John C Castle

Summary

Affiliation: Merck Research Laboratories
Country: USA

Publications

  1. pmc Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines
    John C Castle
    Rosetta Inpharmatics LLC, Seattle, WA 98109, USA
    Nat Genet 40:1416-25. 2008
  2. pmc Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles
    Zhengyan Kan
    Rosetta Inpharmatics LLC, Merck and Co, Inc 401 Terry Ave N, Seattle, WA 98109, USA
    Nucleic Acids Res 33:5659-66. 2005
  3. pmc Development of a microarray platform for FFPET profiling: application to the classification of human tumors
    Sven Duenwald
    Translational Sciences, Department of Molecular Profiling, Merck Research Laboratories, Seattle, WA 98109, USA
    J Transl Med 7:65. 2009
  4. pmc 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
  5. pmc Comparative expression pathway analysis of human and canine mammary tumors
    Paolo Uva
    IRBM P Angeletti, Merck MRL Rome, Pomezia, Italy
    BMC Genomics 10:135. 2009
  6. pmc ACC2 is expressed at high levels in human white adipose and has an isoform with a novel N-terminus [corrected]
    John C Castle
    Rosetta Inpharmatics LLC, Seattle, Washington, United States of America
    PLoS ONE 4:e4369. 2009
  7. pmc Definition, conservation and epigenetics of housekeeping and tissue-enriched genes
    Xinwei She
    Rosetta Inpharmatics LLC, Seattle, WA 98109, USA
    BMC Genomics 10:269. 2009
  8. 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
  9. pmc NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children
    Marissa Vignali
    Seattle Biomedical Research Institute, Seattle, Washington, USA
    J Clin Invest 121:1119-29. 2011
  10. pmc DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
    John C Castle
    Rosetta Inpharmatics LLC, Merck and Co, Inc, Seattle, Washington 98109, USA
    BMC Genomics 11:244. 2010

Collaborators

Detail Information

Publications15

  1. pmc Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines
    John C Castle
    Rosetta Inpharmatics LLC, Seattle, WA 98109, USA
    Nat Genet 40:1416-25. 2008
    ..UCUCU and UGCAUG seem to have similar function but independent action, occurring 5' and 3', respectively, of 33% of the cassette exons upregulated in skeletal muscle but co-occurring for only 2%...
  2. pmc Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles
    Zhengyan Kan
    Rosetta Inpharmatics LLC, Merck and Co, Inc 401 Terry Ave N, Seattle, WA 98109, USA
    Nucleic Acids Res 33:5659-66. 2005
    ....
  3. pmc Development of a microarray platform for FFPET profiling: application to the classification of human tumors
    Sven Duenwald
    Translational Sciences, Department of Molecular Profiling, Merck Research Laboratories, Seattle, WA 98109, USA
    J Transl Med 7:65. 2009
    ..Methods are needed to profile these FFPET samples that are linked to clinical outcomes to generate hypotheses that could lead to classifiers for clinical applications...
  4. pmc 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...
  5. pmc Comparative expression pathway analysis of human and canine mammary tumors
    Paolo Uva
    IRBM P Angeletti, Merck MRL Rome, Pomezia, Italy
    BMC Genomics 10:135. 2009
    ....
  6. pmc ACC2 is expressed at high levels in human white adipose and has an isoform with a novel N-terminus [corrected]
    John C Castle
    Rosetta Inpharmatics LLC, Seattle, Washington, United States of America
    PLoS ONE 4:e4369. 2009
    ..The results demonstrate a significant difference in ACC expression between human and rodents, which may introduce difficulties for the use of rodent models for development of ACC inhibitors...
  7. pmc Definition, conservation and epigenetics of housekeeping and tissue-enriched genes
    Xinwei She
    Rosetta Inpharmatics LLC, Seattle, WA 98109, USA
    BMC Genomics 10:269. 2009
    ..The genomic features of these two groups of genes expressed in opposing patterns may shed light on the mechanisms by which cells maintain basic and tissue-specific functions...
  8. 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...
  9. pmc NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children
    Marissa Vignali
    Seattle Biomedical Research Institute, Seattle, Washington, USA
    J Clin Invest 121:1119-29. 2011
    ..Our study provides proof of principle that NSR-seq represents an approach that can be used to study clinical isolates of parasites causing severe malaria syndromes as well other blood-borne pathogens and blood-related diseases...
  10. pmc DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
    John C Castle
    Rosetta Inpharmatics LLC, Merck and Co, Inc, Seattle, Washington 98109, USA
    BMC Genomics 11:244. 2010
    ..DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number...
  11. doi Digital transcriptome profiling using selective hexamer priming for cDNA synthesis
    Christopher D Armour
    Department of Molecular Informatics, Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck and Co, Inc, Seattle, Washington, USA
    Nat Methods 6:647-9. 2009
    ..In this study we validated the technique by profiling human whole brain and universal human reference RNA using ultra-high-throughput sequencing...
  12. pmc SNPs occur in regions with less genomic sequence conservation
    John C Castle
    Rosetta Inpharmatics LLC, Seattle, Washington, United States of America
    PLoS ONE 6:e20660. 2011
    ..Together, these results confirm that SNPs, reflecting recent genetic variation, occur more frequently in regions with less evolutionarily conservation...
  13. pmc Activity of the Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR
    Hidetada Hirakawa
    Department of Microbiology, University of Washington, Seattle, Washington 98195 7242, USA
    J Bacteriol 193:2598-607. 2011
    ..These data raise the possibility that this antisense RNA or other RpaR-activated noncoding RNAs mediate the indirect activation of genes in the RpaR-controlled regulon...
  14. pmc Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways
    David M Levine
    Rosetta Inpharmatics LLC, Merck and Co, Inc, Terry Avenue North, Seattle, WA 98109, USA
    Genome Biol 7:R93. 2006
    ..Although many methods for measuring pathway expression have been proposed, a systematic analysis of the performance of multiple methods over multiple independent data sets has not previously been reported...
  15. doi Genome-scale RNAi screen for host factors required for HIV replication
    Honglin Zhou
    Department of Virus and Cell Biology, Merck and Co, Inc, West Point, PA 19486, USA
    Cell Host Microbe 4:495-504. 2008
    ..This study highlights both the power and shortcomings of large scale loss-of-function screens in discovering host-pathogen interactions...