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JOURNAL CLUB

The Section on Statistical Genetics holds a monthly journal club meeting on the first Friday, of each month. Each month a faculty member, post-doctoral fellow, or a student is chosen to lead the discussion.This person selects an article related to statistical genetics usually pertaining to his or her area of expertise.

You are welcome to attend. Please see the information below.

The next meeting will be held
On: Friday, August 01, 2014
Time: 11:30 am -12:30 pm
Location: Learning Resources Center 114
Leaders: Dr. Michael Sandel
Topics to be discussed: The problem with haplogroup association studies: A call for mtDNA meta-analyses
Reference: The problem with haplogroup association studies: A call for mtDNA meta-analyses http://onlinelibrary.wiley.com/doi/10.1111/acel.12186/full
optional reading: http://www.biomedcentral.com/1471-2164/15/257/
http://link.springer.com/article/10.1007/s00439-013-1402-4

Journal club meetings are organized by Drs Degui Zhi and Xiang-Yang Lou.

Topics Discussed in Previous Meetings

  • 2014
  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • 2004
  • 2003
  • 2002
  • 2001

2014

No Journal Club meeting in July 2014 (Holiday)

June 6, 2014
Leaders: Dr. Hemant K. Tiwari
Topics to be discussed: The effectiveness of breakfast recommendation on weight loss: an RCT
Reference: Dhurandhar, E. J., J. Dawson, A. Alcorn, L. H. Larsen, E. A. Thomas, M. Cardel, A. C. Bourland, A. Astrup, M.-P. St-Onge, J. O. Hill, C. M. Apovian, J. M. Shikany and D. B. Allison (2014). The effectiveness of breakfast recommendations on weight loss: a randomized controlled trial. The American Journal of Clinical Nutrition. [doi:10.3945/ajcn.114.089573]

No Journal Club meeting in May 2014

April 4, 2014
Leaders: Dr. John Dawson
Topics to be discussed: Challenges and Issues in Analyzing Different Genomic and Proteomic Data
Reference:Not available

March 7, 2014
Leaders: Dr. Bertha A. Hidalgo
Topics to be discussed: Epigenome-wide Association Study of Fasting Measures of Glucose, Insulin, and HOMA-IR in GOLDN
Reference: Hidalgo, B., Irvin, M.R., Sha, J., Zhi, D., Aslibekyan, S., Absher, D., Tiwari, H.K., Kabagambe, E.K., Ordovas, J.M., and Arnett, D.K. (2014). Epigenome-Wide Association Study of Fasting Measures of Glucose, Insulin, and HOMA-IR in the Genetics of Lipid Lowering Drugs and Diet Network Study. Diabetes 63, 801-807. [doi: 10.2337/db13-1100]

February 7, 2014
Leaders: Dr. Tonia S. Schwartz
Topics to be discussed: The use of next generation sequencing in non-model organisms: New opportunities and challenges for addressing questions related to human health and food resources
Reference:

  1. Salem, M., et al., RNA-Seq identifies SNP markers for growth traits in rainbow trout. PLoS One, 2012. 7(5): p. e36264. [doi:10.1371/journal.pone.0036264]
  2. Ubaida Mohien, C., et al., A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Mol Cell Proteomics, 2013. 12(1): p. 120-31. [doi:10.1074/mcp.M112.019596]

No Journal Club meeting in January 2014

2013

December 6, 2013
Leaders:  Dr. Nengjun Yi
Topics to be discussed: Hierarchical Models for Genetic Association Studies
Reference: No specific references

November 1, 2013
Leaders:  Dr. Ana I. Vazquez
Topics to be discussed: Prediction of Cancer Risk & Cancer Outcomes
Reference: Vazquez, A.I., de los Campos, G., Klimentidis, Y.C., Rosa, G.J., Gianola, D., Yi, N., and Allison, D.B. (2012). A comprehensive genetic approach for improving prediction of skin cancer risk in humans. Genetics 192, 1493-1502. [doi: 10.1534/genetics.112.141705]

October 4, 2013
Leaders:  Mr. Guodong Wu (Mentor for this presentation: Dr. Degui Zhi)
Topics to be discussed: Subsampling and Permutation in Penalized Regression, and their application in GWAS
Reference:

  1. Alexander, D.H. and K. Lange, Stability Selection for Genome-Wide Association. Genetic Epidemiology, 2011. 35(7): p. 722-728. [doi: 10.1002/gepi.20623]
  2. Meinshausen, N. and P. Buhlmann, Stability selection. Journal of the Royal Statistical Society Series B-Statistical Methodology, 2010. 72: p. 417-473. [doi: 10.1111/j.1467-9868.2010.00740.x]

September 6, 2013
Leaders:  Dr. Tapan Shirish Mehta
Topics to be discussed: Mendelian Randomization
Reference:

  1. Sheehan, N.A., Didelez, V., Burton, P.R., and Tobin, M.D. (2008). Mendelian randomisation and causal inference in observational epidemiology. Plos Medicine 5, 1205-1210. [doi: 10.1371/journal.pmed.0050177]
  2. Burgess, S., Butterworth, A., Malarstig, A., and Thompson, S.G. (2012). Use of Mendelian randomisation to assess potential benefit of clinical intervention. BMJ 345, e7325.[doi: 10.1136/bmj.e7325]

August 2, 2013
Leaders:  Dr. Paulino Perez Rodriguez (Mentor: Dr. Gustavo A de los Campos)
Topics to be discussed: Prediction of genetic values using Neural Networks: Cases of study in plants and animals
Reference:

  1. Gonzalez-Camacho JM, de Los Campos G, Perez P, Gianola D, Cairns JE, Mahuku G, Babu R, Crossa J (2012) Genome-enabled prediction of genetic values using radial basis function neural networks. Theor Appl Genet 125:759-771 [doi: 10.1007/s00122-012-1868-9]
  2. Perez-Rodriguez P, Gianola D, Gonzalez-Camacho JM, Crossa J, Manes Y, Dreisigacker S (2012) Comparison between linear and non-parametric regression models for genome-enabled prediction in wheat. G3: Genes|Genomes|Genetics (Bethesda) 2:1595-1605 [doi: 10.1534/g3.112.003665]
  3. Perez-Rodriguez P, Gianola D, Weigel KA, Rosa GJ, Crossa J (2013) Technical Note: An R package for fitting Bayesian regularized neural networks with applications in animal breeding. J Anim Sci [doi: 10.2527/jas.2012-6162]

July 5, 2013
Leaders:  Dr. Jacqueline J Harris
Topics to be discussed: Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease
Reference: Zhang B, Gaiteri C, Bodea LG, Wang Z, McElwee J, Podtelezhnikov AA, Zhang C, et al. (2013) Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell 153:707-720. [doi:10.1016/j.cell.2013.03.030]

No Journal Club meeting in June 2013

May 3, 2013
Leader: Dr. John Dawson (Mentor for the presentation: Dr. David B. Allison)
Topics to be discussed: EBSeq: Setting, Theory, Implementation and an Application
Reference: Leng, N., Dawson, J. A., Thomson, J. A., et al. (2013). EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29, 1035-1043 [doi:10.1093/bioinformatics/btt087]

April 5, 2013
Leader:

