Jason M Johnson

Summary

Affiliation: Merck Research Laboratories
Country: USA

Publications

  1. ncbi request reprint Protein family annotation in a multiple alignment viewer
    Jason M Johnson
    Pfizer Discovery Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
    Bioinformatics 19:544-5. 2003
  2. 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
  3. ncbi request reprint Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    Lee P Lim
    Rosetta Inpharmatics, Merck and Co, 401 Terry Avenue N, Seattle, Washington 98109, USA
    Nature 433:769-73. 2005
  4. 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
  5. ncbi request reprint 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. pmc Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression
    Peter S Linsley
    Rosetta Inpharmatics, LLC, 401 Terry Ave N, Seattle, WA 98109, USA
    Mol Cell Biol 27:2240-52. 2007

Collaborators

Detail Information

Publications26

  1. ncbi request reprint Protein family annotation in a multiple alignment viewer
    Jason M Johnson
    Pfizer Discovery Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
    Bioinformatics 19:544-5. 2003
    ..The application merges display features such as dendrograms, secondary and tertiary protein structure with SRS retrieval, subgroup comparison, and extensive user-annotation capabilities...
  2. 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...
  3. ncbi request reprint Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    Lee P Lim
    Rosetta Inpharmatics, Merck and Co, 401 Terry Avenue N, Seattle, Washington 98109, USA
    Nature 433:769-73. 2005
    ..Moreover, miR-1 and miR-124, and presumably other tissue-specific miRNAs, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans...
  4. 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...
  5. ncbi request reprint 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...
  6. 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
    ....
  7. 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
    ....
  8. 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...
  9. 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%...
  10. pmc Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression
    Peter S Linsley
    Rosetta Inpharmatics, LLC, 401 Terry Ave N, Seattle, WA 98109, USA
    Mol Cell Biol 27:2240-52. 2007
    ..Simultaneous silencing of these genes was more effective at blocking cell cycle progression than disruption of the individual genes. Thus, miR-16 coordinately regulates targets that may act in concert to control cell cycle progression...
  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 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...
  13. pmc Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs
    Christopher K Raymond
    Rosetta Inpharmatics, Seattle, WA 98109, USA
    RNA 11:1737-44. 2005
    ..We used the method for quantitative analysis of six microRNAs across 12 tissue samples. The data confirm striking variation in the patterns of expression of these noncoding regulatory RNAs...
  14. 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...
  15. pmc A quantitative atlas of polyadenylation in five mammals
    Adnan Derti
    Department of Informatics IT, Merck and Co, Inc, Boston, Massachusetts 02115, USA
    Genome Res 22:1173-83. 2012
    ..These quantitative maps of polyA usage in evolutionarily and functionally related samples constitute a resource for understanding the regulatory mechanisms underlying alternative polyadenylation...
  16. 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...
  17. doi request reprint Global survey of genomic imprinting by transcriptome sequencing
    Tomas Babak
    Rosetta Inpharmatics, LLC, a wholly owned subsidiary of Merck and Co, 401 Terry Avenue North, Seattle, WA 98109, USA
    Curr Biol 18:1735-41. 2008
    ..Such an approach will allow researchers to study imprinting without restricting themselves to individual loci or specific transcripts...
  18. 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...
  19. 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
    ....
  20. ncbi request reprint Expression of alternatively spliced sodium channel alpha-subunit genes. Unique splicing patterns are observed in dorsal root ganglia
    Christopher K Raymond
    Rosetta Inpharmatics LLC, Seattle, Washington 98109, USA
    J Biol Chem 279:46234-41. 2004
    ..Consistent down-regulation of all transcripts was observed, as well as significant changes in the splicing patterns of SCN8A and SCN9A...
  21. 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...
  22. pmc A human homeotic transformation resulting from mutations in PLCB4 and GNAI3 causes auriculocondylar syndrome
    Mark J Rieder
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Am J Hum Genet 90:907-14. 2012
    ..This work defines the molecular basis of ACS as a homeotic transformation (mandible to maxilla) in humans...
  23. pmc Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing
    Aimee L Jackson
    Rosetta Inpharmatics, LLC, Seattle, WA 98109, USA
    RNA 12:1197-205. 2006
    ....
  24. ncbi request reprint Protein interaction networks
    Matteo Pellegrini
    Rosetta Inpharmatics LLC, 401 Terry Ave, Seattle, WA 98109, USA
    Expert Rev Proteomics 1:239-49. 2004
    ..It is clear that the evolution of these experimental and computational approaches is rapidly changing our view of biology, and promises to provide us with an unprecedented ability to model cells and organisms at a system-wide level...
  25. ncbi request reprint PDE4B5, a novel, super-short, brain-specific cAMP phosphodiesterase-4 variant whose isoform-specifying N-terminal region is identical to that of cAMP phosphodiesterase-4D6 (PDE4D6)
    York Fong Cheung
    Molecular Pharmacology Group, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
    J Pharmacol Exp Ther 322:600-9. 2007
    ..Understanding the distinct tissue specificity of PDE4 isoforms will be important for understanding phosphodiesterase biology and opportunities for therapeutic intervention...
  26. pmc Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2
    Juan I Young
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 102:17551-8. 2005
    ..Thus, we uncovered a previously uncharacterized function of MeCP2 that involves regulation of splicing, in addition to its role as a transcriptional repressor...