Eric E Schadt

Summary

Publications

  1. doi request reprint Molecular networks as sensors and drivers of common human diseases
    Eric E Schadt
    Pacific Biosciences, 1505 Adams Drive, Menlo Park, California 94025, USA
    Nature 461:218-23. 2009
  2. pmc 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
  3. pmc Computational solutions to large-scale data management and analysis
    Eric E Schadt
    Pacific Biosciences, Menlo Park, California 94025, USA
    Nat Rev Genet 11:647-57. 2010
  4. doi request reprint A window into third-generation sequencing
    Eric E Schadt
    Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
    Hum Mol Genet 19:R227-40. 2010
  5. pmc 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
  6. pmc 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
  7. pmc 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
  8. pmc 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
  9. ncbi request reprint 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
  10. pmc Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting
    John R Lamb
    Rosetta Inpharmatics, LLC, Seattle, Washington, United States of America
    PLoS ONE 6:e20090. 2011

Collaborators

Detail Information

Publications53

  1. doi request reprint Molecular networks as sensors and drivers of common human diseases
    Eric E Schadt
    Pacific Biosciences, 1505 Adams Drive, Menlo Park, California 94025, USA
    Nature 461:218-23. 2009
    ....
  2. pmc 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
    ....
  3. pmc Computational solutions to large-scale data management and analysis
    Eric E Schadt
    Pacific Biosciences, Menlo Park, California 94025, USA
    Nat Rev Genet 11:647-57. 2010
    ..Here we discuss how we can master the different types of computational environments that exist - such as cloud and heterogeneous computing - to successfully tackle our big data problems...
  4. doi request reprint A window into third-generation sequencing
    Eric E Schadt
    Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA
    Hum Mol Genet 19:R227-40. 2010
    ....
  5. pmc 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...
  6. pmc 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...
  7. pmc 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...
  8. pmc 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...
  9. ncbi request reprint 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
    ....
  10. pmc Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting
    John R Lamb
    Rosetta Inpharmatics, LLC, Seattle, Washington, United States of America
    PLoS ONE 6:e20090. 2011
    ..The relationships between these two sets of predictive genes and the general process of tumorigenesis and disease progression remains unclear...
  11. pmc 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...
  12. pmc Integrating external biological knowledge in the construction of regulatory networks from time-series expression data
    Kenneth Lo
    Department of Microbiology, University of Washington, Box 358070, Seattle, WA 98195, USA
    BMC Syst Biol 6:101. 2012
    ..We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge...
  13. ncbi request reprint 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...
  14. pmc 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...
  15. pmc 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...
  16. pmc 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...
  17. pmc 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
    ....
  18. pmc 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...
  19. pmc 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...
  20. pmc 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
    ....
  21. pmc 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...
  22. pmc 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...
  23. doi request reprint 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
    ....
  24. pmc Inferring causal genomic alterations in breast cancer using gene expression data
    Linh M Tran
    Sage Bionetworks, Seattle, WA 98109, USA
    BMC Syst Biol 5:121. 2011
    ..Many valuable studies lack genomic data to detect CNV; therefore, methods that are able to infer CNVs from gene expression data would help maximize the value of these studies...
  25. pmc Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation
    Jun Zhu
    Sage Bionetworks, Seattle, Washington, United States of America
    PLoS Biol 10:e1001301. 2012
    ....
  26. pmc 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...
  27. pmc Identification of genes and networks driving cardiovascular and metabolic phenotypes in a mouse F2 intercross
    Jonathan M J Derry
    Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck and Co, Seattle, Washington, United States of America
    PLoS ONE 5:e14319. 2010
    ..Overall this study demonstrates how integrating gene expression data with QTL analysis in a network-based framework can aid in the elucidation of the molecular drivers of disease that can be translated from mice to humans...
  28. pmc 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...
  29. pmc 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
    ....
  30. pmc 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...
  31. pmc Construction of regulatory networks using expression time-series data of a genotyped population
    Ka Yee Yeung
    Department of Microbiology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 108:19436-41. 2011
    ..Applying our construction method to previously published data demonstrates that our method is competitive with leading network construction algorithms in the literature...
  32. pmc Systematic detection of polygenic cis-regulatory evolution
    Hunter B Fraser
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Genet 7:e1002023. 2011
    ..These coordinated adaptations may contribute to divergence in a wide range of morphological, physiological, and behavioral phenotypes...
  33. pmc 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
    ....
  34. pmc Identification of causal genes, networks, and transcriptional regulators of REM sleep and wake
    Joshua Millstein
    Sage Bionetworks, Seattle, WA, USA
    Sleep 34:1469-77. 2011
    ..Thus, the aim of this study was to use systems genetics and statistical approaches to uncover the genetic networks underlying 2 primary sleep traits in the mouse: 24-h duration of REM sleep and wake...
  35. pmc Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques
    Wan Lin Su
    Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
    Mol Syst Biol 7:490. 2011
    ....
  36. pmc 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...
  37. ncbi request reprint 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...
  38. doi request reprint 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...
  39. doi request reprint Assessing the prospects of genome-wide association studies performed in inbred mice
    Wan Lin Su
    Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
    Mamm Genome 21:143-52. 2010
    ....
  40. pmc 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
    ....
  41. pmc 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
    ....
  42. pmc 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...
  43. doi request reprint 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
    ....
  44. ncbi request reprint Embracing complexity, inching closer to reality
    Eric E Schadt
    Rosetta Inpharmatics, 401 Terry Avenue North, Seattle, WA 98109, USA
    Sci STKE 2005:pe40. 2005
    ....
  45. pmc A hybrid approach for the automated finishing of bacterial genomes
    Ali Bashir
    Pacific Biosciences, Menlo Park, California, USA
    Nat Biotechnol 30:701-7. 2012
    ..This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly...
  46. doi request reprint 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...
  47. ncbi request reprint 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...
  48. pmc Gene bionetwork analysis of ovarian primordial follicle development
    Eric E Nilsson
    Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
    PLoS ONE 5:e11637. 2010
    ..This is one of the first applications of network analysis to a normal developmental process. These observations provide insights into potential therapeutic targets for preventing ovarian disease and promoting female reproduction...
  49. pmc The origin of the Haitian cholera outbreak strain
    Chen Shan Chin
    Pacific Biosciences, Menlo Park, CA, USA
    N Engl J Med 364:33-42. 2011
    ..Although cholera has been present in Latin America since 1991, it had not been epidemic in Haiti for at least 100 years. Recently, however, there has been a severe outbreak of cholera in Haiti...
  50. pmc 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
    ....
  51. ncbi request reprint 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...
  52. pmc 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
    ....
  53. ncbi request reprint 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...