Publications

Algorithms for the selection of fluorescent reporters

Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into …
Prashant Vaidyanathan, Evan Appleton, David Tran, Alexander Vahid, George Church, Douglas Densmore
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Scalable dynamic characterization of synthetic gene circuits

The dynamic behavior of synthetic gene circuits plays a key role in ensuring their correct function. However, our ability to accurately …
Neil Dalchau, Paul K. Grant, Prashant Vaidyanathan, Colin Gravill, Carlo Spaccasassi, Andrew Phillips

Functional synthesis of genetic systems

Synthetic genetic regulatory networks (or genetic circuits) can operate in complex biochemical environments to process and manipulate …
Prashant Vaidyanathan

Metrics for Signal Temporal Logic Formulae

Signal Temporal Logic (STL) is a formal language for describing a broad range of real-valued, temporal properties in cyber-physical …
Curtis Madsen, Prashant Vaidyanathan, Sadra Sadraddini, Cristian-Ioan Vasile, Nicholas A. DeLateur, Ron Weiss, Douglas Densmore, Calin Belta
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A Computational Workflow for the Automated Generation of Models of Genetic Designs

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. …
Göksel Misirli, Tramy Nguyen, James Alastair McLaughlin, Prashant Vaidyanathan, Timothy S. Jones, Douglas Densmore, Chris Myers, Anil Wipat

Grid-based temporal logic inference

This paper introduces a new algorithm to infer temporal logic properties of a system from data consisting of a set of finite time …
Prashant Vaidyanathan, Rachael Ivison, Giuseppe Bombara, Nicholas A. DeLateur, Ron Weiss, Douglas Densmore, Calin Belta

Genetic circuit design automation

Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. …
Alec AK Nielsen, Bryan S. Der, Jonghyeon Shin, Prashant Vaidyanathan, Vanya Paralanov, Elizabeth A. Strychalski, David Ross, Douglas Densmore, Christopher A. Voigt
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Genetic circuit design automation

A Framework for Genetic Logic Synthesis

Digital electronic circuits have inspired synthetic biologists to program living cells with synthetic decision-making circuits by …
Prashant Vaidyanathan, Bryan S Der, Swapnil Bhatia, Nicholas Roehner, Ryan Silva, Christopher A Voigt, Douglas Densmore

A new encryption technique for the secured transmission and storage of text information with medical images

Modern day hospital management systems rely heavily on electronic data processing to maintain patient records. These electronic medical …
Prashant Vaidyanathan, Nitish Malhotra, Jagadish Nayak