John C Castle

Summary

Affiliation: University of Mainz
Country: Germany

Publications

  1. pmc Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification
    John C Castle
    Institute for Translational Oncology and Immunology, Mainz, Germany
    PLoS ONE 5:e11779. 2010
  2. 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
  3. 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
  4. 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
  5. doi request reprint 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. pmc A boy with homozygous microdeletion of NEUROG1 presents with a congenital cranial dysinnervation disorder [Moebius syndrome variant]
    Julia C Schröder
    Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstrasse 1, D 55101, Mainz, Germany
    Behav Brain Funct 9:7. 2013

Collaborators

Detail Information

Publications12

  1. pmc Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification
    John C Castle
    Institute for Translational Oncology and Immunology, Mainz, Germany
    PLoS ONE 5:e11779. 2010
    ..This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available...
  2. 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...
  3. 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%...
  4. 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...
  5. doi request reprint 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. pmc A boy with homozygous microdeletion of NEUROG1 presents with a congenital cranial dysinnervation disorder [Moebius syndrome variant]
    Julia C Schröder
    Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstrasse 1, D 55101, Mainz, Germany
    Behav Brain Funct 9:7. 2013
    ..Further findings included scaphocephaly, plagiocephaly, long palpebral fissures, high narrow palate, low-set posteriorly rotated ears, torticollis, hypoplastic genitalia and faulty foot posture. Parents were consanguineous...
  11. doi request reprint 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...
  12. 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...