City, UT 84108, USA
Genet Epidemiol 35:S115-9. 2011..The second unexpected result was that applying principal components analysis to genome-wide genotype data can apparently control not only for population structure but also for linkage disequilibrium... - Accelerated gene counting for haplotype frequency estimationAlun Thomas
Department of Medical Informatics and the Center for High Performance Computing, University of Utah, 391 Chipeta Way, Suite D, Salt Lake City, UT 84108, USA
Ann Hum Genet 67:608-12. 2003..The method is illustrated by haplotype frequency estimation from a sample of 45 individuals genotyped at 26 single nucleotide polymorphisms in the PIK3R1 gene... - GCHap: fast MLEs for haplotype frequencies by gene countingAlun Thomas
Department of Medical Informatics and Center for High Performance Computing, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA
Bioinformatics 19:2002-3. 2003..AVAILABILITY: The Java classes and Javadocs pages for GCHap can be obtained from bioinformatics.med.utah.edu/~alun.. - Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene countingAlun Thomas
Department of Medical Informatics, University of Utah, 391 Chipeta Way, Suite D, Salt Lake City, 84108, USA
Bioinformatics 22:771-2. 2006..AVAILABILITY: The Java classes and Javadocs pages for \mathsf\hbox GeneCountAlleles can be obtained from bioinformatics.med.utah.edu/~alun, which also has more information on its use and file formats... - Replication of the 10q11 and Xp11 prostate cancer risk variants: results from a Utah pedigree-based studyNicola J Camp
Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
Cancer Epidemiol Biomarkers Prev 18:1290-4. 2009..We also nominally replicated the association of prostate cancer with rs5945619 (Xp11). In particular, it seems that the susceptibility locus at 10q11 maybe involved in familial, early-onset disease... - Haplotype association analyses in resources of mixed structure using Monte Carlo testingRyan Abo
Department of Biomedical Informatics, University of Utah, Salt Lake City, USA
BMC Bioinformatics 11:592. 2010..Both traditional association statistics and transmission/disequilibrium statistics can be performed. The method includes a phasing algorithm that can be used in large pedigrees and optional use of pseudocontrols... - Estimating the parameters of a model for protein-protein interaction graphsVikrant Deshmukh
Department of Biomedical Informatics, University of Utah, 26 South 2000 East, Room 5775, Salt Lake City, UT 84112 5750, USA
Math Med Biol 23:279-95. 2006..Characterization of this model lays the foundation for its use as a prior distribution in a Bayesian analysis of yeast two-hybrid networks that can potentially aid in identifying false-positive and false-negative results... 
A unique genome-wide association analysis in extended Utah high-risk pedigrees identifies a novel melanoma risk variant on chromosome arm 10qCraig Teerlink
Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
Hum Genet 131:77-85. 2012..Our approach illustrates an example of using high-risk pedigrees for the identification of new melanoma predisposition variants...- A multivariate time series approach to modeling and forecasting demand in the emergency departmentSpencer S Jones
Department of Biomedical Informatics, University of Utah, Health Sciences Education Building, 26 S 2000 E, Salt Lake City, UT 84112 5750, USA
J Biomed Inform 42:123-39. 2009..The goals of this investigation were to study the temporal relationships between the demands for key resources in the emergency department (ED) and the inpatient hospital, and to develop multivariate forecasting models... - Characterization of linkage disequilibrium structure, mutation history, and tagging SNPs, and their use in association analyses: ELAC2 and familial early-onset prostate cancerNicola J Camp
Genetic Epidemiology Division, Department of Medical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA
Genet Epidemiol 28:232-43. 2005.... - A chromosome 16 quantitative trait locus regulates allogeneic bone marrow engraftment in nonmyeloablated miceThai M Cao
Department of Medicine, University of Utah, Salt Lake City, UT 84132, USA
Blood 114:202-10. 2009..K strain, that are permissive for allogeneic BM engraftment. Further identification of Bmgr5 genes by positional cloning may reveal new and effective approaches for overcoming BM engraftment obstacles... - Identification of regions of positive selection using Shared Genomic Segment analysisZheng Cai
Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
Eur J Hum Genet 19:667-71. 2011..Others are suggested to be novel regions. Our finding illustrates the utility of SGS as a method for identifying regions of selection, and some of these regions have been proposed to be candidate regions for harboring disease genes... - Automated construction and testing of multi-locus gene-gene associationsRyan Abo
Department of Biomedical Informatics, University of Utah School of Medicine, UT, USA
