Edwin van den Oord
Edwin J.C.G. van den Oord, Ph.D.
Professor
Center for Biomarker Research and
Precision Medicine
Virginia
Commonwealth University
McGuire
Hall, Room 216A
P. O. Box 980533
Richmond, VA 23298-0581
Fax (804) 828 8359
e-mail: ejvandenoord@vcu.edu
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 Ĺberg 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, Ĺberg 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 Ĺberg, Jozsef
Bukszár, Patrick F. Sullivan, Edwin J.C.G. van den
Oord. In press Schizophrenia Research. * equal
contributions.
QQ-plots for
paper: Adkins, DE, Ĺberg, 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, Ĺberg 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).
lga972 now replaces code
used for the calculations performed in the article: Van den Oord, E. J. C. G.,
& Sullivan, P. F.
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.
Links to R, Mplus, Mx, and LEM
This page
does not reflect an official position of Virginia Commonwealth University.
Last
updated on 10/21/2019