  1. Dr. Xikui Wang
    Professor and Head,  Department of Statistics, University of Manitoba Winnipeg, Manitoba, Canada R3T 2N2
  2. Dr. Jianshe Yu
    President and Professor of Guangzhou University, China

Topics to be discussed: 

  1. Response adaptive design of clinical trials
  2. Periodic solutions of delay differential equations

March 01, 2013
Leader: Dr. Juan Diego Hernandez Jarquin (Mentor for the presentation: Dr. Gustavo A de los Campos)
Topic to be discussed: Introducing Highly Dimensional Genomic and Environmental Covariates Into Models for Prediction of Complex Traits

Abstract: Genome-enabled prediction (GEP) is becoming increasingly important in fields such as personalized medicine, plant and animal breeding. Because of genetic by environmental interaction (G×E) the effects of genes can change across environmental conditions; therefore, modeling G×E can enhance our ability to predict complex traits and diseases. Modern information systems allow capturing very detailed information about environmental conditions. This information can potentially be incorporated into GEP models. Due to the highly dimensional nature of the genetic and environmental information, modeling interactions between markers and environmental covariates (ECs) is challenging. And as of today we lack a well-established methodology to combine genomic and environmental information into models that account for all possible main effects and all possible interactions between molecular marker and ECs. Here, we propose an extension of the Genomic Best Linear Unbiased Predictor (GBLUP, a Ridge Regression-type predictor) that incorporates highly dimensional marker genotypes, highly dimensional environmental covariates (ECs) and all the interactions. Main effects and interactions are modeled using co-variance structures in a mixed effects context. These co-variance structures are functions of marker genotypes and of ECs. Interactions are modeled using a multiplicative mode of action. The proposed model was evaluated using data from Arvalis consisting of 139 wheat lines evaluated in 340 environments, in an incomplete field trial. A total of 2,395 SNPs and 68 ECs were available. Starting from a baseline model that accounts only for the main effects of lines and environments we build a sequence of models with various degrees of complexity. Estimates of variance components indicated that the main effects of markers, the main effects of ECs and the interactions between markers and ECs accounted for 22.6, 35.2 and 8.9 percent of the within-environment phenotypic variability. Relative to our baseline model the incorporation of molecular markers and of ECs, as well as their interactions increased the predictive correlation by roughly 20%, from a predictive correlation of 0.425 to a correlation of 0.513.

Reference:

  1. Makowsky, R., Pajewski, N.M., Klimentidis, Y.C., Vazquez, A.I., Duarte, C.W., Allison, D.B. and de los Campos, G. (2011) Beyond Missing Heritability: Prediction of Complex Traits, Plos Genetics, 7. [doi:10.1371/journal.pgen.1002051]
  2. VanRaden, P.M. (2008) Efficient Methods to Compute Genomic Predictions, J Dairy Sci, 91, 4414-4423. [doi:10.3168/jds.2007-0980]
  3. Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Madden, P.A., Heath, A.C., Martin, N.G., Montgomery, G.W., Goddard, M.E. and Visscher, P.M. (2010) Common SNPs explain a large proportion of the heritability for human height, Nat Genet, 42, 565-569. [doi:10.1038/ng.608]

February 01, 2013
Leader: Dr. Michael W. Sandel (Mentor for the presentation: Dr. Hermant Tiwari)
Topic to be discussed: What is a gene?
Reference:

  1. Lin, M., Eng, C., Hawk, E.T., Huang, M., Lin, J., Gu, J., Ellis, L.M. and Wu, X. (2012) Identification of polymorphisms in ultraconserved elements associated with clinical outcomes in locally advanced colorectal adenocarcinoma, Cancer, 118, 6188-6198. [doi:10.1002/cncr.27653]
  2. Ryu, T., Seridi, L. and Ravasi, T. (2012) The evolution of ultraconserved elements with different phylogenetic origins, BMC Evol Biol, 12, 236. [doi:10.1186/1471-2148-12-236]

No Journal Club meeting in January 2013




 

2012

December 07, 2012
Leader: Dr. Laura Kelly Vaughan
Topic to be discussed: Prospects for phylogeny-assisted genetic association of disease risk and prognosis
Reference:

  1. Djebali, S., C. A. Davis, et al. (2012). Landscape of transcription in human cells. Nature 489(7414): 101-8. [doi:10.1038/nature11233]
  2. Harrow, J., A. Frankish, et al. (2012). GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research 22(9): 1760-74 [doi:10.1101/gr.135350.111]
  3. Web resources (please also use the link below to go to the Nature ENCODE portal and follow thread #3 to read the pertinent parts of the recent ENCODE papers): http://www.nature.com/encode/#/threads/characterization-of-intergenic-regions-and-gene-definition

November 02, 2012
Leader: Dr. Richard Kennedy
Topic to be discussed: Voxelwise genome-wide association study (vGWAS)
Reference: Stein JL, Hua X, Lee S, Ho AJ, Leow AD, Toga AW, Saykin AJ, Shen L, Foroud T, Pankratz N and others. 2010. Voxelwise genome-wide association study (vGWAS). Neuroimage 53(3):1160-1174. [doi:10.1016/j.neuroimage.2010.02.032]

October 04, 2012
Leader: Dr. Bertha Hidalgo (Mentor for the presentation: Dr. Hemant Tiwari)
Topic to be discussed: An integrated encyclopedia of DNA elements in the human genome
Reference: Bernstein, B.E., et al., An integrated encyclopedia of DNA elements in the human genome. Nature, 2012. 489(7414): p. 57-74. [doi: 10.1038/nature11247]

September 06, 2012
Leader: Dr. Bertha Hidalgo (Mentor for the presentation: Dr. Hemant Tiwari)
Topic to be discussed: Disease Mapping with population structure
Reference:

  1. Population Structure of Hispanics in the United States: The Multi-Ethnic Study of Atherosclerosis. [doi:10.1371/journal.pgen.1002640]
  2. New approaches to disease mapping in admixed populations [doi:10.1038/nrg3002]
  3. Methods for Detecting and Correcting for Population Stratification [doi:10.1002/0471142905.hg0122s73]

August 02, 2012
Leader: Dr. Jun Li (Mentor for the presentation: Dr. Nengjun Yi)
Topic to be discussed: A general framework for detecting disease associations with rare variants in sequencing studies
Reference: Lin, D.Y., and Tang, Z.Z. (2011). A General Framework for Detecting Disease Associations with Rare Variants in Sequencing Studies. Am J Hum Genet 89, 354-367. [doi: 10.1016/j.ajhg.2011.07.015]

July 5, 2012
Leader: Mr. Peng Li (Mentor for the presentation: Dr. Nianjun Liu)
Topic to be discussed: Rare-variant association testing for sequencing data with the sequence kernel association test
Reference: Wu, M.C., Lee, S., Cai, T.X., Li, Y., Boehnke, M., and Lin, X.H. (2011). Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test. Am J Hum Genet 89, 82-93.[doi:10.1016/j.ajhg.2011.05.029]

June 7, 2012
Leader: Dr. Gustavo de los Campos
Topic to be discussed: Genetic Architecture of Complex Traits: Understanding and Using Additive Genetic Variability
Reference: Hill WG, Goddard ME, Visscher PM. 2008. Data and theory point to mainly additive genetic variance for complex traits. Plos Genetics 4(2). [doi:10.1371/journal.pgen.1000008]

