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Combinational logic design in Synthetic Biology

Douglas Densmore, J. Christopher Anderson
2009 2009 IEEE International Symposium on Circuits and Systems  
In the growing field of Synthetic Biology, devices are emerging which are being classified as "combinational logic".  ...  Combinational logic circuits are a fundamental building block in today's digital electronics.  ...  We will illustrate that these abstractions may be difficult to maintain as cleanly in synthetic biology.  ... 
doi:10.1109/iscas.2009.5117745 dblp:conf/iscas/DensmoreA09 fatcat:oyol27jvevbvloaoa5j3ayvg2m

Ribocomputing devices for sophisticated in vivo logic computation

Alexander A. Green, Jongmin Kim, Duo Ma, Pamela A. Silver, James J. Collins, Peng Yin
2016 Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication - NANOCOM'16  
circuits evaluating logic expressions in test tubes.  ...  devices to rapidly evaluate complex logic in living cells.  ...  These design strategies can be used in combination with existing protein-based layered circuit architecture for even more complex information processing in cells.  ... 
doi:10.1145/2967446.2970373 dblp:conf/nanocom/GreenKMSCY16 fatcat:6y7cis6n7nepzdjrgpgxjyswoe

SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology

Liqiang Wang, Kun Qian, Yan Huang, Nana Jin, Hongyan Lai, Ting Zhang, Chunhua Li, Chunrui Zhang, Xiaoman Bi, Deng Wu, Changliang Wang, Hao Wu (+6 others)
2015 Scientific Reports  
Basic genetic logic gates have been designed to combine biological science with digital logic.  ...  Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology.  ...  SynBioLGDB therefore provides a global view of genetic logic gates in synthetic biology.  ... 
doi:10.1038/srep08090 pmid:25627341 pmcid:PMC4308699 fatcat:letsdkhowfat5gzfvtrc72yk2m


2009 Biocomputing 2010  
Here we propose to adapt co-design methodologies for synthetic biology.  ...  We show that the logical operations can be implemented in three different design domains: (1) the transcriptional domain using synthetically designed hybrid promoters, (2) the protein domain using bi-molecular  ...  Introduction The need for co-design of synthetic biology systems A major focus in the field of synthetic biology from the field's inception has been the design of biological "devices" [1] .  ... 
doi:10.1142/9789814295291_0041 fatcat:nwtdco36szd3bkqscucnunlfcm

Advances in Crop Synthetic Biology: A Platform that Bridges the Expertise of Crop Molecular Biologists, Engineers, Software Developers and Mathematical Modelers

Mariam Sticklen
2015 Advances in Crop Science and Technology  
Citation: Sticklen M (2015) Advances in Crop Synthetic Biology: A Platform that Bridges the Expertise of Crop Molecular Biologists, Engineers, Software Developers and Mathematical Modelers.  ...  Plant synthetic biology has been recently effectively applied in embedding of completely artificial genetic code circuits into naturally existing plants used as framework of "chassis" [1].  ...  If the system was to be synthetically made using the technologies associated with synthetic biology, it should be possible to logically design circuits networks of crop cell walls consisting of cellulase  ... 
doi:10.4172/2329-8863.1000171 fatcat:3p7ucfeq5nadxfrosh3m2fkazy

Synthetic biology: advancing biological frontiers by building synthetic systems

Yvonne Y Chen, Kate E Galloway, Christina D Smolke
2012 Genome Biology  
Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy.  ...  circuit design in synthetic biology.  ...  (e) Combining logic processing with communication circuitry enables a synthetic biological edge detection system.  ... 
doi:10.1186/gb-2012-13-2-240 pmid:22348749 pmcid:PMC3334564 fatcat:wfm6apuxqfd67e3nwozavkocti

Principles of Synthetic Biology: A MOOC for an Emerging Field

Daniel A Anderson, Ross D Jones, Adam P Arkin, Ron Weiss
2019 Synthetic Biology  
PoSB seeks to teach synthetic biology through five key fundamentals: (i) parts and layers of abstraction, (ii) biomolecular modeling, (iii) digital logic abstraction, (iv) circuit design principles and  ...  Our course, Principles of Synthetic Biology (PoSB), was released on the massively open online course platform edX in 2016.  ...  We expect that students with a background in biology will particularly benefit from the course's insights into model design, digital logic and design-build-test approaches.  ... 
doi:10.1093/synbio/ysz010 pmid:32995535 pmcid:PMC7445764 fatcat:biydvnfyjvdydprbswviubqh7e

Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks

Christina M. Agapakis, Pamela A. Silver
2009 Molecular Biosystems  
Synthetic biology has been used to describe many biological endeavors over the past thirty years-from designing enzymes and in vitro systems, to manipulating existing metabolisms and gene expression, to  ...  This review covers the canonical examples as well as some recent advances in synthetic biology in terms of what we know and what we can learn about the networks underlying biology, and how this endeavor  ...  While synthetic networks are typically designed to be orthogonal to existing biology to avoid complex cross-talk interactions, 26 the ability to combine synthetic and natural genetic networks is a valuable  ... 
doi:10.1039/b901484e pmid:19562109 fatcat:g5ajztk3dvfsdpzith24h2k73i

