Eric Schadt

Summary

Affiliation: Merck Research Laboratories
Country: USA

Publications

  1. ncbi Genomics and genome-wide association studies: an integrative approach to expression QTL mapping
    James H Degnan
    Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Genomics 92:129-33. 2008
  2. ncbi Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California-Los Angeles, Los Angeles, CA 90095-1732, USA
    Mamm Genome 17:466-79. 2006
  3. ncbi Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing
    John Castle
    Rosetta Inpharmatics, Merck and Co, Inc, 12040 115th Ave NE, Kirkland, Washington 98034, USA
    Genome Biol 4:R66. 2003
  4. ncbi Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels
    Alessandra C Cervino
    Rosetta Inpharmatics, LLC, Seattle, WA 98109, USA
    Genomics 86:505-17. 2005
  5. ncbi Novel integrative genomics strategies to identify genes for complex traits
    E E Schadt
    Rosetta Inpharmatics, LLC, a wholly owned subsidiary of Merck and Co, Inc, Seattle, WA 98109, USA
    Anim Genet 37:18-23. 2006
  6. ncbi Moving toward a system genetics view of disease
    Solveig K Sieberts
    Rosetta Inpharmatics, LLC, 401 Terry Avenue N, Seattle, Washington 98109, USA
    Mamm Genome 18:389-401. 2007
  7. ncbi Dosage compensation is less effective in birds than in mammals
    Yuichiro Itoh
    Department of Physiological Science, University of California, Los Angeles, CA 90095, USA
    J Biol 6:2. 2007
  8. ncbi Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease
    Radu Dobrin
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, Seattle, Washington 98109, USA
    Genome Biol 10:R55. 2009
  9. ncbi DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies
    Iiris Hovatta
    The Salk Institute for Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 8:R25. 2007
  10. ncbi Genomic analysis of metabolic pathway gene expression in mice
    Anatole Ghazalpour
    Department of Human Genetics, Molecular Biology Institute, University of California, Los Angeles, CA 90095 1679, USA
    Genome Biol 6:R59. 2005

Collaborators

Detail Information

Publications80

  1. ncbi Genomics and genome-wide association studies: an integrative approach to expression QTL mapping
    James H Degnan
    Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Genomics 92:129-33. 2008
    ..We demonstrate that our family-based screening approach performs well in the analysis of integrative genomic datasets and that screening using either heritability or conditional power produces similar, though not identical, results...
  2. ncbi Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California-Los Angeles, Los Angeles, CA 90095-1732, USA
    Mamm Genome 17:466-79. 2006
    ..In this review we discuss the basic concepts and applications of this integrative genomic approach to cardiovascular and metabolic diseases...
  3. ncbi Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing
    John Castle
    Rosetta Inpharmatics, Merck and Co, Inc, 12040 115th Ave NE, Kirkland, Washington 98034, USA
    Genome Biol 4:R66. 2003
    ....
  4. ncbi Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels
    Alessandra C Cervino
    Rosetta Inpharmatics, LLC, Seattle, WA 98109, USA
    Genomics 86:505-17. 2005
    ....
  5. ncbi Novel integrative genomics strategies to identify genes for complex traits
    E E Schadt
    Rosetta Inpharmatics, LLC, a wholly owned subsidiary of Merck and Co, Inc, Seattle, WA 98109, USA
    Anim Genet 37:18-23. 2006
    ..A number of novel genes for disease phenotypes have been identified as a result of these approaches, highlighting the utility of integrating orthogonal sources of data to get at the underlying causes of disease...
  6. ncbi Moving toward a system genetics view of disease
    Solveig K Sieberts
    Rosetta Inpharmatics, LLC, 401 Terry Avenue N, Seattle, Washington 98109, USA
    Mamm Genome 18:389-401. 2007
    ....
  7. ncbi Dosage compensation is less effective in birds than in mammals
    Yuichiro Itoh
    Department of Physiological Science, University of California, Los Angeles, CA 90095, USA
    J Biol 6:2. 2007
    ..Dosage compensation is not understood in birds, in which females (ZW) and males (ZZ) differ in the number of Z chromosomes...
  8. ncbi Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease
    Radu Dobrin
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, Seattle, Washington 98109, USA
    Genome Biol 10:R55. 2009
    ....
  9. ncbi DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies
    Iiris Hovatta
    The Salk Institute for Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 8:R25. 2007
    ....
