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  • Solar Physics  (3)
  • Computational Methods  (2)
  • 2010-2014  (5)
  • 1950-1954
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  • 2010-2014  (5)
  • 1950-1954
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  • 1
    Publication Date: 2013-09-26
    Description: It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense–antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2014-08-15
    Description: High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A , a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2019-07-13
    Description: The Helioseismic and Magnetic Imager (HMI) instrument and investigation as a part of the NASA Solar Dynamics Observatory (SDO) is designed to study convection-zone dynamics and the solar dynamo, the origin and evolution of sunspots, active regions, and complexes of activity, the sources and drivers of solar magnetic activity and disturbances, links between the internal processes and dynamics of the corona and heliosphere, and precursors of solar disturbances for space-weather forecasts. A brief overview of the instrument, investigation objectives, and standard data products is presented.
    Keywords: Solar Physics
    Type: GSFC-E-DAA-TN9963 , Solar Physics; 275; 2-Jan; 207-227
    Format: application/pdf
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  • 4
    Publication Date: 2019-07-13
    Description: The magnetic energy and relative magnetic helicity in two emerging solar active regions, AR 11072 and AR 11158,are studied. They are computed by integrating over time the energy and relative helicity fluxes across the photosphere. The fluxes consist of two components: one from photospheric tangential flows that shear and braid field lines (shear term), the other from normal flows that advect magnetic flux into the corona (emergence term). For these active regions: (1) relative magnetic helicity in the active-region corona is mainly contributed by the shear term,(2) helicity fluxes from the emergence and the shear terms have the same sign, (3) magnetic energy in the corona (including both potential energy and free energy) is mainly contributed by the emergence term, and(4) energy fluxes from the emergence term and the shear term evolved consistently in phase during the entire flux emergence course.We also examine the apparent tangential velocity derived by tracking field-line footpoints using a simple tracking method. It is found that this velocity is more consistent with tangential plasma velocity than with the flux transport velocity, which agrees with the conclusion by Schuck.
    Keywords: Solar Physics
    Type: GSFC-E-DAA-TN9037 , The Astrophysical Journal (ISSN ISN 0004-637X); 761; 2; 105
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  • 5
    Publication Date: 2019-08-26
    Description: On 2010 August 1, the northern solar hemisphere underwent significant activity that involved a complex set of active regions near central meridian with, nearby, two large prominences and other more distant active regions. This activity culminated in the eruption of four major coronal mass ejections (CMEs), effects of which were detected at Earth and other solar system bodies. Recognizing the unprecedented wealth of data from the wide range of spacecraft that were available-providing the potential for us to explore methods for CME identification and tracking, and to assess issues regarding onset and planetary impact-we present a comprehensive analysis of this sequence of CMEs.We show that, for three of the four major CMEs, onset is associated with prominence eruption, while the remaining CME appears to be closely associated with a flare. Using instrumentation on board the Solar Terrestrial Relations Observatory spacecraft, three of the CMEs could be tracked out to elongations beyond 50; their directions and speeds have been determined by various methods, not least to assess their potential for Earth impact. The analysis techniques that can be applied to the other CME, the first to erupt, are more limited since that CME was obscured by the subsequent, much faster event before it had propagated far from the Sun; we discuss the speculation that these two CMEs interact. The consistency of the results, derived from the wide variety of methods applied to such an extraordinarily complete data set, has allowed us to converge on robust interpretations of the CME onsets and their arrivals at 1 AU.
    Keywords: Solar Physics
    Type: GSFC-E-DAA-TN9096 , The Astrophysical Journal; 750; 1; 45
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