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  • 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. ...
  • Highly sensitive transient absorption imaging of graphene and graphene oxide in living cells and circulating blood 

    Li, Junjie; Zhang, Weixia; Chung, Ting-Fung; Slipchenko, Mikhail N.; Chen, Yong P.; Cheng, Ji-Xin; Yang, Chen (2015-07-23)
    We report a transient absorption (TA) imaging method for fast visualization and quantitative layer analysis of graphene and GO. Forward and backward imaging of graphene on various substrates under ambient condition was ...
  • Understanding cellular internalization pathways of silicon nanowires 

    McNear, Kelly; Huang, Yimin; Yang, Chen (2017-03-01)
    BACKGROUND: Understanding how cells interact with nanomaterials is important for rational design of nanomaterials for nanomedicine and transforming them for clinical applications. Particularly, the mechanism for one-dimensional ...
  • Use of graphene as protection film in biological environments 

    Zhang, Weixia; Lee, Sudarat; McNear, Kelly L.; Chung, Ting Fung; Lee, Seunghyun; Lee, Kyunghoon; Crist, Scott A.; Ratliff, Timothy L.; Zhong, Zhaohui; Chen, Yong P.; Yang, Chen (2014-02-14)
    Corrosion of metal in biomedical devices could cause serious health problems to patients. Currently ceramics coating materials used in metal implants can reduce corrosion to some extent with limitations. Here we proposed ...
  • Far-field imaging of non-fluorescent species with sub-diffraction resolution 

    Wang, Pu; Slipchenko, Mikhail N.; Mitchell, James; Yang, Chen; Potma, Eric O.; Xu, Xianfan; Cheng, Ji-Xin (2013)
    Super-resolution optical microscopy is opening a new window to unveil the unseen details on the nanoscopic scale. Current far-field super-resolution techniques rely on fluorescence as the read-out1-5. Here, we demonstrate ...
  • Edge-TM: Exploiting transactional memory for error tolerance and energy efficiency 

    Moreshet, Tali; Papagiannopoulou, Dimitra; Marongiu, Andrea; Herlihy, Maurice; Bahar, R. Iris (2017-10-01)
    Scaling of semiconductor devices has enabled higher levels of integration and performance improvements at the price of making devices more susceptible to the effects of static and dynamic variability. Adding safety margins ...

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