Edwin J.C.G. van den Oord, Ph.D.
Virginia Commonwealth University
McGuire Hall, Room 216A
P. O. Box 980533
Richmond, VA 23298-0581
Fax (804) 828 8359
For express mail/FEDEX
McGuire Hall, Room 209B
1112 East Clay Street
Richmond, VA 23298-0581
Downloads (zipped) and links:
Download MWAS results for the paper: Cell-Type-Specific Methylome-wide Association Studies Implicate Neurotrophin and Innate Immune Signaling in Major Depressive Disorder" Biological Psychiatry by Robin F. Chan, Gustavo Turecki, Andrey A. Shabalin, Jerry Guintivano, Min Zhao, Lin Y Xie, Gerard van Grootheest, Zachary A. Kaminsky, Brian Dean, Brenda W.J.H. Penninx, Karolina A. Aberg, and Edwin J.C.G. van den Oord.
Download raw and processed MBD-seq cell type data and their description as used in the paper “Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies” by Hattab M, Shabalin A, Clark S, Zhao M, Kumar G, Chan R, Xie L, Jansen R, Han L, Magnusson P, van Grootheest G, Hultman C, Penninx B, Aberg K, van den Oord EJCG.
Simulation code used in “Evaluating the Evidence of Replication for Genetic Associations With Schizophrenia — In Reply” by Aberg, K, Y Liu, J Bukszár, JL McClay, AN Khachane, OE Andreassen, D Blackwood, A Corvin, S Djurovic, H Gurling, R Ophoff, C Pato, M Pato, BP Riley, BT Webb, KS Kendler, M O'Donovan, N Craddock, G Kirov, M Owen, D Rujescu, D St Clair, T Werge, CM Hultman, LE Delisi, PF Sullivan, and EJCG van den Oord. JAMA Psychiatry 2014, 71, 1195-1196.
All MWAS results with q-value better than 0.01 in “Methylome-Wide Association Study of Schizophrenia: Identifying Blood Biomarker Signatures of Environmental Insults. JAMA Psychiatry “ by Aberg KA, McClay JL, Nerella S, Clark S, Kumar G, Chen W, Khachane AN, Xie LY, Hudson A, Gao G, Harada A, Hultman CM, Sullivan PF, Magnusson PKE, van den Oord EJCG (2014), JAMA Psychiatry, 2014, 71, 255-264.
P-values from replication analyses in the paper Aberg, K, Y Liu, J Bukszár, JL McClay, AN Khachane, OE Andreassen, D Blackwood, A Corvin, S Djurovic, H Gurling, R Ophoff, C Pato, M Pato, BP Riley, BT Webb, KS Kendler, M O'Donovan, N Craddock, G Kirov, M Owen, D Rujescu, D St Clair, T Werge, CM Hultman, LE Delisi, PF Sullivan, and EJCG van den Oord.( 2013). A Comprehensive Family-based Replication Study of Schizophrenia Genes. JAMA Psychiatry 2013;70(6):573-581.
P-values from analyses in the paper "Metabolomics p-values for article "Behavioral metabolomics analysis identifies novel neurochemical signatures in methamphetamine sensitization" by Daniel E. Adkins, Joseph L. McClay, Sarah A. Vunck, Angela M. Batman, Robert E. Vann, Shaunna L. Clark, Renan P. Souza, James J. Crowley, Patrick F. Sullivan, Edwin J.C.G. van den Oord, Patrick M. Beardsley
Software for the paper: Van den Oord EJCG, Bukszar J, Rudolf G, Nerella S, McClay JL, Xie L, and Åberg K, Estimation of CpG coverage in whole methylome next-generation sequencing studies. For the documentation click here. Source code/executables (Windows and Linux) plus example can be downloaded in tar.bz2 format.
GWAS p-values for article by Adkins DE, Clark SL, Åberg K, Hettema JM, Bukszár J, McClay JL,Souza RP, Sullivan PF, van den Oord EJCG.
Genomewide pharmacogenomic study of citalopram-induced side effects in STAR*D.
List of neurotransmitters, genes and CATIE SNPs analyzed in the manuscript "SNP-based analysis of neuroactive ligand-receptor interaction pathways implicates PGE2 as a novel mediator of antipsychotic treatment response: Data from the CATIE Study” by Daniel E. Adkins*, Amit N. Khachane*, Joseph L. McClay, Karolina Åberg, Jozsef Bukszár, Patrick F. Sullivan, Edwin J.C.G. van den Oord. In press Schizophrenia Research. * equal contributions.
