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  • Assessing probabilistic inference by comparing the generalized mean of the model and source probabilities 

    Nelson, Kenric P. (MDPI AG, 2017-06-01)
    An approach to the assessment of probabilistic inference is described which quantifies the performance on the probability scale. From both information and Bayesian theory, the central tendency of an inference is proven to ...
  • Active C4 electrodes for local field potential recording applications 

    Wang, Lu; Freedman, David; Sahin, Mesut; Ünlü, M. Selim; Knepper, Ronald (2016-02-04)
    Extracellular neural recording, with multi-electrode arrays (MEAs), is a powerful method used to study neural function at the network level. However, in a high density array, it can be costly and time consuming to integrate ...
  • Fractional generalizations of filtering problems and their associated fractional Zakai equations 

    Umarov, Sabir; Daum, Frederick; Nelson, Kenric (2014-01-01)
    In this paper we discuss fractional generalizations of the filtering problem. The ”fractional” nature comes from time-changed state or observation processes, basic ingredients of the filtering problem. The mathematical ...
  • High-throughput intensity diffraction tomography with a computational microscope 

    Ling, Ruilong; Tahir, Waleed; Lin, Hsing-Ying; Lee, Hakho; Tian, Lei (2018-01-29)
    We demonstrate a motion-free intensity diffraction tomography technique that enables direct inversion of 3D phase and absorption from intensity-only measurements for weakly scattering samples. We derive a novel linear ...
  • Reduced perplexity: Uncertainty measures without entropy 

    Nelson, Kenric P. (2014)
    A simple, intuitive approach to the assessment of probabilistic inferences is introduced. The Shannon information metrics are translated to the probability domain. The translation shows that the negative logarithmic score ...
  • DeviceEditor visual biological CAD canvas 

    Chen, Joanna; Densmore, Douglas; Ham, Timothy S.; Keasling, Jay D.; Hillson, Nathan J. (2012-02-28)
    BACKGROUND: Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To ...
  • Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems 

    Bilitchenko, Lesia; Liu, Adam; Cheung, Sherine; Weeding, Emma; Xia, Bing; Leguia, Mariana; Anderson, J. Christopher; Densmore, Douglas (2011-04-29)
    BACKGROUND: Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification ...
  • Reducing DNA context dependence in bacterial promoters 

    Carr, Swati B.; Beal, Jacob; Densmore, Douglas M. (2017)
    Variation in the DNA sequence upstream of bacterial promoters is known to affect the expression levels of the products they regulate, sometimes dramatically. While neutral synthetic insulator sequences have been found to ...
  • Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration 

    Woodruff, Lauren B.A.; Gorochowski, Thomas E.; Roehner, Nicholas; Mikkelsen, Tarjei S.; Densmore, Douglas; Gordon, D. Benjamin; Nicol, Robert; Voigt, Christopher A. (2016-11-22)
    Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. ...
  • Automated robotic liquid handling assembly of modular DNA devices 

    Ortiz, Luis; Pavan, Marilene; McCarthy, Lloyd; Timmons, Joshua; Densmore, Douglas M. (2017-12-01)
    Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available "design space" represented by "devices" created as combinations of individual genetic components. ...

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