Literature DB >> 29915814

Scaling Computation and Memory in Living Cells.

Kevin Yehl1,2, Timothy Lu1,2,3,4,5.   

Abstract

The semiconductor revolution that began in the 20th century has transformed society. Key to this revolution has been the integrated circuit, which enabled exponential scaling of computing devices using silicon-based transistors over many decades. Analogously, decreasing costs in DNA sequencing and synthesis, along with the development of robust genetic circuits, are enabling a "biocomputing revolution". First-generation gene circuits largely relied on assembling various transcriptional regulatory elements to execute digital and analog computing functions in living cells. Basic design rules and computational tools have since been derived so that such circuits can be scaled in order to implement complex computations. In the past five years, great strides have been made in expanding the biological programming toolkit to include recombinase- and CRISPR-based gene circuits that execute complex cellular logic and memory. Recent advances have enabled increasingly dense computing and memory circuits to function in living cells while expanding the application of these circuits from bacteria to eukaryotes, including human cells, for a wide range of uses.

Entities:  

Year:  2017        PMID: 29915814      PMCID: PMC6003718          DOI: 10.1016/j.cobme.2017.10.003

Source DB:  PubMed          Journal:  Curr Opin Biomed Eng        ISSN: 2468-4511


  25 in total

1.  Construction of a genetic toggle switch in Escherichia coli.

Authors:  T S Gardner; C R Cantor; J J Collins
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

Review 2.  Epigenetics and gene expression.

Authors:  E R Gibney; C M Nolan
Journal:  Heredity (Edinb)       Date:  2010-05-12       Impact factor: 3.821

3.  Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability.

Authors:  Jesus Fernandez-Rodriguez; Lei Yang; Thomas E Gorochowski; D Benjamin Gordon; Christopher A Voigt
Journal:  ACS Synth Biol       Date:  2015-11-24       Impact factor: 5.110

Review 4.  Synthetic biology for synthetic chemistry.

Authors:  Jay D Keasling
Journal:  ACS Chem Biol       Date:  2008-01-18       Impact factor: 5.100

5.  An estimation of the number of cells in the human body.

Authors:  Eva Bianconi; Allison Piovesan; Federica Facchin; Alina Beraudi; Raffaella Casadei; Flavia Frabetti; Lorenza Vitale; Maria Chiara Pelleri; Simone Tassani; Francesco Piva; Soledad Perez-Amodio; Pierluigi Strippoli; Silvia Canaider
Journal:  Ann Hum Biol       Date:  2013-07-05       Impact factor: 1.533

6.  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

7.  Whole-organism lineage tracing by combinatorial and cumulative genome editing.

Authors:  Aaron McKenna; Gregory M Findlay; James A Gagnon; Marshall S Horwitz; Alexander F Schier; Jay Shendure
Journal:  Science       Date:  2016-05-26       Impact factor: 47.728

8.  A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells.

Authors:  Brian Chaikind; Jeffrey L Bessen; David B Thompson; Johnny H Hu; David R Liu
Journal:  Nucleic Acids Res       Date:  2016-08-11       Impact factor: 16.971

9.  Permanent genetic memory with >1-byte capacity.

Authors:  Lei Yang; Alec A K Nielsen; Jesus Fernandez-Rodriguez; Conor J McClune; Michael T Laub; Timothy K Lu; Christopher A Voigt
Journal:  Nat Methods       Date:  2014-10-26       Impact factor: 28.547

10.  Rapidly evolving homing CRISPR barcodes.

Authors:  Reza Kalhor; Prashant Mali; George M Church
Journal:  Nat Methods       Date:  2016-12-05       Impact factor: 28.547

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  3 in total

Review 1.  Synthetic Biology Goes Cell-Free.

Authors:  Aidan Tinafar; Katariina Jaenes; Keith Pardee
Journal:  BMC Biol       Date:  2019-08-08       Impact factor: 7.431

2.  A multiplexed, electrochemical interface for gene-circuit-based sensors.

Authors:  Peivand Sadat Mousavi; Sarah J Smith; Jenise B Chen; Margot Karlikow; Aidan Tinafar; Clare Robinson; Wenhan Liu; Duo Ma; Alexander A Green; Shana O Kelley; Keith Pardee
Journal:  Nat Chem       Date:  2019-11-25       Impact factor: 24.427

3.  A synthetic distributed genetic multi-bit counter.

Authors:  Tianchi Chen; M Ali Al-Radhawi; Christopher A Voigt; Eduardo D Sontag
Journal:  iScience       Date:  2021-11-29
  3 in total

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