Journal Articles

  • switchBox: an R package for k-Top Scoring Pairs classifier development
    [Jan 2015]

    Summary: k–Top Scoring Pairs (kTSP) is a classification method for prediction from high-throughput data based on a set of the paired measurements. Each of the two possible orderings of a pair of measurements (e.g. a reversal in the expression of two genes) is associated with one of two classes. The kTSP prediction rule is the aggregation of voting among such individual two-feature decision rules based on order switching. kTSP, like its predecessor, Top Scoring Pair (TSP), is a parameter-free classifier relying only on ranking of a small subset of features, rendering it robust to noise and potentially easy to interpret in biological terms. In contrast to TSP, kTSP has comparable accuracy to standard genomics classification techniques, including Support Vector Machines and Prediction Analysis for Microarrays. Here, we describe ‘switchBox’, an R package for kTSP-based prediction.

    Availability: The ‘switchBox’ package is freely available from Bioconductor: http://www.bioconductor.org.

    Contact: bahman@jhu.edu

    Supplementary information: Supplementary data are available at Bioinformatics online.

    Categories: Journal Articles
  • Enlight: web-based integration of GWAS results with biological annotations
    [Jan 2015]

    Summary: Identifying causal variants remains a key challenge in post-GWAS (genome-wide association study) era, as many GWAS single-nucleotide polymorphisms (SNPs) (including imputed ones) fall into non-coding regions, making it difficult to associate statistical significance with predicted functionality. Therefore, we created a web-based tool, Enlight, which overlays functional annotation information, such as histone modification states, methylation patterns, transcription factor binding sites, eQTL and higher-order chromosomal structure, to GWAS results.

    Availability and implementation: Accessible by a Web browser at http://enlight.usc.edu.

    Contact: kaiwang@usc.edu

    Categories: Journal Articles
  • NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks
    [Jan 2015]

    Summary: The wide variety of published approaches for the problem of regulatory network inference makes using multiple inference algorithms complex and time-consuming. Network Analysis and Inference Library (NAIL) is a set of software tools to simplify the range of computational activities involved in regulatory network inference. It uses a modular approach to connect different network inference algorithms to the same visualization and network-based analyses. NAIL is technology-independent and includes an interface layer to allow easy integration of components into other applications.

    Availability and implementation: NAIL is implemented in MATLAB, runs on Windows, Linux and OSX, and is available from SourceForge at https://sourceforge.net/projects/nailsystemsbiology/ for all researchers to use.

    Contact: daniel.hurley@unimelb.edu.au

    Supplementary information: Supplementary data are available at Bioinformatics online.

    Categories: Journal Articles
  • Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions
    [Jan 2015]

    Summary: In chemoinformatics and bioinformatics fields, one of the main computational challenges in various predictive modeling is to find a suitable way to effectively represent the molecules under investigation, such as small molecules, proteins and even complex interactions. To solve this problem, we developed a freely available R/Bioconductor package, called Compound–Protein Interaction with R (Rcpi), for complex molecular representation from drugs, proteins and more complex interactions, including protein–protein and compound–protein interactions. Rcpi could calculate a large number of structural and physicochemical features of proteins and peptides from amino acid sequences, molecular descriptors of small molecules from their topology and protein–protein interaction and compound–protein interaction descriptors. In addition to main functionalities, Rcpi could also provide a number of useful auxiliary utilities to facilitate the user’s need. With the descriptors calculated by this package, the users could conveniently apply various statistical machine learning methods in R to solve various biological and drug research questions in computational biology and drug discovery.

    Availability and implementation: Rcpi is freely available from the Bioconductor site (http://bioconductor.org/packages/release/bioc/html/Rcpi.html).

    Contact: oriental-cds@163.com

    Categories: Journal Articles
  • Blown-up brains reveal nanoscale details
    [Jan 2015]

    Nature -

    Blown-up brains reveal nanoscale details

    Nature 517, 7534 (2015). http://www.nature.com/doifinder/10.1038/nature.2015.16667

    Author: Ewen Callaway

    Material used in diaper absorbant can make brain tissue bigger and enable ordinary microscopes to resolve features down to 60 nanometres.

