Ben Bolstad

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. Dissertation. University of California, Berkeley. Postscript or PDF

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

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.

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

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

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

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.

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

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

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

Bolstad BM (2008) Preprocessing and Normalization for Affymetrix GeneChip Expression Microarrays in Methods in Microarray Normalization Phillip Stafford (Ed), CRC Press, 2008 Publisher Website

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

Brettschneider J, Collin F, Bolstad BM, and Speed TP. (2008) Quality Assessment for Short Oligonucleotide Microarray Data Technometrics 50(3):241-264

Brettschneider J, Collin F, Bolstad BM, and Speed TP. (2008) Rejoinder for "Quality Assessment for Short Oligonucleotide Microarray Data" Technometrics 50(3):279-283

McCall MN, Bolstad BM, Irizarry RA. (2010) Frozen robust multiarray analysis (fRMA). Biostatistics. 2010 Apr;11(2):242-53. Link

Click here for a PubMed search on some of these papers.

Click here for Google Scholar Citations.

Unpublished material

Bolstad, B (2013) PLM Extensions Unfinished Manuscript PDF file (really primarily written in 2008))

Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide Array Data Unpublished Manuscript PDF file

Bolstad, B. M. (2002) Comparing the effects of background, normalization and summarization on gene expression estimates. Unpublished Manuscript PDF file

Bolstad, B. M. (2002) Investigating the effects of simple filtering on detecting differential gene expression. Unpublished Manuscript PDF file

Bolstad, B. M. (2002) Using MM in place of PM for detecting differential gene expression Unpublished Manuscript PDF file

Bolstad, B. M. (1998) Comparing some iterative methods of parameter estimation for censored gamma data University of Waikato Dissertation PDF file PS file

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

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

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

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

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

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

Bolstad, B. M., Detection of Long Contiguous Stretches of Homozygosity using the Affymetrix Cytogenetics Research Solution Microarrays. (Program #1435) Presented at the 59th Annual Meeting of The American Society of Human Genetics, October 21, 2009, Honolulu, Hawaii. Poster available here

Hu, Z., Berntsen, t., Chen, J., Flaucher, D., Flaucher, Huynh, V., Nautiyal, S., Ngo, N., Pankratz, D., Abdueva, D., Bolstad, B., Carlton, V., Liu, B., Veitch, J., and Collins, J. Development and performance of a simple assay for high resolution copy number analysis on the Affymetrix 2.7M Cytogenetics Research Array. (Program #1436) Presented at the 59th Annual Meeting of The American Society of Human Genetics, October 21, 2009, Honolulu, Hawaii. Poster available here

Ron Sapolsky, Anju Shukla, Sumathi Venkatapathy, Chuan Chen, Carsten Bruckner, Vicky Huynh, Liansen Liu, Xuan Shen, Kent Suyenaga, Patrick Weaver, Wai Wu, Bitao Liu, Matt Ghent, Benjamin Bolstad, Farooq Siddiqui, Diana Abdueva, Mirjana Alvi, Eric Fung, Jeanette Schmidt and Lawrence Greenfield Molecular Inversion Probe analysis using OncoScan™ FFPE Assay Kit to detect copy number aberrations and somatic mutations in lung tumor DNA samples from formalin-fixed paraffin-embedded (FFPE) tissue. AACR Annual Meeting 2014 ; April 5-9, 2014; San Diego, CA

J. Schmidt, B. Liu, M. Ghent, B. Bolstad, F. Siddiqui, D. Abdueva, M. Marjanovic, R. Saplosky, A. Shukla, S. Venkatapathy, C. Chen, C. Bruckner, V. Huynh, L. Liu, K. Suyenaga, P. Weaver, L. Greenfield, E. Fung. A new method for high-fidelity copy number analysis in solid tumor samples and its implementation in OncoScan®FFPE Assay Kit Presented as ASHF 2014 Poster available here

Tina Chen; Ben Bolstad; Alan H. Roter; Radha Duttagupta; Eric T. Fung; and Gargi P. Mamtora: Assessment of Mosaicism Performance for Affymetrix CytoScan® Dx Assay Using a Simulated Titration Experiment Molecular Medicine Tri-Conference 2015 Poster

Roter, A., Bolstad, B., Nguyen, S., Shapero, M., and Schmidt, J. Characterization of Exon-Level Genomic Copy Number Changes in 1,855 Normal Individuals. Presented at ACMG 2019 Poster available here

Shapero, M., Nguyen, S., Bolstad, B., Schmidt J., and Roter, A. Exon-Level Detection of Human Copy Number Variation Using High-Density DNA Oligonucleotide Arrays Presented at ACMG 2019 Poster available here