Searching journal content for articles similar to Valen et al. 19 (2): 255.

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  1. Research: Genome-wide analysis of promoter architecture in Drosophila melanogaster
    • Roger A. Hoskins,
    • Jane M. Landolin,
    • James B. Brown,
    • Jeremy E. Sandler,
    • Hazuki Takahashi,
    • Timo Lassmann,
    • Charles Yu,
    • Benjamin W. Booth,
    • Dayu Zhang,
    • Kenneth H. Wan,
    • Li Yang,
    • Nathan Boley,
    • Justen Andrews,
    • Thomas C. Kaufman,
    • Brenton R. Graveley,
    • Peter J. Bickel,
    • Piero Carninci,
    • Joseph W. Carlson,
    • and Susan E. Celniker
    Genome Res. February 2011 21: 182-192; Published in Advance December 22, 2010, doi:10.1101/gr.112466.110
    ..., and not independent promoters. Discussion Genome-wide analysis of core promoter architecture in D. melanogaster has been limited by the availability of TSS data. Previous studies have relied on 59 ESTs generated from large-insert cDNA libraries, including libraries constructed usingmethods that do not trap the 59 cap...
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  2. Method: Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
    • Hideya Kawaji,
    • Marina Lizio,
    • Masayoshi Itoh,
    • Mutsumi Kanamori-Katayama,
    • Ai Kaiho,
    • Hiromi Nishiyori-Sueki,
    • Jay W. Shin,
    • Miki Kojima-Ishiyama,
    • Mitsuoki Kawano,
    • Mitsuyoshi Murata,
    • Noriko Ninomiya-Fukuda,
    • Sachi Ishikawa-Kato,
    • Sayaka Nagao-Sato,
    • Shohei Noma,
    • Yoshihide Hayashizaki,
    • Alistair R.R. Forrest,
    • Piero Carninci,
    • and The FANTOM Consortium
    Genome Res. April 2014 24: 708-717; Published in Advance March 27, 2014, doi:10.1101/gr.156232.113
    ...in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies...
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  3. Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
    • Hsin-Yen Larry Wu,
    • Isaiah D. Kaufman,
    • and Polly Yingshan Hsu
    Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
    ....Visualization is emphasized in cell biology research to generate hypotheses and results. However, in omics studies, the visualization of sequencing data within genes of interest remains underutilized owing to a lack of appropriate tools. Recent advancements in plotting tools in the R programming language (R Core Team 2025...
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  4. Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
    • Robert A. Policastro,
    • R. Taylor Raborn,
    • Volker P. Brendel,
    • and Gabriel E. Zentner
    Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
    ...) Jitter plot of the number of genes with a promoter-proximal TSR in each sample. Error bars represent standard deviation.We next compared the dinucleotide frequencies of TSSs detected by STRIPE-seq, SLIC-CAGE, and nanoCAGE. STRIPE-seq and SLIC-CAGE both preferentially detected all four Y−1R+1 combinations...
  5. Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
    • Tim R. Mercer,
    • Marcel E. Dinger,
    • Cameron P. Bracken,
    • Gabriel Kolle,
    • Jan M. Szubert,
    • Darren J. Korbie,
    • Marjan E. Askarian-Amiri,
    • Brooke B. Gardiner,
    • Gregory J. Goodall,
    • Sean M. Grimmond,
    • and John S. Mattick
    Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
    ...to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic...
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