QQ-plots for paper: Adkins, DE, Åberg, K; McClay JA, Bukszar J., Zhao, Z, Jia, P, Stroup, S, Perkins, DO, McEvoy, JP, Lieberman, JA, Sullivan, PF, van den Oord, EJCG (2009). Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. Molecular Psychiatry
QQ-plots and GWAS p-values for article by McClay JL, Adkins DE, Åberg K, Stroup S, Perkins DO, Vladimirov VI, Lieberman JA, Sullivan PF, van den Oord EJCG. (2009) Genome-wide pharmacogenomic analysis of response to treatment with antipsychotics. Molecular Psychiatry, E-pub 2009 Sep 1.
Mplus and Mx scripts for the paper by York TP, Vargas-Irwin C, Anderson WH, Van den Oord EJCG (2009). The use of finite mixture models to handle drug response heterogeneity in pharmacogenetic studies. Pharmacogenomics, 10, 753-767.
Supplemental material and all GWAS p-values related to the paper Van den Oord, EJCG, Kuo, P., Hartmann, A., Webb, B., Möller, H., Hettema, J, Giegling, I, Bukszár, J, and Rujescu, D. (2008). Genomewide association analysis followed by a replication study implicates a novel neuroticism gene. Archives of General Psychiatry, 65:1062-1071.
Supplemental material for the paper: Genetics and Diagnostic Refinement by Van den Oord, E. J. C. G., Joseph L McClay, Timothy P. York, Lenn Murrelle, and Jaime R. Robles (2007) in Behavior Genetics, 37, 535-545.
Supplemental material and Splus/R code used in the article by Bukszár, J. & Van den Oord, E. J. C. G (2006). Optimization of two-stage genetic case-control designs where data are combined using an accurate and efficient approximation for Pearson’s statistic. Biometrics, 62, 1132-1137.
Forrester diagrams of model parts, Stella models, picture showing full model, and S-PLUS/R scripts for the paper Joseph L McClay and Edwin JCG van den Oord (2006). Variance component analysis of polymorphic metabolic systems. Journal of Theoretical Biology, 240, 149-159.
Supplemental material for the paper by Timothy P. York, Lindon J. Eaves, & Edwin J. C. G. van den Oord (2006). Multivariate adaptive regression splines: A powerful method for detecting disease-risk relationship differences among subgroups. Statistics in Medicine, 25, 1355-1367.
Supplemental figures and tables + zipped Splus/R code used to calculate power for 2×2 and 2×3 tables in the MS: Bukszár, J. & Van den Oord, E. J. C. G. (2005). Accurate and efficient power calculations for 2×m tables in unmatched case-control designs. Statistics in Medicine, 24, 2632-2646.
Supplemental material for the paper: Van den Oord, E. J. C. G. (2005). Controlling false discoveries in candidate gene studies. Molecular Psychiatry, 10, 230 -231
Link to the program lga972 and its manual. The program is discussed in the paper: Robles, J.R. & van den Oord, E.J.C.G. (2004). lga972: A cross-platform application for optimizing LD studies using a genetic algorithm. Bioinformatics, 20, 3244-3245.
Details of the calculations performed in the MS: Van den Oord, E. J. C. G., & Sullivan, P. F. (2003). False discoveries and models for gene discovery. Trends in Genetics, 19, 537-542.
lga972 now replaces code used for the calculations performed in the article: Van den Oord, E. J. C. G., & Sullivan, P. F. (2003). A framework for controlling false discovery rates and minimizing the amount of genotyping in gene-finding studies. Human Heredity, 56, 188-199.
Program Assign plus documentation for FP-TDI SNP genotype scoring in Mplus as discussed in the article: Van den Oord, E. J. C. G., Jiang, Y., Riley, B. P., Kendler, K. S., & Chen, X. (2003). FP-TDI SNP Scoring by manual and statistical procedures: A study of error rates and types. BioTechniques, 34, 610-624.
Program MxScript plus documentation discussed in the paper: Van den Oord, E. J. C. G., & Snieder, H. (2002). Including measured genotypes in statistical models to study the interplay of multiple factors affecting complex traits. Behavior Genetics, 32, 1-19.
Mx scripts and Mplus scripts used in the article: Van den Oord, E. J. C. G. (2000). The use of mixture models to perform quantitative tests for linkage disequilibrium, maternal effects, and parent-of-origin effects with incomplete subject-parent triads. Behavior Genetics, 30, 335-343.
LEM scripts plus documentation as discussed in paper: Van den Oord, E. J. C. G. & Vermunt, J. K. (2000). Testing for linkage disequilibrium, maternal effects, and imprinting with (in)complete case-parent triads, by use of the computer program LEM. American Journal of Human Genetics, 66, 335-338.
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Last updated on 10/21/2019