May 3, 2012
Leader: Mr. Guodong Wu (Mentor for the presentation: Dr. Degui Zhi)
Topic to be discussed: Pathway analysis for GWAS
Reference:

  1. Eleftherohorinou H, Hoggart CJ, Wright VJ, Levin M, Coin LJM. 2011. Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways. Human Molecular Genetics 20(17):3494-3506. [doi:10.1093/hmg/ddr248]
  2. Wang K, Li MY, Bucan M. 2007. Pathway-based approaches for analysis of genomewide association studies. American Journal of Human Genetics 81(6):1278-1283. [doi:10.1086/522374]
  3. Wang K, Li MY, Hakonarson H. 2010. Analysing biological pathways in genome-wide association studies. Nature Reviews Genetics 11(12):843-854. [doi:10.1038/nrg2884]

April 5, 2012
Leader: Dr. Curtis Holliman (Mentors for the presentation: Drs. Hemant Tiwari and Degui Zhi)
Topic to be discussed: RNA-seq data analysis
Reference:

  1. Li, H., Lovci, M.T., Kwon, Y.S., Rosenfeld, M.G., Fu, X.D., and Yeo, G.W. (2008). Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model. Proceedings of the National Academy of Sciences of the United States of America 105, 20179-20184. [doi:10.1073/pnas.0807121105]
  2. Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. [doi:10.1093/bioinformatics/btp616]
  3. Robinson, M.D., and Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11. [doi:10.1186/gb-2010-11-3-r25]
  4. Young, M.D., Wakefield, M.J., Smyth, G.K., and Oshlack, A. (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11. [doi:10.1186/gb-2010-11-2-r14]

March 1, 2012
Leader: Dr. Xiang-Yang Lou
Topic to be discussed: The future of family studies in finding genes underlying complex human diseases
Reference:

  1. Bowden DW, An SS, Palmer ND, Brown WM, Norris JM, Haffner SM, Hawkins GA, Guo XQ, Rotter JI, Chen YDI and others. 2010. Molecular basis of a linkage peak: exome sequencing and family-based analysis identify a rare genetic variant in the ADIPOQ gene in the IRAS Family Study. Human Molecular Genetics 19(20):4112-4120. [doi:10.1093/hmg/ddq327]
  2. Cirulli ET, Goldstein DB. 2010. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature Reviews Genetics 11(6):415-425. [doi:10.1038/nrg2779]
  3. Guo XQ, Saad MF, Langefeld CD, Williams AR, Cui JR, Taylor KD, Norris JM, Jinagouda S, Darwin CH, Mitchell BD and others. 2006. Genome-wide linkage of plasma adiponectin reveals a major locus on chromosome 3q distinct from the adiponectin structural gene - The IRAS family study. Diabetes 55(6):1723-1730. [doiI:10.2337/db05-0428]
  4. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A and others. 2009. Finding the missing heritability of complex diseases. Nature 461(7265):747-53. [doi:10.1038/nature08494]
  5. Ott J, Kamatani Y, Lathrop M. 2011. Family-based designs for genome-wide association studies. Nature Reviews Genetics 12(7):465-474. [doi:10.1038/nrg2989]

February 02, 2012
Leader: Dr. Samad Jahandideh (Mentor for the presentation: Dr. Degui Zhi)
Topic to be discussed: Machine Learning Prediction: Protein Active Sites or Medical Outcomes
Reference:

  1. Sankararaman, S., Sha, F., Kirsch, J.F., Jordan, M.I. and Sjolander, K. (2010) Active site prediction using evolutionary and structural information, Bioinformatics, 26, 617-624. [doi:10.1093/bioinformatics/btq008]
  2. Tu, J.V. (1996) Advantages and disadvantages of using artificial neural networks versus logistic regression for predicting medical outcomes, Journal of Clinical Epidemiology, 49, 1225-1231. [doi:10.1016/S0895-4356(96)00002-9]

No Journal Club meeting in January 2012

2011

No Journal Club meeting in December 2011

November 03, 2011
Leader: Dr. Henry Robertson (Mentor for the presentation: Dr. Gustavo de los Campos)
Topic to be discussed: Genetic Epidemiology of Diabetes
Reference: Heron, E.A., O'Dushlaine, C., Segurado, R., Gallagher, L., and Gill, M. (2011). Exploration of empirical Bayes hierarchical modeling for the analysis of genome-wide association study data. Biostatistics 12, 445-461. [doi: 10.1093/biostatistics/kxq072]

October 06, 2011
Leader: Ms. Celeste T. Yang (Mentor for the presentation: Dr. Xiangqin Cui)
Topic to be discussed: A multivariate test for similarity of two dissolution profiles
Reference: Saranadasa H, Krishnamoorthy K (2005) A multivariate test for similarity of two dissolution profiles. Journal of Biopharmaceutical Statistics 15:265-278. [doi: 10.1081/BIP-200049832]

September 01, 2011
Leader: Dr. Kui Zhang
Topic to be discussed: Hidden Markov Model for Haplotype Inference, Genotype Imputation, and Admixture Mapping
Reference:

  1. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes. Genet Epidemiol 34:816-834 [doi: 10.1002/gepi.20533]
  2. Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78:629-644 [doi:10.1086/502802]
  3. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S (2009) Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations. Plos Genetics 5:e1000519 [doi:10.1371/journal.pgen.1000519]

No Journal Club meeting in August 2011

July 07, 2011
Leader: Dr. Richard Reynolds
Topic to be discussed: Association screening of common and rare genetic variants by penalized regression
Reference: Hua Zhou, Mary E. Sehl, Janet S. Sinsheimer and Kenneth Lange. Association screening of common and rare genetic variants by penalized regression Bioinformatics. Vol. 26 no. 19 2010, 2375–2382 [doi:10.1093/bioinformatics/btq448]

June 02, 2011
Leader: Dr. Jacqueline Harris (Mentor for the presentation: Dr. Christine W. Duarte)
Topic to be discussed: Exploratory Structural Equation Modeling
Reference: Asparouhov, T., and Muthen, B. (2009). Exploratory Structural Equation Modeling. Struct. Equ. Modeling 16, 397-438. [doi: 10.1080/10705510903008204]

May 05, 2011
Leader: Drs. Kathryn Kaiser and Robert Makowsky (Mentor for the presentation of Dr. Kathryn Kaiser: David Allison)
Topic to be discussed: Meta-analyses: Methodological Considerations and an Example on Quantitative Measures of Genetic Variation
Reference:

  1. Bowden J, Tierney JF, Copas AJ, Burdett S (2011) Quantifying, displaying and accounting for heterogeneity in the meta-analysis of RCTs using standard and generalised Q statistics. BMC Med Res Methodol 11: 41. [doi:10.1186/1471-2288-11-41]
  2. Reed DH, Frankham R (2001) How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 55: 1095-1103. [PMID: 11475045]
  3. Moher D, Liberati A, Tetzlaff J, Altman DG, Grp P (2009) Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement. Journal of Clinical Epidemiology 62: 1006-1012. [doi: 10.1016/j.jclinepi.2009.06.005]

 

