Su, Wan-Lin, Modrek, Barmak, GuhaThakurta, Debraj, Edwards, Stephen, Shah, Jyoti K, Kulkarni, Amit V, ...
Abstract Background Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing,...
Mapping the Genetic Architecture of Gene Expression in Human Liver (2008)
Eric E. Schadt, Cliona Molony, Eugene Chudin, Ke Hao, Xia Yang, Pek Y. Lum, ...
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order...
Statistical power of phylo-HMM for evolutionarily conserved element detection (2007)
Fan, Xiaodan, Zhu, Jun, Schadt, Eric E, Liu, Jun S
Abstract Background An important goal of comparative genomics is the identification of functional elements through conservation analysis. Phylo-HMM was recently introduced to detect conserved...
Linkage Disequilibrium in Wild Mice (2007)
Cathy C. Laurie, Deborah A. Nickerson, Amy D. Anderson, Bruce S. Weir, Robert J. Livingston, Matthew D. Dean, ...
Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only...
Linkage disequilibrium in wild mice (2007)
Cathy C. Laurie, Deborah A. Nickerson, Amy D Anderson, Bruce Weir, Robert J. Livingston, Matthew D. Dean, ...
Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci (QTL) for complex traits related to human disease. Hundreds of QTL have been detected, but only...
Jun Zhu, Matthew C. Wiener, Chunsheng Zhang, Arthur Fridman, Eric Minch, Pek Y. Lum, ...
To dissect common human diseases such as obesity and diabetes, a systematic approach is needed to study how genes interact with one another, and with genetic and environmental factors, to determine...
Dosage compensation is less effective in birds than in mammals (2007)
Itoh, Yuichiro, Melamed, Esther, Yang, Xia, Kampf, Kathy, Wang, Susanna, Yehya, Nadir, ...
Abstract Background In animals with heteromorphic sex chromosomes, dosage compensation of sex-chromosome genes is thought to be critical for species survival. Diverse molecular mechanisms have...
Hovatta, Iiris, Zapala, Matthew A, Broide, Ron S, Schadt, Eric E, Libiger, Ondrej, Schork, Nicholas J, ...
Abstract Background Expression quantitative trait locus (eQTL) mapping is used to find loci that are responsible for the transcriptional activity of a particular gene. In recent eQTL studies,...
Jun Zhu, Matthew C. Wiener, Chunsheng Zhang, Arthur Fridman, Eric Minch, Pek Y. Lum, ...
To dissect common human diseases like obesity and diabetes, a systematic approach is needed to study how genes interact with one another, and how genetic and environmental factors and interactions...
GuhaThakurta, Debraj, Xie, Tao, Anand, Manish, Edwards, Stephen W, Li, Guoya, Wang, Susanna S, ...
Abstract Background Changes in gene expression are known to be responsible for phenotypic variation and susceptibility to diseases. Identification and annotation of the genomic sequence variants that...
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight (2006)
Anatole Ghazalpour, Sudheer Doss, Bin Zhang, Susanna Wang, Christopher Plaisier, Ruth Castellanos, ...
Systems biology approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. We use microarray and genetic marker...
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight (2006)
Anatole Ghazalpour, Sudheer Doss, Bin Zhang, Susanna Wang, Christopher Plaisier, Ruth Castellanos, ...
Gene mapping approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. Recently, several groups have proposed...
Susanna Wang, Nadir Yehya, Eric E. Schadt, Hui Wang, Thomas A. Drake, Aldons J. Lusis
The integration of expression profiling with linkage analysis has increasingly been used to identify genes underlying complex phenotypes. The effects of gender on the regulation of many physiological...
Genomic analysis of metabolic pathway gene expression in mice (2005)
Ghazalpour, Anatole, Doss, Sudheer, Sheth, Sonal S, Ingram-Drake, Leslie A, Schadt, Eric E, Lusis, Aldons J, ...
