Published Articles
These are some of the articles I have been involved with:
| Sandrine Dudoit,Yee Hwa Yang and Ben Bolstad (2002) Using R
for the Analysis of DNA Microarray Data, R News, 2, 1, 24-32 Rnews
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| Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003), A Comparison of Normalization
Methods for High Density Oligonucleotide Array Data Based
on Bias and Variance. Bioinformatics 19(2):185-193 Supplemental
information. Note that this paper was named a hot paper by ISI Essential Science Indicators in July 2004.
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| Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15
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| Barczak, A., Rodriguez, M. W., Hanspers, K., Koth, L. L., Tai, Y. C., Bolstad, B. M., Speed, T. P., and Erle, D. J. (2003), Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis Genome Research link
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| Gautier, L., Cope, L.M., Bolstad, B. M., and Irizarry, R. A. (2004) affy - Analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 20(3):307-315
gziped Postscript pre-print
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| Bolstad, B. M., Collin, F., Simpson, K. M., Irizarry, R. A. and Speed, T. P. (2004) Design and low level analysis of microarray experiments. International Review of Neurobiology 60:25-58.
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| Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, and Zhang J. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5(10):R80 Full text
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Bolstad BM, Irizarry RA, Gautier L, and Wu Z. (2005) Preprocessing High-density Oligonucleotide Arrays in Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey V, Huber W, Irizarry R, and Dudoit S. (Eds.), Springer, 2005. Publisher Website
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| Bolstad BM, Collin F, Brettschneider J, Simpson K, Cope L, Irizarry RA, and Speed TP. (2005) Quality Assessment of Affymetrix GeneChip Data in
Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey V, Huber W, Irizarry R, and Dudoit S. (Eds.), Springer, 2005. Publisher Website |
| Bolstad BM (2006) Pre-processing Microarray Data in Fundamentals of Data Mining for Genomics and Proteomics Dubitzky W, Granzow M, Berrar DP (Eds.), Springer, 2006. Publisher Website Chapter Supplementary Information
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| Bolstad BM (2008) Preprocessing and Normalization for Affymetrix GeneChip Expression Microarrays in Methods in Microarray Normalization Phillip Stafford (Ed), CRC Press, 2008 Publisher Website
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| Bolstad BM, Ghosh S and Turpaz Y (2008) SNP Array-Based Analysis for Detection of Chromosomal Aberrations and Copy Number Variations in Methods in Microarray Normalization Phillip Stafford (Ed), CRC Press, 2008 Publisher Website
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Click here for a PubMed search on some of these papers
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Published Abstracts
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Evans S.J., Li J., Choudary P.V., Tomita H., Vawter M.P., Turner C.A., Lopez J.F., Thompson R.C., Meng, F., Bolstad, B.M., Speed, T.P., Myers R.M., Bunney, W.E., Jones E.G., Watson, S., Akil H. (2004) Dysregulation of Specific Growth Factor System Gene Expression in Limbic Structures of Subjects with Major Depressive Disorder. Society for Neuroscience 34th Annual Meeting link
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Tomita H., Vawter M.P., Shao L., Atz M.E., Overman K.M., Meng F., Neal C.R., Stead, J.D.H, Evans, S.J., Choudary, P.V., Li, J., Bolstad, B.M., Cartagena P., Walsh, D.M., Speed, T.P., Myers, R.M., Jones, E.G., Watson S., Akil, H., Bunney, W.E. (2004) Gene Expression Profiles of G-protein Signaling Pathway Related Genes in Postmortem Brains of Mood Disorder Patients. Society for Neuroscience 34th Annual Meeting link
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Vawter, M.P., Tomita, H., Atz, M., Li, J., Meng, F., Overman, K., Shao, L., Bolstad, B, Speed, T.P., Stead, J., Choudary, P.V., Neal, C., Evans, S., Walsh, D., Myers, R., Watson, S.J., Jones, E.G, Akil, H, Bunney, W.E. (2004) Mitochondrial Related Gene Expression In Affective Disorders In Postmortem Brain Society for Neuroscience 34th Annual Meeting link
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Vawter M.P., Tomita H., Evans S., Choudary P., Li J., Bolstad B., Meador-Woodruff J.H., Lopez J, Speed T., Myers R.M., Watson S, Akil H., Jones E.G., and Bunney W.E. (2003) Bipolar and Major Depressive disorder gene expression profiling in three brain regions American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Volume 122B, Issue 1
link
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Vawter, M.P., Evans, S.J., Choudary, P., Atz, M., Tomita, H., Bolstad, B., Li, J, Speed, T.P., Myers, R., Watson, S.J, Jones, E. G., Akil, H. and Bunney W.E. (2003) Patterns of Differential Gene Expression In Schizophrenia Overlap In Cortical Regions. American Society of Human Genetics 53nd annual meeting
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Tomita, H., Vawter, M.P., Evans, S.J., Choudary, P., Li, J., Bolstad, B., Speed, T., Myers, R.M., Jones, E.G., Watson, S.J., Akil, H., and Bunney, W.E. (2003) Effects of Mood Disorders and Suicide on Gene Expression Profiles in Postmortem Brains. American Society of Human Genetics 53nd annual meeting
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