April 7, 2011
Leader: Dr. Wan-Yu Lin (Mentor for the presentation: Dr. Nianjun Liu)
Topic to be discussed: Powerful multi-marker association tests: Unifying genomic distance-based regression and logistic regression.
Reference: Han, F. & Pan, W. (2010). Powerful multi-marker association tests: Unifying genomic distance-based regression and logistic regression. Genetic Epidemiology, 34: 680-688. [doi: 10.1002/gepi.20529]

March 03, 2011
Leader: Dr. Boshao Zhang (Mentor for the presentation: Dr. Nianjun Liu)
Topic to be discussed: Some interpretation issues of the risk estimates from Logistic regression and Cox proportional hazard with applications in genetic studies.
Reference:

  1. Case, L.D., Kimmick, G., Paskett, E.D., Lohman, K., and Tucker, R. (2002). Interpreting measures of treatment effect in cancer clinical trials. Oncologist 7, 181-187. [PMID: 12065789]
  2. Jakobsdottir, J., Gorin, M.B., Conley, Y.P., Ferrell, R.E., and Weeks, D.E. (2009). Interpretation of Genetic Association Studies: Markers with Replicated Highly Significant Odds Ratios May Be Poor Classifiers. Plos Genetics 5, e1000337. [doi:10.1371/journal.pgen.1000337]
  3. Spruance, S.L., Reid, J.E., Grace, M., and Samore, M. (2004). Hazard ratio in clinical trials. Antimicrobial Agents and Chemotherapy 48, 2787-2792. [doi: 10.1128/AAC.48.8.2787-2792.2004]
  4. Zhang, J., and Yu, K.F. (1998). What's the relative risk? A method of correcting the odds ratio in cohort studies of common outcomes. Jama-Journal of the American Medical Association 280, 1690-1691. [doi: 10.1001/jama.280.19.1690 ][PMID: 9832001]

February 03, 2011
Leader: Dr. Guo-Bo Chen (Mentor for the presentation: Dr. Xiang-Yang Lou)
Topic to be discussed: The Meaning of Interaction.
Reference: Wang X, Elston RC, Zhu X (2010) The Meaning of Interaction. Hum Hered 70: 269-277. [doi: 10.1159/000321967]

January 06, 2011
Leader: Dr. Ana Ines Vazquez (Mentor for the presentation: Dr. David B. Allison)
Topic to be discussed: Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins.
Reference: Vazquez AI, Rosa GJ, Weigel KA, de Los Campos G, Gianola D, et al. (2010) Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins. J Dairy Sci 93: 5942-5949. [doi: 10.3168/jds.2010-3335]

2010

December 02, 2010
Leader: Dr. Xiangqin Cui
Topic to be discussed: Comparing next generation sequencing and microarray in RNA expression quantification.
Reference:

  1. Marioni, J. C., C. E. Mason, et al. (2008). "RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays." Genome Research 18(9): 1509-1517. [doi:10.1101/gr.079558.108]
  2. t Hoen, P. A. C., Y. Ariyurek, et al. (2008). "Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms." Nucleic Acids Research 36(21): e141. [doi:10.1093/nar/gkn705]
  3. Willenbrock, H., J. Salomon, et al. (2009). "Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing." Rna-a Publication of the Rna Society 15(11): 2028-2034. [doi:10.1261/rna.1699809]

November 04, 2010
Leader: Dr. Jihua Wu (Mentor for the presentation: Dr. Kui Zhang)
Topic to be discussed: Statistical Methods in GWAS and Recommendations for Their Application.
Reference:
1. Cantor RM (2010) Prioritizing GWAS results: A review of statistical methods and recommendations for their application. American Journal of Human Genetics 86:6–22. [DOI 10.1016/j.ajhg.2009.11.017.]
2. oannidis JPA (2009) Validating, augmenting and refining genome-wide association signals. Nature Reviews Genetics 10:318–329. [doi:10.1038/nrg2544]

October 07, 2010
Leader: Dr. Gustavo de los Campos (Mentor for the presentation: Dr. David B. Allison)
Topic to be discussed: Semi-Parametric Prediction of Genetic Values Using Kernel-Based Methods. Abstract: Prediction of genetic values is a central problem in quantitative genetics and may become relevant for preventive and personalized human medicine. Family-based predictions have been used over many decades. More recently, marker-based prediction methods were developed. A standard approach consist of regressing phenotypes on marker covariates (e.g., SNPs) using a linear model. The linear model can account for additive effects and can be extended to accommodate genetic differences due to dominance. However, genetic predisposition may involve complex forms of epistatic interactions. In principle, the linear model can be extended to account for such interactions. However, when the number of available markers is large, including all possible interactions is feasible only to a very limited extent. An alternative is to use semi-parametric methods such as reproducing kernel Hilbert spaces regressions. In this presentation I will briefly review these methods, discuss their connection with methods commonly encountered in the statistical and machine learning literature (smoothing spline, kriging, support vector machine) and in quantitative genetics (pedigree-based regression) and illustrate the use of the methodology with an application to plant breeding data. References
Reference:

  1. Schaid DJ (2010) Genomic Similarity and Kernel Methods I: Advancements by Building on Mathematical and Statistical Foundations. Human Heredity 70:109–131. [doi: 10.1159/000312641]
  2. Schaid DJ (2010) Genomic Similarity and Kernel Methods II: Methods for Genomic Information. Human Heredity 70:132–140. [doi: 10.1159/000312643]
  3. de los Campos G (2010) Semi-parametric genomic-enabled prediction of genetic values using reproducing 5 kernel Hilbert spaces methods. Genetics Research (in press).

September 02, 2010
Leader: Dr. Degui Zhi
Topic to be discussed: Exome sequencing identifies the cause of a mendelian disorder.
Reference: Ng et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics, Vol. 42, No. 1, 30-35. [doi:10.1038/ng.499]

August 05, 2010
Leader: Dr. Robert Makowsky (Mentor for the presentation: Dr. T. Mark Beasley)
Topic to be discussed: Integration of Genetic, Clinical, and INR Data to Refine Warfarin Dosing.
Reference: Lenzini et al. (2010) Integration of Genetic, Clinical, and INR Data to Refine Warfarin Dosing. Clinical Pharmacology & Therapeutics, Vol. 87, No. 5, 572-578. [doi:10.1038/clpt.2010.13]

July 01, 2010
Leader: Dr. Kofi Placid Adragni (Mentors for the presentation: Drs. Hemant Tiwari and Nianjun Liu)
Topic to be discussed: Sufficient Dimension Reduction of SNPs datasets.
Reference:
1. Cook RD, Li L (2009) Dimension Reduction in Regressions With Exponential Family Predictors. Journal of Computational and Graphical Statistics Sept 2009, Vol. 18, No. 3, 774-791 [doi:10.1198/jcgs.2009.08005].
2. Leek JT, Storey JD (2007) Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis. PLoS Genet 3(9): e161. [doi:10.1371/journal.pgen.0030161].