Abstract Background A segregating population of (C57BL/6J × DBA/2J)F2 intercross mice was studied for obesity-related traits and for global gene expression in liver. Quantitative trait locus...
Schadt, Eric E, Edwards, Stephen W, GuhaThakurta, Debraj, Holder, Dan, Ying, Lisa, Svetnik, Vladimir, ...
Abstract Background Computational and microarray-based experimental approaches were used to generate a comprehensive transcript index for the human genome. Oligonucleotide probes designed from...
The Collaborative Cross, a community resource for the genetic analysis of complex traits (2004)
Churchill, Gary A., Airey, David C., Allayee, Hooman, Angel, Joe M., Attie, Alan D., Beatty, Jackson, ...
The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse...
Castle, John, Garrett-Engele, Phil, Armour, Christopher D, Duenwald, Sven J, Loerch, Patrick M, Meyer, Michael R, ...
Abstract Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire...
Castle, John, Garrett-Engele, Phil, Armour, Christopher D, Duenwald, Sven J, Loerch, Patrick M, Meyer, Michael R, ...
A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized...
Schadt, Eric E, Edwards, Stephen W, GuhaThakurta, Debraj, Holder, Dan, Ying, Lisa, Svetnik, Vladimir, ...
A combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts, providing the first experiment-driven annotation of the human...
Cis-acting expression quantitative trait loci in mice
Doss, Sudheer, Schadt, Eric E., Drake, Thomas A., Lusis, Aldons J.
We previously reported the analysis of genome-wide expression profiles and various diabetes-related traits in a segregating cross between inbred mouse strains C57BL/6J (B6) and DBA/2J (DBA). By...
Genomic analysis of metabolic pathway gene expression in mice
Ghazalpour, Anatole, Doss, Sudheer, Sheth, Sonal S, Ingram-Drake, Leslie A, Schadt, Eric E, Lusis, Aldons J, ...
In order to evaluate metabolic pathways associated with obesity, global gene-expression data were integrated with phenotypic and genetic segregation analyses, identifying 13 metabolic pathways the...
Wang, Susanna, Yehya, Nadir, Schadt, Eric E, Wang, Hui, Drake, Thomas A, Lusis, Aldons J
The integration of expression profiling with linkage analysis has increasingly been used to identify genes underlying complex phenotypes. The effects of gender on the regulation of many physiological...
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight
Ghazalpour, Anatole, Doss, Sudheer, Zhang, Bin, Wang, Susanna, Plaisier, Christopher, Castellanos, Ruth, ...
Systems biology approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. We use microarray and genetic marker...
Castle, John, Garrett-Engele, Phil, Armour, Christopher D, Duenwald, Sven J, Loerch, Patrick M, Meyer, Michael R, ...
A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized...
Schadt, Eric E, Edwards, Stephen W, GuhaThakurta, Debraj, Holder, Dan, Ying, Lisa, Svetnik, Vladimir, ...
A combination of microarray data with extensive genome annotations resulted in a set of 28,456 experimentally supported transcripts, providing the first experiment-driven annotation of the human...
Cis-acting expression quantitative trait loci in mice
Doss, Sudheer, Schadt, Eric E., Drake, Thomas A., Lusis, Aldons J.
We previously reported the analysis of genome-wide expression profiles and various diabetes-related traits in a segregating cross between inbred mouse strains C57BL/6J (B6) and DBA/2J (DBA). By...
Genomic analysis of metabolic pathway gene expression in mice
Ghazalpour, Anatole, Doss, Sudheer, Sheth, Sonal S, Ingram-Drake, Leslie A, Schadt, Eric E, Lusis, Aldons J, ...
In order to evaluate metabolic pathways associated with obesity, global gene-expression data were integrated with phenotypic and genetic segregation analyses, identifying 13 metabolic pathways the...