Foundations and Emerging Paradigms for Computing in Living Cells

Kevin C. Ma, Samuel D. Perli, Timothy K. Lu
2016 Journal of Molecular Biology  
We then review the assembly of these parts into synthetic circuits from the perspectives of digital & analog logic, systems biology, and metabolic engineering, three areas of particular theoretical and  ...  Finally, we discuss notable challenges that the field of synthetic biology still faces in achieving reliable and predictable forward-engineering of artificial biological circuits.  ...  However, the rational design and implementation of analog synthetic gene circuits is relatively new in the field of synthetic biology.  ... 
doi:10.1016/j.jmb.2016.02.018 pmid:26908220 fatcat:opw34obcx5ffhcebduca5vxzmq

Synthetic Biology Speeds Up Drug Target Discovery

Yixuan Xie, Yanfang Yang, Yu He, Xixi Wang, Peng Zhang, Haocheng Li, Shufang Liang
2020 Frontiers in Pharmacology  
Depending on the combination mode of different logic gates, various synthetic circuits are created to carry out multilevel regulations.  ...  Synthetic biology works well in association with the CRISPR system for drug target functional screening.  ...  These logic gates function alone or in combination according to the level of regulation. (B) Drug-responsive synthetic circuits.  ... 
doi:10.3389/fphar.2020.00119 pmid:32174833 pmcid:PMC7054250 fatcat:edqkyjcrnzagllefluhkk24isy

A Schematic Overview on Computational Methodologies for Designing Synthetically Biological Products

Bina Gidwani Shiv Shankar, Shukla Ravindra Pandey, Chanchal Deep Kaur
2015 Current Synthetic and Systems Biology  
This work will support the progress in designing and construction of synthetic genetic products.  ...  The integration of molecular biology with engineering leads to development of an emerging field in research known as synthetic biology.  ...  Synthetic biology is a branch with combination of biological sciences and engineering sciences.  ... 
doi:10.4172/2332-0737.1000122 fatcat:46n5zb6wzfbatifvlh3bzx4zoy

Mathematical models in biology: from molecules to life

Yiannis N. Kaznessis
2011 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
biology.  ...  Augmentation can then be considered as a qualitative shift in abilities.  ...  This modeling formalism was validated, by combining mechanistic-kinetic models with in vivo genetic engineering to build and test a synthetic, bio-logical AND gate. 23 This device is composed of elements  ... 
doi:10.1002/wsbm.142 pmid:21472998 pmcid:PMC3073512 fatcat:qh35uvdiefemnpl57ncqocexgq

Cellular Biosensors with Engineered Genetic Circuits

Behide Saltepe, Ebru Şahin Kehribar, Side Selin Su Yirmibeşoğlu, Urartu Özgür Şafak Şeker
2017 ACS Sensors  
Utilizing the tools of synthetic biology, numerous genetic circuits have been implemented such as engineered logic operation in analog and digital circuits.  ...  In this review, we investigated the recent developments in biocomputation tools such as analog, digital, and mix circuits, logic gates, switches, and state machines.  ...  ■ BIOCOMPUTATION IN SYNTHETIC BIOLOGY Digital Circuits and Logic Operation.  ... 
doi:10.1021/acssensors.7b00728 pmid:29168381 fatcat:fhxelqk5ivbebpmr2ckvk5vfiu

The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms

G. Alterovitz, T. Muso, M. F. Ramoni
2009 Briefings in Bioinformatics  
The field of synthetic biology holds an inspiring vision for the future; it integrates computational analysis, biological data and the systems engineering paradigm in the design of new biological machines  ...  Here we review the informatics challenges in synthetic biology along three dimensions: in silico, in vitro and in vivo.  ...  In other words, systems biology and synthetic biology represent two sides of the same coin: analysis and design [1] .  ... 
doi:10.1093/bib/bbp054 pmid:19906839 pmcid:PMC2810114 fatcat:fmscc3keibgi3libbwksghztlq

Synthetic Gene Expression Circuits for Designing Precision Tools in Oncology

Angela Re
2017 Frontiers in Cell and Developmental Biology  
Synthetic biology streamlines the design and construction of functionalized devices through standardization and rational engineering of basic biological elements decoupled from their natural context.  ...  We describe significant advancements in our capabilities to tailor synthetic genetic circuits to specific applications in tumor diagnosis, tumor cell-and gene-based therapy, and drug delivery.  ...  INTRODUCTION Synthetic biology builds on the transformative assertion that engineering approaches could be used to elucidate design principles of cellular systems and to implement synthetic digital and  ... 
doi:10.3389/fcell.2017.00077 pmid:28894736 fatcat:7q553oyware4pfpois3ls32t7y
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