Research Activities
Bioinformatics
Virology/Bacteriology
Centers
 - UW Toxico Genomics
 - UW - NHLBI Center
 - Center for Pathway Inference Software
Recent Publications
-- Nature Genetics - Integrating large-scale functional genomic data...

-- Nature Biotechnology - Min info spec for in situ hybridization...

-- Nature Biotechnology - Direct multiplexed measurement of gene expression...

-- J Virology - Attenuation of the type I interferon response...

-- J Virology - Independent and cooperative antiviral actions of beta interferon...

-- Carcinogenesis - Comparative genomics of susceptibility to mammary carcinogenesis...

-- OMICS - What is the best reference RNA?...

-- J Virology - Human rhinovirus attenuates the type I interferon response...

-- Science - Rhesus Macaque Genome Sequencing and Analysis Consortium...

-- Cell Microbiology - Hierarchical gene expressio profiles of HUVEC...
Publications
Selected Publications
Title of Paper
Citation
Source Code
AA Genome Announcement D11S Supplementary Material (pdf) Journal of Bacteriology  
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks Nature Genetics. 2008 Jun 15 [Epub ahead of print]  
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nature Biotechnology. 2008 Mar;26(3):305-312  
Direct multiplexed measurement of gene expression with color-coded probe pairs Nature Biotechnology. 2008 Mar;26(3):317-325  
Attenuation of the type I interferon response in cells infected with human rhinovirus. J Virol. 2008 May 10;374(2):399-410  
Independent and cooperative antiviral actions of beta interferon and gamma interferon against herpes simplex virus replication in primary human fibroblasts. J Virol. 2008 Feb;82(4):1934-45  
Comparative genomics of susceptibility to mammary carcinogenesis among inbred rat strains: role of reduced prolactin signaling in resistance of the Copenhagen strain. Carcinogenesis. 2008 Jan;29(1):177-185  
What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments. OMICS. 2007 Summer;11(2):152-165  
Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3. J Virol. 2007 Jun;81(11):6161  
Rhesus Macaque Genome Sequencing and Analysis Consortium Science. 2007 Apr 13;316(5822):222-234  
Hierarchical gene expression profiles of HUVEC stimulated by different lipid A structures obtained from Porphyromonas gingivalis and Escherichia coli. Cell Microbiology. 2007 Apr;9(4):1028-38  
Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3 J Virol. 2006 May;80(10):5021-31. Erratum in: J Virol. 2006 Jul;80(13):6722.  
Clustering Gene Expression Data with Repeated Measurements Genome Biology 2003 4(5): R34 Website
Multiclass classification of microarray data with repeated measurements: application to cancer Genome Biology 2003: 4:R83 Website
Bayesian mixture model based clustering of replicated microarray data Bioinformatics 2004: May 22;20(8):1222-32 Website
From co-expression to co-regulation: how many microarray experiments do we need? Genome Biology 2004 5(7):R48 Website


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