    Categories: Journal Articles
  • [Editorial] Judging synthetic biology risks
    [Jan 2015]

    Last month, the European Commission (EC) Scientific Committees issued a draft opinion on whether existing risk assessment methods are adequate for synthetic biology. This opinion, which was written by a Working Group of 20 experts from Europe and the United States,* could have a substantial impact on shaping European and global synthetic biology policy for years to come. It is open for public comment through 3 February 2015.† Authors: Rainer Breitling, Eriko Takano, Timothy S. Gardner
    Categories: Journal Articles
  • [In Brief] This week's section
    [Jan 2015]

    A roundup of weekly science policy and related news.
    Categories: Journal Articles
  • [In Depth] Laser fusion, with a difference
    [Jan 2015]

    Europe's Laser Mégajoule project blazes its own trail toward nuclear ignition. Author: Daniel Clery
    Categories: Journal Articles
  • [In Depth] U.S. patent office reworks unpopular policy
    [Jan 2015]

    New guidelines lower the barrier for patenting products derived from nature, quelling some biotech fears. Author: Kelly Servick
    Categories: Journal Articles
  • [In Depth] A soft approach kick-starts cybernetic implants
    [Jan 2015]

    Mimicking real tissue, novel materials lead to flexible electrode implants that help paralyzed animals walk again. Author: Robert F. Service
    Categories: Journal Articles
  • [In Depth] Air Force turns a keen eye on space junk
    [Jan 2015]

    Flood of data from new “space fence” radar may overwhelm some satellite operators. Author: Ilima Loomis
    Categories: Journal Articles
  • [In Depth] Beyond the Turing Test
    [Jan 2015]

    Concluding that there is no one test for machine intelligence, AI researchers develop a battery of research challenges. Author: Jia You
    Categories: Journal Articles
  • [Feature] Salvaging science
    [Jan 2015]

    Underwater archaeologist Charles Beeker works to preserve famous wrecks as museums. Author: Michael Bawaya
    Categories: Journal Articles
  • [Feature] On the trail of contagion
    [Jan 2015]

    One team's quest to find a potential Ebola case in Liberia reveals how difficult it will be to end the epidemic. Author: Kai Kupferschmidt
    Categories: Journal Articles
  • [Perspective] Solving imperfect-information games
    [Jan 2015]

    The smallest common poker game, two-player limit Texas Hold'em, is essentially solved [Also see Research Article by Bowling et al.] Author: Tuomas Sandholm
    Categories: Journal Articles
  • [Perspective] Prescribing splicing
    [Jan 2015]

    A model predicts the impact of variations in the human genome on RNA splicing and disease [Also see Research Article by Xiong et al.] Authors: Roderic Guigó, Juan Valcárcel
    Categories: Journal Articles
  • [Perspective] Coping with oxidative stress
    [Jan 2015]

    A crystal structure helps to explain how cells detoxify [Also see Report by Leung et al.] Authors: Ute Krengel, Susanna Törnroth-Horsefield
    Categories: Journal Articles
  • [Perspective] Dynamics of a cold quantum gas
    [Jan 2015]

    A cloud of cold atoms provides a route to understanding complex phase transitions [Also see Report by Navon et al.] Author: Gabriele Ferrari
    Categories: Journal Articles
  • [Perspective] Making sense of amino acid sensing
    [Jan 2015]

    Biochemically and spatially diverse intracellular mechanisms couple the activity of a cell growth regulatory complex to the availability of amino acids [Also see Reports by Wang et al. and Jewell et al.] Author: Robert T. Abraham
    Categories: Journal Articles
  • [Perspective] Designing two-dimensional materials that spring rapidly into three-dimensional shapes
    [Jan 2015]

    Buckling of sheets can be engineered to rapidly create complex shapes [Also see Report by Xu et al.] Authors: Chunhong Ye, Vladimir V. Tsukruk
    Categories: Journal Articles
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