  10. ncbi Genomic analysis of metabolic pathway gene expression in mice
    Anatole Ghazalpour
    Department of Human Genetics, Molecular Biology Institute, University of California, Los Angeles, CA 90095 1679, USA
    Genome Biol 6:R59. 2005
    ..Quantitative trait locus analyses were applied to the subcutaneous fat-mass trait and all gene-expression data. These data were then used to identify gene sets that are differentially perturbed in lean and obese mice...
  11. ncbi Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations
    Debraj GuhaThakurta
    Genetics, Rosetta Inpharmatics LLC, Merck and Co, Inc 401 Terry Avenue North, Seattle, WA 98109, USA
    BMC Genomics 7:235. 2006
    ..This led us to characterize the SNPs in promoter (5 Kb upstream) and non-coding gene regions (introns and 5 Kb downstream) (cis-SNPs) and the effects they may have on putative transcription factor binding sites...
  12. ncbi Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences
    Wan Lin Su
    Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
    BMC Genomics 9:273. 2008
    ..Here, we surveyed the effect of strain and sex on liver gene and exon expression using male and female mice from three different inbred strains...
  13. ncbi Disentangling molecular relationships with a causal inference test
    Joshua Millstein
    Genetics Department, Rosetta Inpharmatics, LLC, Seattle, Washington 98109, USA
    BMC Genet 10:23. 2009
    ..g. a molecular species, which potentially mediates a known causal association between a locus and a quantitative trait...
  14. ncbi Statistical power of phylo-HMM for evolutionarily conserved element detection
    Xiaodan Fan
    Department of Statistics, Harvard University, Boston, MA, USA
    BMC Bioinformatics 8:374. 2007
    ..Phylo-HMM was recently introduced to detect conserved elements based on multiple genome alignments, but the method has not been rigorously evaluated...
  15. ncbi Embracing complexity, inching closer to reality
    Eric E Schadt
    Rosetta Inpharmatics, 401 Terry Avenue North, Seattle, WA 98109, USA
    Sci STKE 2005:pe40. 2005
    ....
  16. ncbi Mapping the genetic architecture of gene expression in human liver
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Biol 6:e107. 2008
    ..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
  17. ncbi Exploiting naturally occurring DNA variation and molecular profiling data to dissect disease and drug response traits
    Eric E Schadt
    Rosetta Inpharmatics, LLC, Seattle, Washington 98109, USA
    Curr Opin Biotechnol 16:647-54. 2005
    ..Key to this integration has been the development and application of sophisticated algorithms to mine the diversity of data...
  18. ncbi Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Reverse engineering gene networks to identify key drivers of complex disease phenotypes
    Eric E Schadt
    Rosetta Inpharmatics, LLC, Seattle, WA 98109, USA
    J Lipid Res 47:2601-13. 2006
    ..Therefore, these networks can lead to defining pathways underlying disease more objectively and to identifying biomarkers and more-robust points for therapeutic intervention...
  19. ncbi Codon and rate variation models in molecular phylogeny
    Eric Schadt
    Department of Biomathematics, UCLA School of Medicine, Los Angeles, CA, USA
    Mol Biol Evol 19:1534-49. 2002
    ..Our phylogeny program LINNAEUS implements algorithms realizing these goals. Readers may consult our companion article in this issue for several examples...
  20. ncbi An integrative genomics approach to infer causal associations between gene expression and disease
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington 98109, USA
    Nat Genet 37:710-7. 2005
    ..We also demonstrate the utility of this approach by identifying and experimentally validating the involvement of three new genes in susceptibility to obesity...
  21. ncbi Applications of codon and rate variation models in molecular phylogeny
    Eric E Schadt
    Department of Biomathematics, UCLA School of Medicine, Los Angeles, USA
    Mol Biol Evol 19:1550-62. 2002
    ..All the new statistical algorithms applied are incorporated in our phylogeny software LINNAEUS, which is tuned for performance and modeling flexibility...
  22. ncbi Genetics of gene expression surveyed in maize, mouse and man
    Eric E Schadt
    Rosetta Inpharmatics, LLC, 12040 115th Avenue N E, Kirkland, Washington 98034, USA
    Nature 422:297-302. 2003
    ..We identify a gene expression pattern strongly associated with obesity in a murine cross, and observe two distinct obesity subtypes. Furthermore, we find that these obesity subtypes are under the control of different loci...