Bioinformatics 27:134-6. 2011..This tool provides a flexible data-mining approach to identifying gene-gene effects that otherwise is currently unavailable. AVAILABILITY: http://bioinformatics.med.utah.edu/Genie/hapConstructor.html... - Evidence for linkage on chromosome 3q25-27 in a large autism extended pedigreeHilary Coon
Neurodevelopmental Genetics Project, Department of Psychiatry, University of Utah, Salt Lake City, Utah 84108, USA
Hum Hered 60:220-6. 2005..No variants likely to contribute to autism were found in the coding sequence, exon-intron boundaries, or the promoter region of this gene... - Accuracy and computational efficiency of a graphical modeling approach to linkage disequilibrium estimationHaley J Abel
University of Utah, Utah, USA
Stat Appl Genet Mol Biol 10:Article 5. 2011..While the times for fitting and imputation are both O(nm), the imputation process is considerably faster; thus, once a model is estimated from a reference data set, the marginal cost of phasing and imputing further samples is very low... - A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial diseaseTobias Rausch
Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
Comput Biol Med 38:826-36. 2008..In particular, the correlation analysis of IBD expression patterns might hint to possible gene-gene interactions and the filtering might be a fruitful approach to distinguish true correlation signals from noise... - Shared genomic segment analysis: the power to find rare disease variantsStacey Knight
Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA Heart Institute, Intermountain Medical Center, Murray, UT, USA Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
Ann Hum Genet 76:500-9. 2012..96 Mb region containing the known causal APC gene with genome-wide significance. SGS is a powerful method for detecting rare variants and a valuable complement to genome-wide association studies and linkage analysis... - Evaluation of record linkage between a large healthcare provider and the Utah Population DatabaseScott L DuVall
VA Salt Lake City Health Care System, Salt Lake City, Utah, USA
J Am Med Inform Assoc 19:e54-9. 2012..Innovative approaches for creating research infrastructure beyond a traditional data system are necessary... - Pairwise shared genomic segment analysis in high-risk pedigrees: application to Genetic Analysis Workshop 17 exome-sequencing SNP dataZheng Cai
Department of Biomedical Informatics, University of Utah, 391 Chipeta Way, Salt Lake City, UT 84108, USA
BMC Proc 5:S9. 2011..7 false positives were identified per pedigree. In conclusion, we have demonstrated the potential of our new pSGS method for localizing rare disease causal variants in common disease using high-risk pedigrees and exome sequence data... - Forecasting daily patient volumes in the emergency departmentSpencer S Jones
Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
Acad Emerg Med 15:159-70. 2008..There are few studies that explore the use of forecasting methods to predict patient volumes in the ED... - Detecting pleiotropy and epistasis using variance components linkage analysis in jPAPSandra J Hasstedt
Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
Hum Hered 72:258-63. 2011..The inclusion of multiple quantitative trait loci in linkage analysis allows the inference of epistasis between loci. A user-friendly graphical user interface facilitates the usage of jPAP... - The impact of a growing minority population on identification of duplicate records in an enterprise data warehouseScott L DuVall
Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
Stud Health Technol Inform 160:1122-6. 2010.... - Population-based risk assessment for other cancers in relatives of hereditary prostate cancer (HPC) casesLisa A Cannon Albright
Department of Medical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA
Prostate 64:347-55. 2005.... - Extending the Fellegi-Sunter probabilistic record linkage method for approximate field comparatorsScott L DuVall
Department of Biomedical Informatics, University of Utah, Utah, USA
J Biomed Inform 43:24-30. 2010..Given the ubiquity of linkage in both clinical and research settings, the incremental improvement of the extension has the potential to make a considerable impact... - Identification of a major susceptibility locus for lethal graft-versus-host disease in MHC-matched miceThai M Cao
Department of Medicine, University of Utah School of Medicine, Salt Lake City, 84132, USA
J Immunol 183:462-9. 2009..Further identification of Gvh genes by positional cloning may yield new insight into genetic control mechanisms regulating GVHD and potentially reveal novel approaches for effective GVHD therapy... - Analysis of high-density single-nucleotide polymorphism data: three novel methods that control for linkage disequilibrium between markers in a linkage analysisKristina Allen Brady
Department of Biomedical Informatics, University of Utah, 391 Chipeta Way, Suite D, Salt Lake City, Utah 84108, USA
BMC Proc 1:S160. 2007..Additional work is required to further understand the effects of LD on linkage results and explore LD control methodology... - Extracting disease risk profiles from expression data for linkage analysis: application to prostate cancerG Bryce Christensen
