Archive
Inference to the best explanation
D. R. Bickel, “The strength of statistical evidence for composite hypotheses: Inference to the best explanation,” Technical Report, Ottawa Institute of Systems Biology, COBRA Preprint Series, Article 71, available at biostats.bepress.com/cobra/ps/art71 (2010).
Shrinkage estimation of expression fold change
Z. Montazeri*, C. M. Yanofsky*, and D. R. Bickel, “Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: Applications to differential gene expression,” Statistical Applications in Genetics and Molecular Biology 9 (1) 23 (2010). Article | Software
* the first two authors contributed equally
Significance v. fold change
C. M. Yanofsky and D. R. Bickel, “Validation of differential gene expression algorithms: Application comparing fold change estimation to hypothesis testing,” BMC Bioinformatics 11, 63 (2010). Article
Empirical null conditioning
D. R. Bickel, “Estimating the null distribution for conditional inference and genome-scale screening,” Technical Report, Ottawa Institute of Systems Biology, arXiv.org:0910.0745 (2009). Full preprint
Shrinkage estimation vs. testing
Z. Montazeri, C. M. Yanofsky, and D. R. Bickel [the first two authors contributed equally], “Shrinkage estimation of gene expression fold change as an alternative to testing hypotheses of equivalent expression,” Technical Report, Ottawa Institute of Systems Biology, COBRA Preprint Series, Article 60, available at tinyurl.com/mwhnj2 (2009). Full preprint
Gene network reconstruction from transcriptional dynamics
D. R. Bickel, Z. Montazeri, P.-C. Hsieh, M. Beatty, S. J. Lawit, and N. J. Bate, “Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: A case for the second derivative,” Bioinformatics 25, 772-779 (2009).
Fold change estimation versus hypothesis testing
D. R. Bickel and C. M. Yanofsky, “Validation of differential gene expression algorithms: Application comparing fold change estimation to hypothesis testing,” Preprint, Ottawa Institute of Systems Biology, COBRA Preprint Series, Article 50, available at tinyurl.com/bw9jod (2009).
Strength of evidence for composite hypotheses
D. R. Bickel, “The strength of statistical evidence for composite hypotheses with an application to multiple comparisons,” Preprint, Ottawa Institute of Systems Biology, COBRA Preprint Series, Article 49, available at tinyurl.com/7yaysp (2008).
Application: cis- & trans-effects on gene expression
M. Guo, S. Yang, M. Rupe, B. Hu, D. R. Bickel, L. Arthur, and O. Smith, “Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS) reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue,” Plant Molecular Biology 66, 551-563 (2008).
Estimating levels of differential gene expression
D. R. Bickel, “Correcting the estimated level of differential expression for gene selection bias: Application to a microarray study,” Statistical Applications in Genetics and Molecular Biology 7 (1) 10, http://www.bepress.com/sagmb/vol7/iss1/art10 (2008).
David Bickel, statistician 
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