June 03, 2010
Leader: Dr. Lekki Wood (Mentors for the presentation: Drs. Donna Arnett and David B. Allison)
Topic to be discussed: Whole genome approaches to quantitative genetics.
Reference: Visscher (2009) Whole genome approaches to quantitative genetics. Genetica 136: 351-358. [doi:10.1007/s10709-008-9301-7]

May 06, 2010
Leader: Mr. Tapan Mehta and Mr. Vinodh Srinivasasainagendra
Topic to be discussed: Increasing Reproducibility in Genomic Research.
Reference:
1.Ioannidis et al. (2009) Repeatability of published microarray gene expression analyses. Nature Genetics 41: 149-155. [doi:10.1038/ng.295]
2. Koenker & Zeileis (2007) Reproducible econometric research (A critical review of the state of the art). EPub at http://epub.wu-wien.ac.at.

April 01, 2010
Leader: Dr. Kirk Yancy Williams (Mentor for the presentation: Dr. Degui Zhi)
Topic to be discussed: Rare Variants Create Synthetic Genome-Wide Associations.
Reference: Dickson et al. (2010). Rare Variants Create Synthetic Genome-Wide Associations. PLoS Biology 8: e1000294 [doi:10.1371/journal.pbio.1000294]

March 04, 2010
Leader: Drs. Christine W. Duarte, Degui Zhi and Xiang-Yang Lou
Topic to be discussed: Application of Bayesian networks to genetic dissection and prognostic modeling for complex diseases.
Reference:
1. Ramoni et al. (2009) Predictive Genomics of Cardioembolic Stroke. Stroke 40: S67-S70. [doi: 10.1161/STROKEAHA.108.533273]
2. Sebastiani et al. (2005). Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia. Nature Genetics 37: 435–440. [doi:10.1038/ng1533]

February 04, 2010
Leader: Dr. Kirk Yancy Williams (Mentor for the presentation: Dr. David B. Allison)
Topic to be discussed: Analysis of 30 genes (355 SNPS) related to energy homeostasis for association with adiposity in European-American and Yup'ik Eskimo populations.
Reference: Chung et al. (2009) Analysis of 30 genes (355 SNPS) related to energy homeostasis for association with adiposity in European-American and Yup'ik Eskimo populations. Human Heredity 67: 193-205 [doi: 10.1159/000181158]

No Journal Club meeting in Jan 2010

2009

December 03, 2009
Leader: Dr. Xiang-Yang Lou
Topic to be discussed: A forest-based approach to identifying gene and gene-gene interactions
Reference: PNAS vol. 104 (2007 Dec): 19199-19203 [doi:10.1073/pnas.0709868104]

November 05, 2009
Leader: Dr. Richard Kennedy (Mentor for the presentation: Dr. Hemant Tiwari)
Topic to be discussed: Schafer et al. (2009) Integrated Analysis of Copy Number Alterations and Gene Expression: A Bivariate Assessment of Equally Directed Abnormalities. Bioinformatics Advance Access Published October 14, 2009 Xiang-Yang [PMID: 19828576]

October 01, 2009
Leader: Dr. Boshao Zhang (Mentor for the presentation: Dr. Nianjun Liu)
Topic to be discussed: Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip.
Reference:Spencer et al. (2009) Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip. PLoS Genet. 5(5): e1000477.

September 03, 2009
Leader: Dr. Guolian Kang (Mentor for the presentation: Dr. Guimin Gao)
Topic to be discussed: Robust genome-wide scans with genetic model selection using case-control design.
Reference:
1. Zheng et al. (2009) Robust genome-wide scans with genetic model selection using case-control design. Statistics and Its Interface. 2:145-151.
2. Zheng and Tony NG. (2008) Genetic model selection in two-phase analysis for case–control association studies. Biostatistics 9: 391-399.

There will be no journal club meeting in August. due to the JSM.

July 02, 2009
Leader: Dr. Degui Zhi
Topic to be discussed: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.
Reference: Brunner et al. (2009) Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19:1044-1056

June 04, 2009
Leader: Mr. Amit Patki
Topic to be discussed: Principal components analysis corrects for stratification in genome-wide association studies.
Reference: Price et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics 38:904-909

May 07, 2009
Leader: Dr. Yann Klimentidis (Mentor for the presentation: Dr. David Allison)
Topic to be discussed: Increased constraints on MC4R during primate and human evolution.
Reference: Hughes et al. (2009) Increased constraints on MC4R during primate and human Evolution. Hum Genet 124:633–647

March 05, 2009
Leader: Dr. Xiangqin Cui
Topic to be discussed: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.
Reference: Weber et al. (2007). Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457-466

February 05, 2009
Leader: Mr. Nathan E Wineinger (Mentor for the presentation: Hemant Tiwari)
Topic to be discussed: Extending genome-wide association studies to copy-number variation.
Reference: McCarroll S.A. (2008) Extending genome-wide association studies to copy-number variation. Human Molecular Genetics 17:R135-R142

2008

December 04, 2008
Leader: Dr. Laura Kelly Vaughan
Topic to be discussed: On the utility of gene set methods in genomewide association studies of quantitative traits.
Reference: Chasman D.I. On the utility of gene set methods in genomewide association studies of quantitative traits. Genet. Epidemiol. 2008 32: 658-668.

November 06, 2008
Leader: Dr. Richard Kennedy (Mentor for the presentation: Dr. Hemant Tiwari)
Topic to be discussed: A fast and flexible method for the segmentation of aCGH data.
Reference: Ben-Yaacov and Eldar. A fast and flexible method for the segmentation of aCGH data. Bioinformatics 2008 24: i139-i145.

October 02, 2008
Leader: Dr. Nicholas M. Pajewski (Mentor for the presentation: David Allison)
Topic to be discussed: Observational Associations: The p-value versus the Bayes Factor.
Reference:
1. Ioannidis, J.P. Effect of Formal Statistical Significance on the Credibility of Observed Associations.
Am. J. Epidemiology 2008 Aug 15;168(4):374-83
2. Katki, H.A. Evidence-based Evaluation of p Values and Bayes Factors (Discussion).
Am. J. Epidemiology 2008 Aug 15;168(4):384-88
3. Ioannidis, J.P. The Author Responds to "Evaluating p Values and Bayes Factors."
Am. J. Epidemiology 2008L Aug 15;168(4): 389-90.

September 4, 2008
Leader: Dr. Richard J. Reynolds (Mentor for the presentation: Nengjun Yi)
Topic to be discussed: An ensemble learning approach jointly modeling main and interaction effects in genetic association studies.
Reference: Zhang et al (2008) An ensemble learning approach jointly modeling main and interaction effects in genetic association studies. Genetic Epidemiology 32:285-300.

August 7, 2008
Leader: Dr. Nengjun Yi
Topic to be discussed: Least angle and l1 penalized regression: A review.
Reference:
1. Yi N, Xu S, (2008) Bayesian LASSO for quantitative trait loci mapping. Genetics 179: 1045-1055
2. Hesterberg et al. (2008) Least angle and l1 penalized regression: A review. Statistics Surveys 2: 61-93

June 5, 2008
Leader: Dr. Guolian kang (Mentor for the presentation: Guimin Gao)
Topic to be discussed: Genomewide Weighted Hypothesis Testing in Family-Based Association Studies, with an Application to a 100K Scan.
Reference: Ionita-Laza et al. (2007) Am J Hum Genet, 81: 607-614

May 1, 2008
Leader: Dr. Stephen Erickson (Mentor for the presentation: David Allison)
Topic to be discussed: Variations in DNA elucidate molecular networks that cause disease..
Reference: Chen et al.  Variations in DNA elucidate molecular networks that cause disease. Nature. 2008 27; 452(7186):429-35

April 3, 2008
Leader: Dr. Kui Zhang
Topic to be discussed: Two new multilocus methods for association mapping.
Reference: (1) Malo et al. (2008) Accommodating linkage disequilibrium in genetic-association analysis via ridge regression. Am. J. of Hum .Genet. 82:375-385.
(2) Kwee et al. (2008) A powerful and flexible multilocus association test for quantitative traits. Am. J. of Hum .Genet. 82: 386-397.