  23. ncbi A new paradigm for drug discovery: integrating clinical, genetic, genomic and molecular phenotype data to identify drug targets
    E E Schadt
    Rosetta Inpharmatics LLC, 12040 115th Avenue N E, Kirkland, WA 98034, U S A
    Biochem Soc Trans 31:437-43. 2003
    ....
  24. ncbi A comprehensive transcript index of the human genome generated using microarrays and computational approaches
    Eric E Schadt
    Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, WA 98034, USA
    Genome Biol 5:R73. 2004
    ..Further, expression activity over at least six conditions was more generally assessed using genomic tiling arrays consisting of probes tiled through a repeat-masked version of the genomic sequence making up chromosomes 20 and 22...
  25. ncbi Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data
    Susanna S Wang
    Department of Human Genetics, University of California at Los Angeles, Los Angeles, CA 90095 1679, USA
    Circ Res 101:e11-30. 2007
    ..Thus, global gene expression in peripheral tissues can reflect the systemic perturbations that contribute to atherosclerosis...
  26. ncbi Expression quantitative trait loci: replication, tissue- and sex-specificity in mice
    Atila Van Nas
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genetics 185:1059-68. 2010
    ..We conclude that most local eQTL are highly replicable between mouse crosses, tissues, and sex as compared to distal eQTL, which exhibited modest replicability...
  27. ncbi Cis-acting expression quantitative trait loci in mice
    Sudheer Doss
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Genome Res 15:681-91. 2005
    ....
  28. ncbi Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits
    Margarete Mehrabian
    Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095 1679, USA
    Nat Genet 37:1224-33. 2005
    ....
  29. ncbi Variations in DNA elucidate molecular networks that cause disease
    Yanqing Chen
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, 401 Terry Avenue North, Seattle, Washington 98109, USA
    Nature 452:429-35. 2008
    ..Our analysis provides direct experimental support that complex traits such as obesity are emergent properties of molecular networks that are modulated by complex genetic loci and environmental factors...
  30. ncbi Integrating genetic and network analysis to characterize genes related to mouse weight
    Anatole Ghazalpour
    Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
    PLoS Genet 2:e130. 2006
    ..Our approach results in the identification of genetic targets that influence gene modules (pathways) that are related to the clinical phenotypes of interest...
  31. ncbi Correction for hidden confounders in the genetic analysis of gene expression
    Jennifer Listgarten
    Microsoft Research, 1100 Glendon Avenue, Suite PH1, Los Angeles, CA, USA
    Proc Natl Acad Sci U S A 107:16465-70. 2010
    ..Lastly, our software and the associations we found with it are available at http://www.microsoft.com/science...
  32. ncbi Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks
    Xia Yang
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    Nat Genet 41:415-23. 2009
    ..Integration of gene expression in the design and analysis of traditional F(2) intercross studies allows high-confidence prediction of causal genes and identification of pathways and networks involved...
  33. ncbi Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history
    Laura B Scheinfeldt
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Mol Biol Evol 26:1357-67. 2009
    ..These results provide new insights into the evolutionary history of ALMS1 in humans and suggest that selective events identified in genomewide scans may be more complex than currently appreciated...
  34. ncbi Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network
    Zhidong Tu
    Rosetta Inpharmatics, a wholly owned subsidiary of Merck and Co, Inc, Seattle, Washington 98109, USA
    Genome Res 19:1057-67. 2009
    ..We experimentally validated one of the predictions, S1pr2, as a novel candidate gene for T2D...
  35. ncbi Tissue-specific expression and regulation of sexually dimorphic genes in mice
    Xia Yang
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 16:995-1004. 2006
    ..Moreover, many tissue-specific transcription factor binding sites were found to be enriched in the sexually dimorphic genes...
  36. ncbi Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes
    Hua Zhong
    Department of Genetics, Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Genet 6:e1000932. 2010
    ....
  37. ncbi Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies
    Ke Hao
    Genetics Department, Rosetta Inpharmatics, a Wholly Owned Subsidiary of Merck and Co Inc, Seattle, Washington, USA
    BMC Genet 10:27. 2009
    ..Genome-wide imputation of untyped markers allows us to address these issues in a direct fashion...
