Matt Gethers/Articles of General Interest

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Articles of General Interest

Organized by Topic

Affibody Inactivation


Biologically Encoded Safety Mechanisms

Base Excision Repair

Charge Migration Along DNA

DNA Synthesis

Social Science and Synthetic Biology

Reactive Oxygen Species


Organized Alphabetically

  1. Andrianantoandro E, Basu S, Karig DK, and Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol. 2006;2:2006.0028. DOI:10.1038/msb4100073 | PubMed ID:16738572 | HubMed [Adrianantoandro]
  2. Anderson JC, Voigt CA, and Arkin AP. Environmental signal integration by a modular AND gate. Mol Syst Biol. 2007;3:133. DOI:10.1038/msb4100173 | PubMed ID:17700541 | HubMed [Anderson]
  3. Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, and You L. A synthetic Escherichia coli predator-prey ecosystem. Mol Syst Biol. 2008;4:187. DOI:10.1038/msb.2008.24 | PubMed ID:18414488 | HubMed [Balagadde]
  4. Cherkasov A, Hilpert K, Jenssen H, Fjell CD, Waldbrook M, Mullaly SC, Volkmer R, and Hancock RE. Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs. ACS Chem Biol. 2009 Jan 16;4(1):65-74. DOI:10.1021/cb800240j | PubMed ID:19055425 | HubMed [Cherkasov]
  5. Dasika MS and Maranas CD. OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst Biol. 2008 Mar 3;2:24. DOI:10.1186/1752-0509-2-24 | PubMed ID:18315885 | HubMed [Dasika]
  6. Dhar PK, Thwin CS, Tun K, Tsumoto Y, Maurer-Stroh S, Eisenhaber F, and Surana U. Synthesizing non-natural parts from natural genomic template. J Biol Eng. 2009 Feb 3;3:2. DOI:10.1186/1754-1611-3-2 | PubMed ID:19187561 | HubMed [Dhar]
  7. Drubin DA, Way JC, and Silver PA. Designing biological systems. Genes Dev. 2007 Feb 1;21(3):242-54. DOI:10.1101/gad.1507207 | PubMed ID:17289915 | HubMed [Drubin]
  8. Fu P. A perspective of synthetic biology: assembling building blocks for novel functions. Biotechnol J. 2006 Jun;1(6):690-9. DOI:10.1002/biot.200600019 | PubMed ID:16892318 | HubMed [Fu]
  9. Greber D and Fussenegger M. Mammalian synthetic biology: engineering of sophisticated gene networks. J Biotechnol. 2007 Jul 15;130(4):329-45. DOI:10.1016/j.jbiotec.2007.05.014 | PubMed ID:17602777 | HubMed [Fussenegger]
  10. Gore J and van Oudenaarden A. Synthetic biology: The yin and yang of nature. Nature. 2009 Jan 15;457(7227):271-2. DOI:10.1038/457271a | PubMed ID:19148089 | HubMed [Gore]
  11. Haseltine EL and Arnold FH. Implications of rewiring bacterial quorum sensing. Appl Environ Microbiol. 2008 Jan;74(2):437-45. DOI:10.1128/AEM.01688-07 | PubMed ID:18039819 | HubMed [Haseltine]
  12. Hasty J, McMillen D, and Collins JJ. Engineered gene circuits. Nature. 2002 Nov 14;420(6912):224-30. DOI:10.1038/nature01257 | PubMed ID:12432407 | HubMed [Hasty]
  13. Hasty J, Isaacs F, Dolnik M, McMillen D, and Collins JJ. Designer gene networks: Towards fundamental cellular control. Chaos. 2001 Mar;11(1):207-220. DOI:10.1063/1.1345702 | PubMed ID:12779454 | HubMed [Hasty2]
  14. Kim J, White KS, and Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol. 2006;2:68. DOI:10.1038/msb4100099 | PubMed ID:17170763 | HubMed [Kim]
  15. Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, and Collins JJ. Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8414-9. DOI:10.1073/pnas.0402940101 | PubMed ID:15159530 | HubMed [Kobayashi]
  16. Lindström MS. Emerging functions of ribosomal proteins in gene-specific transcription and translation. Biochem Biophys Res Commun. 2009 Feb 6;379(2):167-70. DOI:10.1016/j.bbrc.2008.12.083 | PubMed ID:19114035 | HubMed [Lindstrom]
  17. Marguet P, Balagadde F, Tan C, and You L. Biology by design: reduction and synthesis of cellular components and behaviour. J R Soc Interface. 2007 Aug 22;4(15):607-23. DOI:10.1098/rsif.2006.0206 | PubMed ID:17251159 | HubMed [Marguet]
  18. Hamad-Schifferli K, Schwartz JJ, Santos AT, Zhang S, and Jacobson JM. Remote electronic control of DNA hybridization through inductive coupling to an attached metal nanocrystal antenna. Nature. 2002 Jan 10;415(6868):152-5. DOI:10.1038/415152a | PubMed ID:11805829 | HubMed [Schifferli]
  19. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol. 2007;3:158. DOI:10.1038/msb4100202 | PubMed ID:18091727 | HubMed [Serrano]
  20. Tigges M, Marquez-Lago TT, Stelling J, and Fussenegger M. A tunable synthetic mammalian oscillator. Nature. 2009 Jan 15;457(7227):309-12. DOI:10.1038/nature07616 | PubMed ID:19148099 | HubMed [Tigges]
  21. Walter JM, Greenfield D, Bustamante C, and Liphardt J. Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2408-12. DOI:10.1073/pnas.0611035104 | PubMed ID:17277079 | HubMed [Walter]
  22. Yonekura S, Nakamura N, Yonei S, and Zhang-Akiyama QM. Generation, biological consequences and repair mechanisms of cytosine deamination in DNA. J Radiat Res. 2009 Jan;50(1):19-26. DOI:10.1269/jrr.08080 | PubMed ID:18987436 | HubMed [Yonekura]

All Medline abstracts: PubMed | HubMed

K. Hamad-Schifferli, "Control of biomolecular activity by nanoparticle antennas," in BioMEMS and Biomedical Nanotechnology, vol II:Micro/Nano Technologies for Genomics and Proteomics, edited by Mihri Ozkan and Michael Heller (Kluwer, New York, 2006), invited contribution.

Synthetic Biology: Social and Ethical Challenges

Measurement of Radio Frequency Permittivity of Biological Tissues with an Open-Ended Coaxial Line: Part I