Archive for the ‘gene expression’ Category

Inference to the best explanation

13 September 2010 Leave a comment

Shrinkage estimation of expression fold change

9 June 2010 Leave a comment

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

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Significance v. fold change

28 January 2010 Leave a comment

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

11 October 2009 Leave a comment

D. R. Bickel, “Estimating the null distribution for conditional inference and genome-scale screening,” Technical Report, Ottawa Institute of Systems Biology, (2009). Full preprint

Shrinkage estimation vs. testing

23 August 2009 Leave a comment

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 (2009). Full preprint

Gene network reconstruction from transcriptional dynamics

28 March 2009 Leave a comment

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).

Open access (PDF) | Supplement & software | Data

Fold change estimation versus hypothesis testing

19 February 2009 Leave a comment

Strength of evidence for composite hypotheses

14 February 2009 Leave a comment
Categories: gene expression, preprints

Application: cis- & trans-effects on gene expression

4 April 2008 Leave a comment

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

10 March 2008 Leave a comment

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, (2008).