March 6, 2008
Leader: Dr. Mary Wojczynski
Topic to be discussed: Copy-number variation and association studies of human disease.
Reference: McCarroll & Altshuler (2007) Copy-number variation and association studies of human disease. Nature Genet. 39:S37-42

February 7, 2008
Leader: Dr. Daniel Shriner (Mentor for the presentation: Dr. Nengjun Yi
Topic to be discussed: What is a gene?
Reference: Gerstein et al. (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res. 17:669-681, GersteinSuppl.pdf

2007

December 6, 2007
Leader: Dr. Solomon K. Musani
Topic to be discussed: Identifying QTL by genetic background interactions in association studies.
Reference: Jannink (2007) Identifying QTL by genetic background interactions in association studies. Genetics 176: 553-561

November 1, 2007
Leader: Dr. Georgina Ankra-Badu(Mentor for the presentation: Dr. Nengjun Yi)
Topic to be discussed: The ubiquitous nature of Epistasis in determining susceptibility to common human diseases.
Reference:
1. Moore (2003) The ubiquitous nature of Epistasis in determining susceptibility to common human diseases. Hum Hered 56:73-82.
2. Moore (2005) A global view of epistasis. Nature Genetics 37: 13-14
3. Phillips (1998) The language of gene interaction. Genetics 149: 1167-1171

October 4, 2007
Leader: Dr. Douglas K. Childers (Mentor for the presentation: Dr. Kui Zhang)
Topic to be discussed: Pathway-based approaches for analysis of genome-wide association studies.
Reference: Wang et. al. (2007) Am J Hum Genet

September 6, 2007
Leader: Mr. William R Prucka (Mentor for the presentation: Dr. Christopher Coffey)
Topic to be discussed: Imaging Genomics: Mapping the influence of genetics on brain structure and function.
Reference: Glahn et. al. (2007) Human Brain Mapping 28:461-463; 488-501

August 2, 2007
Leader: Dr. David Redden
Topic to be discussed: How to review a paper.
Reference: Benos et al. (2003) Advances in physiology education. 27:47-52
Sternberg R. J. (2003) Monitor on psychology. 34: 5

June 7, 2007
Leader: Dr. Miguel Padilla (Mentor for the presentation: Dr. Mark Beasley)
Topic to be discussed: The design of simulation studies in medical statistics.
Reference: Burton A. et al. (2006) Statistics in Medicine. 25:4279-4292

May 3, 2007
Leader: Mr. Samprit Banerjee (Mentor for the presentation: Dr. Nengjun Yi)
Topic to be discussed: Bayesian Modeling of Multivariate Quantitative Traits using Seemingly Unrelated Regression.
Reference: Verzilli C.J. et al. (2005) Genet. Epidemiol. 28:313-325

April 5, 2007
Leader: Dr. Stephen Erickson (Mentor for the presentation: Drs. Allison and Tiwari)
Topic to be discussed: Integrating copy number polymorphisms into array CGH analysis using a robust HMM.
Reference: Bioinformatics 2006 22(14):e431-e439

March 1, 2007
Leader: Dr. Xiangqin Cui
Topic to be discussed: Relative impact of nucleotide and copy number variation on gene expression phenotypes
Reference: Stranger et al. Science (2007) 315 (5813):848-53

February 1, 2007
Leader: Mr. Amit Patki (Mentor for the presentation: Drs. Hemant Tiwari and Mark Beasley)
Topic to be discussed: Implementation of a combined association-linkage model for quantitative traits in linear mixed model procedures of statistical packages
Reference: Beem A.L. and Boomsma D. L. (2006) Twin Res. And Hum. Genet. 9:325-333

January 4, 2007
Leader: Dr. Yun Joo Yoo (Mentor: Dr. Kui Zhang)
Topic to be discussed: Case-control single-marker and haplotypic association analysis of pedigree data
Reference: Browning et al., 2005 Genet Epidemiol 28:110-122

2006

December 8, 2006
Leader: Dr. Shiju Zhang (Mentor: Dr. Grier Page)
Topic to be discussed: Reducing the dimensionality of data with neural networks
Reference: Hinton and Salakhutdinov, 2006 Science 313:504-507

November 2, 2006
Leader: Dr. Dale J. Benos
Topic to be discussed: Ethics and scientific publication
Reference: Advan Physiol Educ. 29:59-74 (2005)

October 5, 2006
Leader: Dr. Jan P. Dumanski
Topic to be discussed: Copy-number polymorphisms: mining the tip of an iceberg
Reference: Trends Genet. 2005 Jun; 21(6):315-7

September 7, 2006
Leader: Dr. Peter Sorensen
Topic to be discussed: Uncovering the Genetic Architecture of Obesity using Genetic Genomics
Reference: Schadt. E. E et al. Nat Genet. 2005 Jul: 37(7):710-7;
Lum P. Y et al. Journal of Neurochemistry 2006, 97 (Suppl. 1): 50-62

August 3, 2006
Leader: Dr. Jasmin Divers
Topic to be discussed: Optimal two-stage genotyping design for genome-wide association scans
Reference: Wang et al. 2006. Genetic Epidemiol. 30: 356-366

July 6, 2006
Leader: Dr. Issa Coulibaly
Topic to be discussed: Methodological aspects of the genetic dissection of gene expression
Reference: Carlborg et al. Bioinformatics. 2005; 21: 2383-2393

June 1, 2006
Leader: Dr. Solomon Musani
Topic to be discussed: Genome-wide strategies for detecting multiple loci that influence complex diseases
Reference: Marchini et al. Nature Genetics, 2005; 37: 413-417,, Supplementary Note,

May 4, 2006
Leader: Dr. Mahyar Sabripour (mentor for the presentation: Dr. Ann Loraine)
Topic to be discussed: Biological profiling of gene groups utilizing Gene Ontology
Reference: Bluthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D. Genome Inform Ser Workshop Genome Inform. 2005;16(1):106-15

April 6, 2006
Leader: Dr. Kelly Vaughan (mentor for the presentation: Dr. Hemant Tiwari)
Topic to be discussed: Rational Inferences about Departures from Hardy-Weinberg Equilibrium
Reference: Wittke-Thompson JK, Pluzhnikov A, Cox N (2005). Am J Hum Genet 76: 967-986

March 2, 2006
Leader: Dr. Miguel Padilla
Topic to be discussed: Perception of the parent- adolescent relationship: a longitudinal investigation
Reference: (1) McGue et.al. (2005) Developmental Psychology, 41: 971-984,
(2) Patridge T. (2005) Developmental Psychology, 41: 985-988

February 2, 2006
Leader: Dr. Tesfaye Baye Mersha
Topic to be discussed: Linkage disequilibrium maps and association mapping
Reference: (1) Morton NE (2005) The journal of clinical investigation 115:1425-1430 ,
(2) PNAS August 16, 2005, vol. 102, no. 33, 11835–11839

January 5, 2006
Leader: Dr. Daniel Shriner
Topic discussed: The optimal discovery procedure: a new approach to simultaneous significance testing and The optimal discovery procedure II: Applications to Comparative Microarray Experiments
Reference:Collection of Biostatistics Research Archive

2005

December 1, 2005
Leader: Dr. John Hartman
Topic discussed: The synthetic genetic interaction spectrum of essential genes [doi:10.1038/ng1640]
Reference: Nature Genetics Oct. 2005, pg. 1147

November 3, 2005
Leader: Dr. Guimin Gao
Topic discussed: Family-based tests for associating haplotypes with general phenotype data: application to asthma genetics
Reference: Horvath et al, Genet Epidemiol. 2004, 26(1):61-9

October 6, 2005
Leader: Dr. Nianjun Liu
Topic discussed: Am. J. Hum. Genet., 77:27-40, 2005

September 1,2005
Leader: Dr. Rui Feng
Topic discussed: Genomic screening and replication using the same data set in family-based association testing.
Reference: Nat. Genet. 2005 37: 683-691

July 07, 2005
Leader: Dr. Ann Loraine
Topic discussed: DNA Tiling Microarray Analysis
Reference:Genome Biology, 2005, 6:R52. Genomics, 2005, 85:1-15.

June 2, 2005
Leader: Dr. Grier Page and Dr. Stephen Barnes
Topic discussed: A Comparison of cDNA, Oligonucleotide, and Affymetrix GeneChip Gene Expression Microarray Platforms
Reference:Journal of Biomolecular Techniques, 2004, Vol. 15:276-284. [PMID: 15585824]

May 2,2005
Leader: Dr. Samprit Banerjee
Topic to be discussed: Mapping Quantitative Trait Loci With Censored Observations
Reference:Genetics, 2004, Vol. 168:1689-1698.

April 7,2005
Leader: Dr. Jasmin Divers
Topic to be discussed: On a Semiparametric Test to Detect Associations Between Quantitative Traits and Candidate Genes Using Unrelated Individuals
Reference:Genetic Epidemiology, 2003, 24, 44-56.

March 3, 2005
Leader: Dr. Leona C. Fitzmaurice
Topic to be discussed: Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research
Reference: http://grants.nih.gov/grants/guide/notice-files/NOT-OD-05-022.html

February 3, 2005
Leader: Amit Patki
Article to be discussed: Modeling quantitative trait loci and interpretation of models by Zeng, Z. et al.
From Journal: Genetics, 2005, Ahead of Print.

January 6, 2005
Leader: Dr. Xianqin Cui
Article to be discussed:
(1) Randomization Tests for Multiple Regression by Kennedy, P. et al.
(2) How do bootstrap and permutation tests work by Jenssen, A. et al.
From Journal:
(1) Commun. Statist. - Simula, 1996, 25(4), 923-936.
(2) Annals of Statistics, 2003, 31(3), 768-806.

2004

December 2, 2004
Leader: Dr. Donna Arnett
Article to be discussed: Pharmacogenetics: ethical problems and solutions by Breckenridge A. et al.
From Journal: Nature Reviews - Genetics, 2004, 5:676-680

November 4, 2004
Leader: Dr. Stas Zakharkin
Articles to be discussed:
(1) Artificial gene networks for objective comparison of analysis algorithms by Mendes, P. et al.
(2) Genomic analysis of regulatory network dynamics reveals large topological changes by Luscombe, N. M. et al.
(3) Circuit Simulation of Genetics Network by McAdams, H. H. et al.
From Journals:
(1) Bioinformatics, 2003, 19:90-7, 2003, 19, Suppl. 2, ii122-ii129.
(2) Nature, 2004, 431, 308-312.
(3) Science, 1995, 269(5224), 650-656.

October 7, 2004
Leader: Dr. Xiangqin Cui
Articles to be discussed:
(1) Allelic Variation in Gene Expression Is Common in the Human Genome by Lo, H. et al.
(2) Detection of regulatory variation in mouse genes by Cowles, C. R. et al.
(3) Allele-specific gene expression uncovered by Knight, J.
From Journals:
(1) Genome Research, 2003, 13, 1855-1862.
(2) Nature Genetics, 2002, 32, 432-437.
(3) Trends in Genetics, 2004, 20(3), 113-116.

September 2, 2004
Leader: Dr. Nengjun Yi
Articles to be discussed:
(1) A large-sample QTL study in mice: I. Growth by Rocha, J. et al.
(2) A large-sample QTL study in mice: II. Body composition by Rocha, J. et al.
(3) A large-sample QTL study in mice: III. Reproduction by Rocha, J. et al.
From Journals:
(1) Mammalian Genome, 2004, 15(2), 83-99. [doi: 10.1007/s00335-003-2312-x]
(2) Mammalian Genome, 2004, 15(2), 100-13. [doi: 10.1007/s00335-003-2308-6]

August 5, 2004
Leader: Dr. Daniel Bullard
Articles to be discussed:
(1) Effect of genetic cross on the detection of quantitative trait loci and a novel approach to mapping QTLs by Hitzemann, R. et al.
(2) Multiple Cross and Inbred Strain Haplotype Mapping of Complex-Trait Candidate Genes by Park, Y. et al.
(3) A strategy for the integration of QTL, gene expression, and sequence analyses by Hitzemann, R. et al.
From Journals:
(1) Pharmacology Biochemistry and Behavior, 2000, 67, 767-772 [doi:10.1016/S0091-3057(00)00421-4]
(2) Genome Research, 2002, 13, 118-121.
(3) Mammalian Genome, 2003, 14, 733-747. [doi: 10.1007/s00335-003-2277-9]

July 1, 2004
Leader: Dr. Steve Barnes
Articles to be discussed: Adaptive Gene Picking with Microarray Data: Detecting Important Low Abundance Signals by Lin, Y. et al.

June 3, 2004
Leader: Prashant Yelisetti
Articles to be discussed: (1) Quantitative Quality Control in Microarray Image Processing and Data Acquisition by Wang,X. et al.
(2) Issues in cDNA Microarray Analysis: Quality Filtering, Channel Normalization, Models of Variations and Assessment of Gene Effects by Tseng, GC et al.
From Journals: (1) Nucleic Acid Research, 2001, 29(15), e75
(2) Nucleic Acid Research, 2001, 29(12), 2549-2557.