  38. ncbi Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes
    Pek Yee Lum
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, Seattle, WA 98109, USA
    J Neurochem 97:50-62. 2006
    ..We identify core functional modules making up the brain transcriptional network in mice that are coherent for core biological processes associated with metabolic disease traits including obesity and diabetes...
  39. ncbi Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver
    Xia Yang
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, Seattle, Washington 98109, USA
    Genome Res 20:1020-36. 2010
    ..This systematic survey provides a comprehensive view of the functionality, genetic control, and interactions of P450s...
  40. ncbi Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity
    Susanna Wang
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
    PLoS Genet 2:e15. 2006
    ..These data have implications on the potential effects of sex on the genetic regulation of other complex traits...
  41. ncbi Calibrating the performance of SNP arrays for whole-genome association studies
    Ke Hao
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Genet 4:e1000109. 2008
    ....
  42. ncbi Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation
    Tomas Babak
    Rosetta Inpharmatics, LLC, 401 Terry Ave N, Seattle, WA 98109, USA
    BMC Genomics 11:473. 2010
    ....
  43. ncbi A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background
    Richard C Davis
    Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California, Los Angeles, CA 90095 1679, USA
    Genomics 86:259-70. 2005
    ..These 65 strains cover more than 95% of the autosomal genome and should facilitate the analysis of the many genetic trait differences that have been reported between these parental strains...
  44. ncbi Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice
    Veronica V Colinayo
    Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
    Mamm Genome 14:464-71. 2003
    ..In this intercross, the genes primarily influencing atherosclerosis are distinct from those controlling plasma lipid levels...
  45. ncbi Drug discovery in a multidimensional world: systems, patterns, and networks
    Joel T Dudley
    Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, USA
    J Cardiovasc Transl Res 3:438-47. 2010
    ..When available, specific applications to cardiovascular drug discovery are highlighted and discussed...
  46. ncbi Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks
    Atila Van Nas
    Department of Human Genetics, University of California, Los Angeles, California 90095 1679, USA
    Endocrinology 150:1235-49. 2009
    ..This study indicates that gonadal hormones play a strong role in sex differences in gene expression. In addition, it results in the identification of sex-specific gene coexpression networks related to genetic and metabolic traits...
  47. ncbi Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
    Jun Zhu
    Rosetta Inpharmatics, LLC, Seattle, Washington 98109, USA
    Nat Genet 40:854-61. 2008
    ..We then prospectively validate predictions, providing direct experimental evidence that predictive networks can be constructed by integrating multiple, appropriate data types...
  48. ncbi Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases
    Kai Wang
    Department of Genetics, Rosetta Inpharmatics, Seattle, Washington, USA
    PLoS Comput Biol 5:e1000616. 2009
    ..Taken together, our approach represents a novel step forward in integrating gene co-expression networks from multiple large scale datasets to leverage not only common information but also differences that are dataset-specific...
  49. ncbi Integrating pathway analysis and genetics of gene expression for genome-wide association studies
    Hua Zhong
    Rosetta Inpharmatics, LLC, and Merck and Co, Inc, 401 Terry Avenue North, Seattle, WA 98109, USA
    Am J Hum Genet 86:581-91. 2010
    ..The integration of pathways and eSNPs provides putative functional bridges between GWAS and candidate genes or pathways, thus serving as a potential powerful approach to identifying biological mechanisms underlying GWAS findings...
  50. ncbi A genome-wide set of congenic mouse strains derived from CAST/Ei on a C57BL/6 background
    Richard C Davis
    Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA 90095 1679, USA
    Genomics 90:306-13. 2007
    ....
  51. ncbi An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association
    Charles R Farber
    Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, California, USA
    J Bone Miner Res 24:105-16. 2009
    ..Integration of multiple genetic and genomic data sets can substantially improve the efficiency of QTL fine-mapping and candidate gene identification...
  52. ncbi Ultrafine mapping of SNPs from mouse strains C57BL/6J, DBA/2J, and C57BLKS/J for loci contributing to diabetes and atherosclerosis susceptibility
    Richard C Davis
    Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, 47 123 CHS, Los Angeles, CA 90095 1679, USA
    Diabetes 54:1191-9. 2005
    ..To further prioritize these candidates, we identified those cis-acting expression quantitative trait loci whose expression significantly correlates with diabetes-related phenotypes...
