Research Topics
Genomes and Genes | Jason M JohnsonSummaryAffiliation: Merck Research Laboratories Country: USA Publications
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Detail Information
Publications
Protein family annotation in a multiple alignment viewerJason M Johnson
Pfizer Discovery Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
Bioinformatics 19:544-5. 2003..AVAILABILITY: The program and source code are freely available from the authors under the GNU General Public License at http://www.pfizerdtc.com..- Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experimentsJason 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... - Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAsLee 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... 
Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathwaysDavid M Levine
Rosetta Inpharmatics LLC, Merck and Co, Inc, Terry Avenue North, Seattle, WA 98109, USA
Genome Biol 7:R93. 2006..We also provide a comprehensive picture of the tissue distribution of human gene pathways and a useful public archive of human pathway expression data...- Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarraysJason 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... 
Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variationTomas Babak
Rosetta Inpharmatics, LLC, 401 Terry Ave N, Seattle, WA 98109, USA
BMC Genomics 11:473. 2010....- Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicingJohn Castle
Rosetta Inpharmatics, Merck and Co, Inc, 12040 115th Ave NE, Kirkland, Washington 98034, USA
Genome Biol 4:R66. 2003.... - Definition, conservation and epigenetics of housekeeping and tissue-enriched genesXinwei 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... - Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell linesJohn 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%... - Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progressionPeter 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... - Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differencesWan 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... - DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencingJohn 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... - Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAsChristopher 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... - 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... - A quantitative atlas of polyadenylation in five mammalsAdnan 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... 
Digital transcriptome profiling using selective hexamer priming for cDNA synthesisChristopher 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...- Global survey of genomic imprinting by transcriptome sequencingTomas 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... - A comprehensive transcript index of the human genome generated using microarrays and computational approachesEric 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... - Evolutionarily conserved and diverged alternative splicing events show different expression and functional profilesZhengyan Kan
Rosetta Inpharmatics LLC, Merck and Co, Inc. 401 Terry Ave N, Seattle, WA 98109, USA
Nucleic Acids Res 33:5659-66. 2005.... - Expression of alternatively spliced sodium channel alpha-subunit genes. Unique splicing patterns are observed in dorsal root gangliaChristopher 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... - Mapping the genetic architecture of gene expression in human liverEric 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... - A human homeotic transformation resulting from mutations in PLCB4 and GNAI3 causes auriculocondylar syndromeMark 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... - Position-specific chemical modification of siRNAs reduces "off-target" transcript silencingAimee L Jackson
Rosetta Inpharmatics, LLC, Seattle, WA 98109, USA
RNA 12:1197-205. 2006.... - Protein interaction networksMatteo 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... - 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... - Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2Juan 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...