Literature DB >> 22688678

Biomolecular computing systems: principles, progress and potential.

Yaakov Benenson1.   

Abstract

The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.

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Year:  2012        PMID: 22688678     DOI: 10.1038/nrg3197

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  111 in total

1.  Reprogramming control of an allosteric signaling switch through modular recombination.

Authors:  John E Dueber; Brian J Yeh; Kayam Chak; Wendell A Lim
Journal:  Science       Date:  2003-09-26       Impact factor: 47.728

2.  Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms.

Authors:  Sang-Hyun Park; Ali Zarrinpar; Wendell A Lim
Journal:  Science       Date:  2003-01-02       Impact factor: 47.728

Review 3.  Manufacturing molecules through metabolic engineering.

Authors:  Jay D Keasling
Journal:  Science       Date:  2010-12-03       Impact factor: 47.728

4.  Deterministic characterization of stochastic genetic circuits.

Authors:  Matthew Scott; Terence Hwa; Brian Ingalls
Journal:  Proc Natl Acad Sci U S A       Date:  2007-04-19       Impact factor: 11.205

5.  An information-bearing seed for nucleating algorithmic self-assembly.

Authors:  Robert D Barish; Rebecca Schulman; Paul W K Rothemund; Erik Winfree
Journal:  Proc Natl Acad Sci U S A       Date:  2009-03-24       Impact factor: 11.205

6.  Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology.

Authors:  Baojun Wang; Richard I Kitney; Nicolas Joly; Martin Buck
Journal:  Nat Commun       Date:  2011-10-18       Impact factor: 14.919

Review 7.  Synthetic biology.

Authors:  Steven A Benner; A Michael Sismour
Journal:  Nat Rev Genet       Date:  2005-07       Impact factor: 53.242

8.  Shape, size, and robustness: feasible regions in the parameter space of biochemical networks.

Authors:  Adel Dayarian; Madalena Chaves; Eduardo D Sontag; Anirvan M Sengupta
Journal:  PLoS Comput Biol       Date:  2009-01-02       Impact factor: 4.475

9.  Programming gene expression with combinatorial promoters.

Authors:  Robert Sidney Cox; Michael G Surette; Michael B Elowitz
Journal:  Mol Syst Biol       Date:  2007-11-13       Impact factor: 11.429

10.  A fast, robust and tunable synthetic gene oscillator.

Authors:  Jesse Stricker; Scott Cookson; Matthew R Bennett; William H Mather; Lev S Tsimring; Jeff Hasty
Journal:  Nature       Date:  2008-10-29       Impact factor: 49.962

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  79 in total

1.  Enzymatic Synthesis of Sequence-Defined Synthetic Nucleic Acid Polymers with Diverse Functional Groups.

Authors:  Dehui Kong; Yi Lei; Wayland Yeung; Ryan Hili
Journal:  Angew Chem Int Ed Engl       Date:  2016-10-10       Impact factor: 15.336

2.  Liquid brains, solid brains.

Authors:  Ricard Solé; Melanie Moses; Stephanie Forrest
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-06-10       Impact factor: 6.237

Review 3.  Statistical physics of liquid brains.

Authors:  Jordi Piñero; Ricard Solé
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-06-10       Impact factor: 6.237

Review 4.  Application of CRISPR/Cas System in the Metabolic Engineering of Small Molecules.

Authors:  Rajveer Singh; Shivani Chandel; Arijit Ghosh; Dhritiman Dey; Rudra Chakravarti; Syamal Roy; V Ravichandiran; Dipanjan Ghosh
Journal:  Mol Biotechnol       Date:  2021-03-27       Impact factor: 2.695

5.  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

6.  Physical constraints on biological integral control design for homeostasis and sensory adaptation.

Authors:  Jordan Ang; David R McMillen
Journal:  Biophys J       Date:  2013-01-22       Impact factor: 4.033

7.  Biocomputing based on particle disassembly.

Authors:  Maxim P Nikitin; Victoria O Shipunova; Sergey M Deyev; Petr I Nikitin
Journal:  Nat Nanotechnol       Date:  2014-08-17       Impact factor: 39.213

8.  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

Review 9.  Engineering Gene Circuits for Mammalian Cell-Based Applications.

Authors:  Simon Ausländer; Martin Fussenegger
Journal:  Cold Spring Harb Perspect Biol       Date:  2016-07-01       Impact factor: 10.005

10.  DNA Computing Systems Activated by Electrochemically-triggered DNA Release from a Polymer-brush-modified Electrode Array.

Authors:  Maria Gamella; Andrey Zakharchenko; Nataliia Guz; Madeline Masi; Sergiy Minko; Dmitry M Kolpashchikov; Heiko Iken; Arshak Poghossian; Michael J Schöning; Evgeny Katz
Journal:  Electroanalysis       Date:  2016-08-05       Impact factor: 3.223

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