  53. ncbi A survey of cancer cell lines reveals highly structured and hierarchical relationships within and between DNA and mRNA that may be the result of selection
    Tao Xie
    Rosetta Inpharmatics LLC, Seattle Washington, USA
    OMICS 14:91-7. 2010
    ..Given that the cohort includes many tissue types, our observations may identify a common and important underlying structure present in human tumors...
  54. ncbi Magnitude of stratification in human populations and impacts on genome wide association studies
    Ke Hao
    Genetics Department, Rosetta Inpharmatics, a Wholly Owned Subsidiary of Merck and Co Inc, Seattle, Washington, USA
    PLoS ONE 5:e8695. 2010
    ..For example, rs646776 and rs10903129 have previously been associated with lipid levels and coronary heart disease risk, however, the rs10903129 eQTL was missed in the eigenvector adjusted analysis...
  55. ncbi Microarray standard data set and figures of merit for comparing data processing methods and experiment designs
    Yudong D He
    Rosetta Inpharmatics Inc, 12 040 115th Avenue Northeast, Kirkland, WA 98034, USA
    Bioinformatics 19:956-65. 2003
    ..AVAILABILITY/SUPPLEMENTARY INFORMATION: Expression data and supplementary information are available at http://www.rii.com/publications/2003/HE_SDS.htm..
  56. ncbi The C3a anaphylatoxin receptor is a key mediator of insulin resistance and functions by modulating adipose tissue macrophage infiltration and activation
    Yael Mamane
    Department of Biochemistry and Molecular Biology, Merck Frosst Centre for Therapeutic Research, Kirkland, Quebec, Canada
    Diabetes 58:2006-17. 2009
    ..A mouse genomic F2 cross biology was performed and identified several causal genes linked to type 2 diabetes, including the complement pathway...
  57. ncbi Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments
    Jason M Johnson
    Rosetta Inpharmatics LLC, 401 Terry Avenue North, Seattle, WA 98109, USA
    Trends Genet 21:93-102. 2005
    ..In this article, we discuss different explanations for this phenomenon...
  58. ncbi Simultaneous clustering of multiple gene expression and physical interaction datasets
    Manikandan Narayanan
    Department of Genetics, Rosetta Inpharmatics Merck, Seattle, Washington, United States of America
    PLoS Comput Biol 6:e1000742. 2010
    ....
  59. ncbi Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays
    Jason M Johnson
    Rosetta Inpharmatics LLC, Merck and Co, Inc, 12040 115th Avenue N E, Kirkland, WA 98034, USA
    Science 302:2141-4. 2003
    ..Adding to previous studies, the results indicate that at least 74% of human multi-exon genes are alternatively spliced...
  60. ncbi Pharmacogenetics of metformin response: a step in the path toward personalized medicine
    Marc L Reitman
    Metabolic Disorders Department, Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, NJ 07065, USA
    J Clin Invest 117:1226-9. 2007
    ..We discuss metformin, OCT1, pharmacogenetics, and how the integrative genomics revolution is likely to change our understanding and treatment of diabetes...
  61. ncbi Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics
    Haijin Meng
    Department of Medicine, Cardiology Division, University of California Los Angeles, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 104:4530-5. 2007
    ..Our results demonstrate the power of the integrative genomics in discovering causal genes and pathways underlying complex traits...
  62. ncbi Integrative genomics and drug development
    Pek Y Lum
    Department of Genetics, Rosetta Inpharmatics, LLC, 401 Terry Avenue North, Seattle, WA 98109, USA
    Pharmacogenomics 10:203-12. 2009
    ....
  63. ncbi Identification and validation of genes affecting aortic lesions in mice
    Xia Yang
    Department of Molecular Profiling, Rosetta Inpharmactics LLC, a Wholly Owned Subsidiary of Merck and Co Inc, Seattle, Washington, USA
    J Clin Invest 120:2414-22. 2010
    ..Our findings therefore validate the ability of causality testing procedures to provide insights into the mechanisms underlying atherosclerosis development...
  64. ncbi A systems biology approach to drug discovery
    Jun Zhu
    Rosetta Inpharmatics, LLC, a Wholly Owned Subsidiary of Merck and Co Inc, Seattle, WA 98109, USA
    Adv Genet 60:603-35. 2008
    ..To highlight these different approaches in practice, we step through an example on how Insig2 was identified as a causal factor for plasma cholesterol levels in mice...
  65. ncbi Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations
    Jun Zhu
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Comput Biol 3:e69. 2007
    ....