Department of Biomedical Informatics, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, Utah 84108 1266, USA
BMC Proc 1:S82. 2007..Our results do indicate there exists potential to augment our current knowledge about the relationships among genes associated with complex diseases using expression data... - Enumeration and simulation of marriage node graphs on zero-loop pedigreesAlun Thomas
Department of Medical Informatics and Center for High Performance Computing, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA
Math Med Biol 20:261-75. 2003..The enumeration method leads naturally to a scheme for simulating from a uniform distribution on such pedigrees. This is extended to simulating pedigrees for which the underlying marriage node graph is a tree of any particular size... - Use of strain typing data to estimate bacterial transmission rates in healthcare settingsBrian R Jackson
Department of Medical Informatics, University of Utah, Salt Lake City, Utah, USA
Infect Control Hosp Epidemiol 26:638-45. 2005..A modest level of surveillance sampling substantially improves the estimation accuracy... - Pedigree association: assigning individual weights to pedigree members for genetic association analysisStacey Knight
Biomedical Informatics Department, University of Utah, 26 South 2000 East Room 5775 HSEB, Salt Lake City, Utah 84112, USA
BMC Proc 3:S121. 2009..We compare this new method with an existing weighting algorithm, a naïve analysis (relatedness is ignored), and an empirical method that appropriately accounts for all relationships (the gold standard)... - An application of the latent p value method to assess linkage in asthma pedigreesCraig C Teerlink
Department of Internal Medicine, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah 84108 1266, USA craig teerlink utah edu
Hum Hered 70:1-8. 2010..It is particularly applicable to genome-wide genetic linkage analysis for test statistics with poorly defined analytical distributions... - A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)Stephen A Goff
Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
Science 296:92-100. 2002..Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops... - Common polymorphism G(-248)A in the promoter region of the bax gene results in significantly shorter survival in patients with chronic lymphocytic Leukemia once treatment is initiatedJane Starczynski
Department of Haematology, Heartlands Hospital, Bordesley Green E, Birmingham, UK B91 1JR
J Clin Oncol 23:1514-21. 2005..This retrospective study assessed the clinical impact of a common single nucleotide polymorphism of the pro-apoptotic bax gene in patients with chronic lymphocytic leukemia... - Effect of linkage disequilibrium between markers in linkage and association analysesJosee Dupuis
Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA 02118, USA
Genet Epidemiol 31:S139-48. 2007.... - The P2X7 receptor gene polymorphism 1513 A-->C has no effect on clinical prognostic markers, in vitro sensitivity to fludarabine, Bcl-2 family protein expression or survival in B-cell chronic lymphocytic leukaemiaJane Starczynski
Department of Haematology, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, UK
Br J Haematol 123:66-71. 2003..These results indicate that the 1513 A-->C polymorphism of the P2X7 gene is unlikely to play a significant role in the pathogenesis or disease progression of B-CLL... - An analysis of unclassified missense substitutions in human BRCA1Sean V Tavtigian
International Agency for Research on Cancer, Lyon, France
Fam Cancer 5:77-88. 2006.... - Bryostatin induces protein kinase C modulation, Mcl-1 up-regulation and phosphorylation of Bcl-2 resulting in cellular differentiation and resistance to drug-induced apoptosis in B-cell chronic lymphocytic leukemia cellsAlun Thomas
Department of Haematology, Llandough Hospital, Penlan Road, Penarth, Vale of Glamorgan, CF64 2XX, UK
Leuk Lymphoma 45:997-1008. 2004....
Research Grants
- ASSOCIATION BETWEEN PHENOTYPES AND DISEQUALIBRIATE LOCIAlun Thomas; Fiscal Year: 2006..This proposal is to extend graphical modeling methods already developed by the investigators for haploid data to diploid data, larger genomic regions, admixed populations and family data. ..
- Graphical models for linkage disequilibrium in genetic mappingAlun Thomas; Fiscal Year: 2007..For this aim of the project we intend to apply the methods developed to dense genotype assays obtained for distantly related breast cancer cases in extended Utah pedigrees. ..
- Graphical models for linkage disequilibrium in genetic mappingAlun Thomas; Fiscal Year: 2009..For this aim of the project we intend to apply the methods developed to dense genotype assays obtained for distantly related breast cancer cases in extended Utah pedigrees. ..
- Graphical models for linkage disequilibrium in genetic mappingAlun Thomas; Fiscal Year: 2010..For this aim of the project we intend to apply the methods developed to dense genotype assays obtained for distantly related breast cancer cases in extended Utah pedigrees. ..