Wang, Susanna, Yehya, Nadir, Schadt, Eric E, Wang, Hui, Drake, Thomas A, Lusis, Aldons J
The integration of expression profiling with linkage analysis has increasingly been used to identify genes underlying complex phenotypes. The effects of gender on the regulation of many physiological...
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight
Ghazalpour, Anatole, Doss, Sudheer, Zhang, Bin, Wang, Susanna, Plaisier, Christopher, Castellanos, Ruth, ...
Systems biology approaches that are based on the genetics of gene expression have been fruitful in identifying genetic regulatory loci related to complex traits. We use microarray and genetic marker...
Tissue-specific expression and regulation of sexually dimorphic genes in mice
Yang, Xia, Schadt, Eric E., Wang, Susanna, Wang, Hui, Arnold, Arthur P., Ingram-Drake, Leslie, ...
We report a comprehensive analysis of gene expression differences between sexes in multiple somatic tissues of 334 mice derived from an intercross between inbred mouse strains C57BL/6J and C3H/HeJ....
Hovatta, Iiris, Zapala, Matthew A, Broide, Ron S, Schadt, Eric E, Libiger, Ondrej, Schork, Nicholas J, ...
Gene expression profiles of five brain regions from six inbred mouse strains suggest that many regulatory networks are highly specific to particular brain regions.
Zhu, Jun, Wiener, Matthew C, Zhang, Chunsheng, Fridman, Arthur, Minch, Eric, Lum, Pek Y, ...
To dissect common human diseases such as obesity and diabetes, a systematic approach is needed to study how genes interact with one another, and with genetic and environmental factors, to determine...
Pharmacogenetics of metformin response: a step in the path toward personalized medicine
Reitman, Marc L., Schadt, Eric E.
Type 2 diabetes mellitus affects 9.6% of the adults in the United States and more than 200 million people worldwide. Diabetes can be a devastating disease, but it can now be treated with nine classes...
Linkage Disequilibrium in Wild Mice
Laurie, Cathy C, Nickerson, Deborah A, Anderson, Amy D, Weir, Bruce S, Livingston, Robert J, Dean, Matthew D, ...
Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only...
Meng, Haijin, Vera, Iset, Che, Nam, Wang, Xuping, Wang, Susanna S., Ingram-Drake, Leslie, ...
The genetic factors contributing to the complex disorder of myocardial calcification are largely unknown. Using a mouse model, we fine-mapped the major locus (Dyscalc1) contributing to the dystrophic...
Moving toward a system genetics view of disease
Sieberts, Solveig K., Schadt, Eric E.
Testing hundreds of thousands of DNA markers in human, mouse, and other species for association to complex traits like disease is now a reality. However, information on how variations in DNA impact...
Dosage compensation is less effective in birds than in mammals
Itoh, Yuichiro, Melamed, Esther, Yang, Xia, Kampf, Kathy, Wang, Susanna, Yehya, Nadir, ...
Mapping the Genetic Architecture of Gene Expression in Human Liver
Schadt, Eric E, Molony, Cliona, Chudin, Eugene, Hao, Ke, Yang, Xia, Lum, Pek Y, ...
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order...
Calibrating the Performance of SNP Arrays for Whole-Genome Association Studies
Hao, Ke, Schadt, Eric E., Storey, John D.
To facilitate whole-genome association studies (WGAS), several high-density SNP genotyping arrays have been developed. Genetic coverage and statistical power are the primary benchmark metrics in...
Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences
Su, Wan-Lin, Modrek, Barmak, GuhaThakurta, Debraj, Edwards, Stephen, Shah, Jyoti K, Kulkarni, Amit V, ...
Keller, Mark P., Choi, YounJeong, Wang, Ping, Belt Davis, Dawn, Rabaglia, Mary E., Oler, Angie T., ...
Insulin resistance is necessary but not sufficient for the development of type 2 diabetes. Diabetes results when pancreatic beta-cells fail to compensate for insulin resistance by increasing insulin...