Publications by Researcher Staff with the Bioinformatics Consulting Center

Publications by researcher staff with the Bioinformatics Consulting Center

<http://bcc.cbio.psu.edu/> at Penn State University, for the academic year 2004-2005.

This file is saved at: <http://www.stat.psu.edu/~jlr/BCC/2005/Pubs04-05.doc>

Hershey Publications:

Liu W, Icitovic N, Shaffer ML, Chase GA. The impact of population heterogeneity on risk estimation in genetic counseling. BMC Medical Genetics 5(1)18, 2004.

Liu W, Zhao W, Chase GA: Genome scan meta-analysis for hypertension. American Journal of Hypertension 17: 1100-1106, 2004.

Drubin D, Smith JS, Liu W, Zhao W, Chase GA: Clawson GA: Comparison of cryopreservation and standard needle biopsy for gene expression profiling of human breast cancer specimens. Breast Cancer Research and Treatment 90: 93–96, 2005.

Liu W, Zhao W, Shaffer ML, Icitovic N, Chase GA: Modeling clinical trials in heterogeneous samples. Statistics in Medicine (in press).

UP publications:

Belinda Giardine, Cathy Riemer, Yi Zhang, Istvan Albert, Jim Kent, Webb
Miller, Anton Nekrutenko and Ross Hardison
Galaxy: A platform for interactive large-scale genome analysis
Accepted for publication in Genome Research

Wen-Yu Chung, Reka Albert, Istvan Albert, Anton Nekrutenko, and Kateryna Makova,
Evolution And Robustness Of Human Gene Co-Expression Network: The Role
Of Duplicate Genes
Submitted and currently under review.

King D.C., Taylor J., Elnitski L., Chiaromonte F., Miller W. and

Hardison R.C. (2005) Evaluation of regulatory potential and conservation

scores for detecting cis-regulatory modules in aligned mammalian genome

sequences. Genome Research, to appear.

Li B., Zha H. and Chiaromonte F. (2005) Contour regression: a general

approach to dimension reduction. Annals of Statistics, to appear.

Makova K.D., Yang S. and Chiaromonte F. (2004) Insertions and deletions

are male-biased too: a whole-genome analysis in rodents. Genome Research,

14, 567-573.

Kolbe D., Taylor J., Elnitski L., Eswara P., Li J., Miller W., Hardison

R.C. and Chiaromonte F. (2004) Regulatory potential scores from

genome-wide 3-way alignments of human, mouse and rat. Genome Research, 14,

700-707.

Yang S., Smit A.F., Schwartz S., Chiaromonte F., Roskin K. M., Haussler

D., Miller W. and Hardison R.C. (2004) Patterns of insertions and their

covariation with substitutions in the rat, mouse and human genomes. Genome

Research, 14, 517-527.

Hardison R.C., Chiaromonte F., Kolbe D., Wang H., Petrykowska H.,

Elnitski L., Yang S., Giardine B., Zhang Y., Riemer C., Schwartz S.,

Haussler D., Roskin K., Weber R., Diekhans M., Kent W.J., Weiss M.J.,

Welch J. and Miller W. (2004) Global prediction and tests for erythroid

regulatory regions. Cold Spring Harbor Symposia in Quantitative Biology:

The Genome of Homo Sapiens, 68, 335-345.

Chiaromonte F., Weber R. J., Roskin K.M., Diekhans M., Kent W.J. and

Haussler D. (2004) The share of human genomic DNA under selection

estimated from human-mouse genomic alignments. Cold Spring Harbor Symposia

in Quantitative Biology: The Genome of Homo Sapiens, 68, 245-255.

Li B., Cook R.D. and Chiaromonte F. (2004) Dimension reduction for the

conditional mean in regressions with categorical predictors. Annals of

Statistics, 30, 1636-1668.

Li B., Zha H. and Chiaromonte F. (2004) Linear contour learning: a

method for supervised dimension reduction. Proceedings of the 20th

Conference on Uncertainty in Artificial Intelligence. ACM International

Conference Proceeding Series. 349-356.