  66. ncbi A systematic approach to multifactorial cardiovascular disease: causal analysis
    Stephen M Schwartz
    Department of Pathology, University of Washington, Seattle, WA, USA
    Arterioscler Thromb Vasc Biol 32:2821-35. 2012
    ..We will describe this approach using the term causal analysis. Finally, we will describe how causal analysis is already being used to decipher the interactions among cytokines as causes of cardiovascular disease...
  67. ncbi A family-based test for correlation between gene expression and trait values
    Peter Kraft
    Department of Biostatistics, University of California at Los Angeles, Los Angeles, CA 90095 1772, USA
    Am J Hum Genet 72:1323-30. 2003
    ....
  68. ncbi Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments
    Eric E Schadt
    Department of Genetics, Rosetta Inpharmatics, LLC, a Merck and Co, Inc, 401 Terry Avenue North, Seattle, WA 98109, USA
    Genetica 136:259-69. 2009
    ....
  69. ncbi Disruption of the aortic elastic lamina and medial calcification share genetic determinants in mice
    Susanna S Wang
    Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
    Circ Cardiovasc Genet 2:573-82. 2009
    ..Disruption of the elastic lamina, as an early indicator of aneurysm formation, and vascular calcification frequently occur together in atherosclerotic lesions of humans...
  70. ncbi The effect of food intake on gene expression in human peripheral blood
    Amy S Leonardson
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, Seattle, WA 98109, USA
    Hum Mol Genet 19:159-69. 2010
    ..Our results suggest that the pair of fasted/fed blood expression profiles provide more comprehensive information about an individual's metabolic states...
  71. ncbi Integrating genetic and gene expression data to study the metabolic syndrome and diabetes in mice
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095 1732, USA
    Am J Ther 12:503-11. 2005
    ..Recent advances in genetics and gene expression technology have greatly increased the knowledge to be derived from this approach when applied to traditional genetic studies...
  72. ncbi Characterizing dynamic changes in the human blood transcriptional network
    Jun Zhu
    Department of Genetics, Rosetta Inpharmatics, LLC, a wholly owned subsidiary of Merck and Co, Inc, Seattle, Washington, USA
    PLoS Comput Biol 6:e1000671. 2010
    ..The results could have broader implications for the design of studies of disease association and drug response in clinical trials...
  73. ncbi A network view of disease and compound screening
    Eric E Schadt
    Eric E Schadt is at Rosetta Inpharmatics, LLC, Merck and Co, Inc, 401 Terry Avenue North, Seattle, Washington 98109, USA
    Nat Rev Drug Discov 8:286-95. 2009
    ..In this article, we describe how such an approach offers a novel way to understand biology, characterize disease and ultimately develop improved therapies, and discuss the challenges to realizing these goals...
  74. ncbi Linkage disequilibrium in wild mice
    Cathy C Laurie
    Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 3:e144. 2007
    ....
  75. ncbi Sequence variation in NPC1L1 and association with improved LDL-cholesterol lowering in response to ezetimibe treatment
    Jason S Simon
    Discovery Technologies, Schering Plough Research Institute, NJ 07090, USA
    Genomics 86:648-56. 2005
    ....
  76. ncbi Genetics of gene expression and its effect on disease
    Valur Emilsson
    deCODE Genetics, 101 Reykjavik, Iceland
    Nature 452:423-8. 2008
    ..A core network module in humans and mice was identified that is enriched for genes involved in the inflammatory and immune response and has been found to be causally associated to obesity-related traits...
  77. ncbi A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
    Mark P Keller
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53076, USA
    Genome Res 18:706-16. 2008
    ....
  78. ncbi Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice
    Iiris Hovatta
    The Salk Institute for Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nature 438:662-6. 2005
    ..Both of these genes are involved in oxidative stress metabolism, linking this pathway with anxiety-related behaviour...
  79. ncbi Systems biology and its potential role in radiobiology
    Ludwig Feinendegen
    Department of Nuclear Medicine, University Hospital, Heinrich Heine University, Dusseldorf, Germany
    Radiat Environ Biophys 47:5-23. 2008
    ..In this context, we discuss in this article examples of relatively small, yet very useful models that elucidate selected aspects of the effects of exposure to ionizing radiation and may shine a light on the path before us...
  80. ncbi The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Gary A Churchill
    The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
    Nat Genet 36:1133-7. 2004
    ..The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease...