JOURNAL CLUB
The Section on Statistical Genetics holds a monthly journal club meeting on the first Thursday of each month. The meeting is held during lunch time with pizza and drinks provided. 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.
The next meeting is held
On: Thursday, November 06, 2008
Time: 11:30 am-1:00 pm
Location: NB G026 (Nursing building)
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
Journal club meetings are organized by Dr. Guimin Gao. Feel free to contact him for more information.
Topics Discussed in Previous Meetings
2008
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
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.
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.
(2) Mammalian Genome, 2004, 15(2), 100-13.
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
(2) Genome Research, 2002, 13, 118-121.
(3) Mammalian Genome, 2003, 14, 733-747.
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.