May 6, 2004
Leader: Dr. Kim
Articles to be discussed: (1)A multivariate analysis of repeated measures: linkage of the albinism gene (Tyr) to a QTL influencing ethanol-induced anesthesia in laboratory mice by Markel, P. D. et al.
(2) QTL Analysis of Multiple Behavioral Measures of Anciety in Mice by Henderson, N. D. et al.
(3) Pleiotropic QTL Analysis by Mangin, B. et al.
From Journals: (1) Psychiatric Genetics, 1994, 4(6): 205-210
(2) Behavior Genetics, 2004, 34(3): 267-293
(3) Biometrics, 1998, 54(1): 88-99

April 1, 2004
Leader: Dr. Musani
Article discussed: (1) Simultaneous Detection and Fine Mapping of Quantitative Trait Loci in Mice Using Heterogeneous Stocks by Mott, R. et al.
(2) A Method for Fine Mapping Quantitative Trait Loci in Outbred Animal Stocks by Mott, R. et al.
(3) From Mouse to Human: Fine Mapping of Quantitative Trait Loci in a Model Organism by McPeek, M.
From Journal: (1) Genetics, 2002, 160: 1609–1618
(2) PNAS, 2000, 97 (23), 12649–12654
(3) PNAS, 2000, 97 (23), 12389–12390

March 4, 2004
Leader: Dr. Bartolucci
Articles to be discussed: (1) A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-test and Statistical Inferences of Gene Changes
(2) Significance Analysis of Microarrays Applied to the Ionizing Radiation Response
Authors: (1) Bladi, P., Long, A.D.
(2) Tusher, V. G., Tibshirani, R., Chu, G.
From Journals: (1)Bioinformatics, 2001, 17(6): 509-519
(2) PNAS, 2001, 98(9): 5116-5121

February 5, 2004
Leader: Dr. Tanik

2003

December 4, 2003
Leader: Dr. Edwards
Article discussed: That BLUP is a Good Thing: The Estimation of Random Effects
Authors: Robinson, G. K.
From Journal: Statistical Science, 1991, 6(1): 15-32

October 2, 2003
Leader: Dr. Edwards
Article discussed: Analysis of Multilocus Models of Association
Authors: Devlin, B., Roeder, K., Wasserman, L.
From Journal: Genetic Epidemiology, 2003, 25: 36-47

September 4, 2003
Leader: Dr. Kim
Article discussed: Bayesian Analysis of Multilocus Association in Quantitative and Qualitative Traits
Authors: Kilpikari, R., Sillanpaa, M.
From Journal: Genetic Epidemiology, 2003, 25: 132-135

August 7, 2003
Leader: Dr. Jose Fernandez
Article discussed: Control of Confounding of Genetic Associations in Stratified Populations
Authors:
From Journal: American Journal of Human Genetics, 2003, 72: 1492-1504

July 3, 2003
Leader: Drs. Hemant Tiwari and Mark Beasley
Article discussed: Genome Association Studies of Complex Diseases by Case-Control Designs
Authors: Fan, R., Knapp, M.
From Journal: American Journal of Human Genetics, 2003, 72: 850-68

June 5, 2003
Leader: Jelai Wang and Prinal Trivedi
Article discussed: openMosix vs. Beowulf: a case study
Authors: Bar, M., Cozzini, S., Davini, M., Marmodoro, A.
From Journal: Link to the article

May 1, 2003
Leader: Dr. Stanislav Zakharkin
Article discussed: Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays
Authors: Coombes, K., Highsmith, W. E., Krogmann, T. A., Baggerly, K. A., Stivers, D. N., Abruzzo, L. V.
From Journal: Journal of Computational Biology, 2002, 9(4): 655-69

April 3, 2003
Leader: Dr. Mark Beasley
Article discussed: An Errors-In-Variables Analysis of Managerial Role Performance
Authors: Warren, R. D., White, J. K., Fuller, W. A.
From Journal: Journal of American Statistical Association, 1974, 69(348): 886-93

March 6, 2003
Leader: Dr. Nengjun Yi
Article discussed: Gene selection: a Bayesian variable selection approach
Authors: Lee et al.
From Journal: Bioinformatics, 2003, 19:90-7

January 2, 2003
Leader: Dr. Cecelia A. Laurie
Article discussed: A direct approach to false discovery rates
Authors: Storey, J.D.
From Journal: Journal of the Royal Statistical Society, Series B, 2002, 64:479-98

2002

December 5, 2002
Leader: Dr. Mark Beasley
Article discussed: Mapping Genes That Underlie Ethnic Differences in Disease Risk: Methods for Detecting Linkage in Admixed Populations, by Conditioning on Parental Admixture
Authors: McKeigue, P.
From Journal: American Journal of Human Genetics, 1998, 63:241-51

November 7, 2002
Leader: Dr. Hemant Tiwari
Article discussed: Case-Control Studies of Association in Structured or Admixed Populations
Authors: Pritchard, J. K., Donnelly, P.
From Journal: Theoretical Population Biology, 2001, 60:227-37

October 3, 2002
Leader: Dr. Hemant Tiwari
Article discussed: Genomic Control, a New Approach to Genetic-Based Association Studies
Authors: Devlin, B., Roeder, K, & Wasserman, L.
From Journal: Theoretical Population Biology, 2001, 60:155-66

September 5, 2002
Leader: Dr. Xiangian Kong
Article discussed: A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington’s disease transgenic model
Authors: Xu, X., Olson, J. M., Zhao, L-P.
From Journal: Human Molecular Genetics, 2002, 11(17): 1977-85

August 1, 2002
Leader: Dongyang Yang
Article discussed: Powerful Regression-Based Quantitative-Trait Linkage Analysis of General Pedigrees
Authors: Sham, P., Purcell, S., Cherny, S. S., Abecasis, G. R.
From Journal: American Journal of Human Genetics, 2002, 71: 238-53

June 4, 2002
Leader: Dr. Rodney Go
Article discussed: A Perspective on Epistasis: Limits of Models Displaying No Main Effect
Authors: Culverhouse, R., Suarez, B. K., Lin, J., Reich, T.
From Journal: American Journal of Human Genetics, 2002, 71: 59-77

May 3, 2002
Leader: Chenxi Wang
Article discussed: A Bayesian approach to the identification of panmictic populations and the assignment of individuals
Authors: Dawson, K.J., Belkhir, K.
From Journal: Genetic Research, 2002, 78: 59-77

April 4, 2002
Leader: Dr. Howard Wiener
Article discussed: Sequence analysis using logic regression
Authors: Kooperberg, C., Ruczinski, I., LeBlanc, M.L., Hsu L.
From Journal: Genetic Epidemiology, 2001, Suppl 1: S626-31

March 7, 2002
Leader: Dr. David Redden
Article discussed: A Combinatorial Partitioning Method to Identify Multilocus Genotypic Partitions that Predict Quantitative Trait Variation
Authors: Nelson, MR, Kardia, SLR, Ferrell, RE, Sing, CF.
From Journal: Genome Research, 2001, 11: 458-70

February 7, 2002
Leader: Dr. Chris Coffey
Article discussed: Mulitfactor-dimensionality reductions reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer
Authors: Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH
From Journal: American Journal of Human Genetics, 2001, 69: 138-47

January 15, 2002
Leader: Dr. Jaap Brand
Article discussed: Using missing data methods in genetic studies with missing mutation status
Authors: Leong, T., Lipsitz, S. R., Ibrahim, J. G.
From Journal: Statistics in Medicine, 1999, 18: 473-85

2001

December 6, 2001
Leader: Dr. Mark Beasley
Article discussed: Future directions of research in statistical genetics
Authors: Horvath, S., Baur, M. P.
From Journal: Statistics in Medicine, 2000, 19: 3337-43
Reference: Genomic screening and replication using the same data set in family-based association testing
Reference: An Entropy-Based Statistic for Genomewide Association Studies

 

The 2001-2002 academic year is generously supported by a donation from Kraft Foods North America, Inc.