Proceedings of the IEEE

Issue 3 • March 2017

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Displaying Results 1 - 23 of 23
  • Front Cover

    Publication Year: 2017, Page(s): C1
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  • Proceedings of the IEEE publication information

    Publication Year: 2017, Page(s): C2
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  • Bioinformatics of DNA

    Publication Year: 2017, Page(s):409 - 410
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  • Spent Nuclear Fuel is not the Problem [Point of View]

    Publication Year: 2017, Page(s):411 - 414
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  • An Enduring Problem: Radioactive Waste From Nuclear Energy [Point of View]

    Publication Year: 2017, Page(s):415 - 418
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  • Bioinformatics of DNA [Scanning the Issue]

    Publication Year: 2017, Page(s):419 - 421
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  • Building and Improving Reference Genome Assemblies

    Publication Year: 2017, Page(s):422 - 435
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1133 KB) | HTML iconHTML

    A genome sequence assembly provides the foundation for studies of genotypic and phenotypic variation, genome structure, and evolution of the target organism. In the past four decades, there has been a surge of new sequencing technologies, and with these developments, computational scientists have developed new algorithms to improve genome assembly. Here we discuss the relationship between sequenci... View full abstract»

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  • Short Read Mapping: An Algorithmic Tour

    Publication Year: 2017, Page(s):436 - 458
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1099 KB) | HTML iconHTML

    Ultra-high-throughput next-generation sequencing (NGS) technology allows us to determine the sequence of nucleotides of many millions of DNA molecules in parallel. Accompanied by a dramatic reduction in cost since its introduction in 2004, NGS technology has provided a new way of addressing a wide range of biological and biomedical questions, from the study of human genetic disease to the analysis... View full abstract»

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  • Reading the Underlying Information From Massive Metagenomic Sequencing Data

    Publication Year: 2017, Page(s):459 - 473
    Cited by:  Papers (4)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1398 KB) | HTML iconHTML

    Microorganisms are everywhere. Recent studies showed that the mixture of microbes or the microbiome on the human body plays important roles in human physiology and diseases. Metagenomic sequencing is a key technology for studying microbiomes. It produces massive amounts of data in the form of short sequencing reads. A single metagenomic sample can contain 10 7 to 10 8 reads o... View full abstract»

    Open Access
  • De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue

    Publication Year: 2017, Page(s):474 - 481
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (555 KB) | HTML iconHTML

    Transposable elements (TEs) constitute the most dynamic and the largest component of large plant genomes: for example, 80% to 90% of the maize genome and the wheat genome may be TEs. De novo TE annotation is therefore a computational challenge, and we investigated, using current tools in the REPET package, new strategies to overcome the difficulties. We tested our methodological developments on th... View full abstract»

    Open Access
  • A Novel Pathway Analysis Approach Based on the Unexplained Disregulation of Genes

    Publication Year: 2017, Page(s):482 - 495
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2630 KB) | HTML iconHTML

    A crucial step in the understanding of any phenotype is the correct identification of the signaling pathways that are significantly impacted in that phenotype. However, most current pathway analysis methods produce both false positives as well as false negatives in certain circumstances. We hypothesized that such incorrect results are due to the fact that the existing methods fail to distinguish b... View full abstract»

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  • DANUBE: Data-Driven Meta-ANalysis Using UnBiased Empirical Distributions—Applied to Biological Pathway Analysis

    Publication Year: 2017, Page(s):496 - 515
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (4909 KB) | HTML iconHTML Multimedia Media

    Identifying the pathways and mechanisms that are significantly impacted in a given phenotype is challenging. Issues include patient heterogeneity and noise. Many experiments do not have a large enough sample size to achieve the statistical power necessary to identify significantly impacted pathways. Meta-analysis based on combining p-values from individual experiments has been used to improve powe... View full abstract»

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  • Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process

    Publication Year: 2017, Page(s):516 - 529
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1984 KB) | HTML iconHTML Multimedia Media

    Neutral models which assume ecological equivalence between species provide null models for community assembly. In Hubbell's unified neutral theory of biodiversity (UNTB), many local communities are connected to a single metacommunity through differing immigration rates. Our ability to fit the full multisite UNTB has hitherto been limited by the lack of a computationally tractable and accurate algo... View full abstract»

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  • Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics

    Publication Year: 2017, Page(s):530 - 541
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1194 KB) | HTML iconHTML

    It is well known that cells in tissue display a large heterogeneity in gene expression due to differences in cell lineage origin and variation in the local environment. Traditional methods that analyze gene expression from bulk RNA extracts fail to accurately describe this heterogeneity because of their intrinsic limitation in cellular and spatial resolution. Also, information on histology in the ... View full abstract»

    Open Access
  • A Parallel Algorithm for $N$-Way Interval Set Intersection

    Publication Year: 2017, Page(s):542 - 551
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1045 KB) | HTML iconHTML

    The comparison of sets of genome intervals (e.g., genes, repeats, ChIP-seq peaks) is essential to genome research, especially as modern sequencing technologies enable ever larger and more complex experiments. Relationships between genomic features are commonly identified by their intersection: that is, if feature sets contain overlapping intervals then it is inferred that they share a common biolo... View full abstract»

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  • Manual for Using Homomorphic Encryption for Bioinformatics

    Publication Year: 2017, Page(s):552 - 567
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2689 KB) | HTML iconHTML

    Biological data science is an emerging field facing multiple challenges for hosting, sharing, computing on, and interacting with large data sets. Privacy regulations and concerns about the risks of leaking sensitive personal health and genomic data add another layer of complexity to the problem. Recent advances in cryptography over the last five years have yielded a tool, homomorphic encryption, w... View full abstract»

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  • What Sparked Video Research in 1877? The Overlooked Role of the Siemens Artificial Eye [Scanning Our Past]

    Publication Year: 2017, Page(s):568 - 576
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  • Future Special Issues/Special Sections of the Proceedings

    Publication Year: 2017, Page(s): 577
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  • Member Get-A-Member (MGM) Program

    Publication Year: 2017, Page(s): 578
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  • Imagine a community hopeful for the future

    Publication Year: 2017, Page(s): 579
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  • Learning Has No Boundaries

    Publication Year: 2017, Page(s): 580
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  • Introducing IEEE Collabratec

    Publication Year: 2017, Page(s): C3
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  • Back Cover

    Publication Year: 2017, Page(s): C4
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The most highly-cited general interest journal in electrical engineering and computer science, the Proceedings is the best way to stay informed on an exemplary range of topics.

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Meet Our Editors

Editor-in-Chief
H. Joel Trussell
North Carolina State University