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Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean(More)
Just Accepted " Just Accepted " manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides " Just Accepted " as a free service to the research community to expedite the dissemination of scientific material as soon(More)
Molecular biologists routinely clone genetic constructs from DNA segments and formulate plans to assemble them. However, manual assembly planning is complex, error prone and not scalable. We address this problem with an algorithm-driven DNA assembly planning software tool suite called Raven (http://www.ravencad.org/) that produces optimized assembly plans(More)
Reality-based interfaces (RBIs) such as tabletop and tangible user interfaces draw upon ideas from embodied cognition to offer a more natural, intuitive, and accessible form of interaction that reduces the mental effort required to learn and operate computational systems. However, to date, little research has been devoted to investigating the strengths and(More)
We present a framework that allows us to construct and formally analyze the behavior of synthetic gene circuits from specifications in a high level language used in describing electronic circuits. Our back-end synthesis tool automatically generates genetic-regulatory network (GRN) topology realizing the specifications with assigned biological "parts" from a(More)
There is a pressing need for design automation tools for synthetic biology systems. Compared to electronic circuits, cellular information processing has more complex elementary components and a greater complexity of interactions among components. Moreover, chemical computation within a cell is strongly a↵ected both by other computations simultaneously(More)
MoClo Planner is an interactive visualization system for collaborative bio-design, utilizing a multi-touch interactive surface. The system integrates the information gathering, design, and specification of complex synthetic biological constructs using the Modular Cloning (MoClo) assembly method. Modular Cloning is a hierarchical DNA construction method that(More)
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