Literature DB >> 24794536

Synthetic analog and digital circuits for cellular computation and memory.

Oliver Purcell1, Timothy K Lu2.   

Abstract

Biological computation is a major area of focus in synthetic biology because it has the potential to enable a wide range of applications. Synthetic biologists have applied engineering concepts to biological systems in order to construct progressively more complex gene circuits capable of processing information in living cells. Here, we review the current state of computational genetic circuits and describe artificial gene circuits that perform digital and analog computation. We then discuss recent progress in designing gene networks that exhibit memory, and how memory and computation have been integrated to yield more complex systems that can both process and record information. Finally, we suggest new directions for engineering biological circuits capable of computation.
Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

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Year:  2014        PMID: 24794536      PMCID: PMC4237220          DOI: 10.1016/j.copbio.2014.04.009

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  47 in total

1.  Programmable single-cell mammalian biocomputers.

Authors:  Simon Ausländer; David Ausländer; Marius Müller; Markus Wieland; Martin Fussenegger
Journal:  Nature       Date:  2012-07-05       Impact factor: 49.962

2.  Rewritable digital data storage in live cells via engineered control of recombination directionality.

Authors:  Jerome Bonnet; Pakpoom Subsoontorn; Drew Endy
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-21       Impact factor: 11.205

3.  Amplifying genetic logic gates.

Authors:  Jerome Bonnet; Peter Yin; Monica E Ortiz; Pakpoom Subsoontorn; Drew Endy
Journal:  Science       Date:  2013-03-28       Impact factor: 47.728

4.  Synthetic circuits integrating logic and memory in living cells.

Authors:  Piro Siuti; John Yazbek; Timothy K Lu
Journal:  Nat Biotechnol       Date:  2013-02-10       Impact factor: 54.908

5.  Synthetic memory circuits for tracking human cell fate.

Authors:  Devin R Burrill; Mara C Inniss; Patrick M Boyle; Pamela A Silver
Journal:  Genes Dev       Date:  2012-07-01       Impact factor: 11.361

6.  Ribozyme-based insulator parts buffer synthetic circuits from genetic context.

Authors:  Chunbo Lou; Brynne Stanton; Ying-Ja Chen; Brian Munsky; Christopher A Voigt
Journal:  Nat Biotechnol       Date:  2012-10-03       Impact factor: 54.908

7.  Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Authors:  Lei S Qi; Matthew H Larson; Luke A Gilbert; Jennifer A Doudna; Jonathan S Weissman; Adam P Arkin; Wendell A Lim
Journal:  Cell       Date:  2013-02-28       Impact factor: 41.582

8.  Genetic programs constructed from layered logic gates in single cells.

Authors:  Tae Seok Moon; Chunbo Lou; Alvin Tamsir; Brynne C Stanton; Christopher A Voigt
Journal:  Nature       Date:  2012-10-07       Impact factor: 49.962

9.  A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells.

Authors:  Tara L Deans; Charles R Cantor; James J Collins
Journal:  Cell       Date:  2007-07-27       Impact factor: 41.582

10.  A synthetic biology framework for programming eukaryotic transcription functions.

Authors:  Ahmad S Khalil; Timothy K Lu; Caleb J Bashor; Cherie L Ramirez; Nora C Pyenson; J Keith Joung; James J Collins
Journal:  Cell       Date:  2012-08-03       Impact factor: 41.582

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  29 in total

Review 1.  Recent advances and opportunities in synthetic logic gates engineering in living cells.

Authors:  Vijai Singh
Journal:  Syst Synth Biol       Date:  2014-08-28

2.  Engineering multicellular systems: using synthetic biology to control tissue self-organization.

Authors:  Marion B Johnson; Alexander R March; Leonardo Morsut
Journal:  Curr Opin Biomed Eng       Date:  2017-12

3.  Synchronized DNA cycling across a bacterial population.

Authors:  Leo Baumgart; William Mather; Jeff Hasty
Journal:  Nat Genet       Date:  2017-07-10       Impact factor: 38.330

Review 4.  Programming Morphogenesis through Systems and Synthetic Biology.

Authors:  Jeremy J Velazquez; Emily Su; Patrick Cahan; Mo R Ebrahimkhani
Journal:  Trends Biotechnol       Date:  2017-12-08       Impact factor: 19.536

5.  Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications.

Authors:  Mitchell S Weisenberger; Tara L Deans
Journal:  J Ind Microbiol Biotechnol       Date:  2018-03-19       Impact factor: 3.346

6.  Bacteriophage-based synthetic biology for the study of infectious diseases.

Authors:  Robert J Citorik; Mark Mimee; Timothy K Lu
Journal:  Curr Opin Microbiol       Date:  2014-07-03       Impact factor: 7.934

Review 7.  Engineering Stem Cell Organoids.

Authors:  Xiaolei Yin; Benjamin E Mead; Helia Safaee; Robert Langer; Jeffrey M Karp; Oren Levy
Journal:  Cell Stem Cell       Date:  2016-01-07       Impact factor: 24.633

8.  Synthetic neural-like computing in microbial consortia for pattern recognition.

Authors:  Ximing Li; Luna Rizik; Valeriia Kravchik; Maria Khoury; Netanel Korin; Ramez Daniel
Journal:  Nat Commun       Date:  2021-05-25       Impact factor: 14.919

Review 9.  CRISPR-Based Synthetic Transcription Factors In Vivo: The Future of Therapeutic Cellular Programming.

Authors:  Matthew Pandelakis; Elizabeth Delgado; Mo R Ebrahimkhani
Journal:  Cell Syst       Date:  2020-01-22       Impact factor: 10.304

10.  Rewritable multi-event analog recording in bacterial and mammalian cells.

Authors:  Weixin Tang; David R Liu
Journal:  Science       Date:  2018-02-15       Impact factor: 47.728

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