Detecting actively translated open reading frames in ribosome profiling data
نویسندگان
چکیده
منابع مشابه
Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We ob...
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3" Anil Raj, Sidney H. Wang, Heejung Shim, Arbel Harpak, 4" Yang I. Li, Brett Engelmann, Matthew Stephens, Yoav Gilad, 5" Jonathan K. Pritchard " 6" " 7" Department of Genetics, Stanford University, Stanford, CA" 8" Department of Human Genetics, University of Chicago, Chicago, IL" 9" Department of Statistics, University of Chicago, Chicago, IL" 10" Department of Biology, Stanford University, St...
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Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around the clock and at high temporal and nucleotide resolution. We discovered, transc...
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Open reading frames (6116) of the budding yeast Saccharomyces cerevisiae were PCR-amplified from genomic DNA using 12,232 primers specific to the ends of the coding sequences; the success rate of amplification was 97%. PCR-products were made accessible to hybridization by being arrayed at very high density on solid support media using various robotic devices. Probes made from total RNA preparat...
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Department of Environmental and Biomolecular Systems, Oregon Health and Science University, Beaverton, Oregon 97006, USA; Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97201, USA; Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Department of Microbiology and De...
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ژورنال
عنوان ژورنال: Nature Methods
سال: 2015
ISSN: 1548-7091,1548-7105
DOI: 10.1038/nmeth.3688