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Items: 1 to 20 of 66

1.

Metabolic perceptrons for neural computing in biological systems.

Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M, Faulon JL.

Nat Commun. 2019 Aug 28;10(1):3880. doi: 10.1038/s41467-019-11889-0.

2.

Optimizing Cell-Free Biosensors to Monitor Enzymatic Production.

Pandi A, Grigoras I, Borkowski O, Faulon JL.

ACS Synth Biol. 2019 Aug 16;8(8):1952-1957. doi: 10.1021/acssynbio.9b00160. Epub 2019 Aug 2.

PMID:
31335131
3.

Microbial Genes for a Circular and Sustainable Bio-PET Economy.

Salvador M, Abdulmutalib U, Gonzalez J, Kim J, Smith AA, Faulon JL, Wei R, Zimmermann W, Jimenez JI.

Genes (Basel). 2019 May 16;10(5). pii: E373. doi: 10.3390/genes10050373. Review.

4.

Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors.

Voyvodic PL, Pandi A, Koch M, Conejero I, Valjent E, Courtet P, Renard E, Faulon JL, Bonnet J.

Nat Commun. 2019 Apr 12;10(1):1697. doi: 10.1038/s41467-019-09722-9.

5.

Custom-made transcriptional biosensors for metabolic engineering.

Koch M, Pandi A, Borkowski O, Batista AC, Faulon JL.

Curr Opin Biotechnol. 2019 Oct;59:78-84. doi: 10.1016/j.copbio.2019.02.016. Epub 2019 Mar 25. Review.

PMID:
30921678
6.

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli.

Jervis AJ, Carbonell P, Vinaixa M, Dunstan MS, Hollywood KA, Robinson CJ, Rattray NJW, Yan C, Swainston N, Currin A, Sung R, Toogood H, Taylor S, Faulon JL, Breitling R, Takano E, Scrutton NS.

ACS Synth Biol. 2019 Jan 18;8(1):127-136. doi: 10.1021/acssynbio.8b00398. Epub 2019 Jan 7.

PMID:
30563328
7.

Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster.

Koch M, Faulon JL, Borkowski O.

Front Bioeng Biotechnol. 2018 Nov 29;6:182. doi: 10.3389/fbioe.2018.00182. eCollection 2018. Review.

8.

RetroRules: a database of reaction rules for engineering biology.

Duigou T, du Lac M, Carbonell P, Faulon JL.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1229-D1235. doi: 10.1093/nar/gky940.

9.

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals.

Carbonell P, Jervis AJ, Robinson CJ, Yan C, Dunstan M, Swainston N, Vinaixa M, Hollywood KA, Currin A, Rattray NJW, Taylor S, Spiess R, Sung R, Williams AR, Fellows D, Stanford NJ, Mulherin P, Le Feuvre R, Barran P, Goodacre R, Turner NJ, Goble C, Chen GG, Kell DB, Micklefield J, Breitling R, Takano E, Faulon JL, Scrutton NS.

Commun Biol. 2018 Jun 8;1:66. doi: 10.1038/s42003-018-0076-9. eCollection 2018.

10.

Enzyme Discovery: Enzyme Selection and Pathway Design.

Carbonell P, Koch M, Duigou T, Faulon JL.

Methods Enzymol. 2018;608:3-27. doi: 10.1016/bs.mie.2018.04.005.

PMID:
30173766
11.

PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts.

Swainston N, Dunstan M, Jervis AJ, Robinson CJ, Carbonell P, Williams AR, Faulon JL, Scrutton NS, Kell DB.

Bioinformatics. 2018 Jul 1;34(13):2327-2329. doi: 10.1093/bioinformatics/bty105.

PMID:
29949952
12.

Building a minimal and generalizable model of transcription factor-based biosensors: Showcasing flavonoids.

Trabelsi H, Koch M, Faulon JL.

Biotechnol Bioeng. 2018 Sep;115(9):2292-2304. doi: 10.1002/bit.26726. Epub 2018 May 24.

13.

A dataset of small molecules triggering transcriptional and translational cellular responses.

Koch M, Pandi A, Delépine B, Faulon JL.

Data Brief. 2018 Feb 27;17:1374-1378. doi: 10.1016/j.dib.2018.02.061. eCollection 2018 Apr.

14.

Selenzyme: enzyme selection tool for pathway design.

Carbonell P, Wong J, Swainston N, Takano E, Turner NJ, Scrutton NS, Kell DB, Breitling R, Faulon JL.

Bioinformatics. 2018 Jun 15;34(12):2153-2154. doi: 10.1093/bioinformatics/bty065.

PMID:
29425325
15.

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.

Koch M, Duigou T, Carbonell P, Faulon JL.

J Cheminform. 2017 Dec 19;9(1):64. doi: 10.1186/s13321-017-0252-9.

16.

RetroPath2.0: A retrosynthesis workflow for metabolic engineers.

Delépine B, Duigou T, Carbonell P, Faulon JL.

Metab Eng. 2018 Jan;45:158-170. doi: 10.1016/j.ymben.2017.12.002. Epub 2017 Dec 9.

17.

Extended Metabolic Space Modeling.

Carbonell P, Delépine B, Faulon JL.

Methods Mol Biol. 2018;1671:83-96. doi: 10.1007/978-1-4939-7295-1_6.

PMID:
29170954
18.

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R.

PLoS One. 2017 Jul 14;12(7):e0179130. doi: 10.1371/journal.pone.0179130. eCollection 2017.

19.

Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways.

Libis V, Delépine B, Faulon JL.

ACS Synth Biol. 2016 Oct 21;5(10):1076-1085. Epub 2016 Mar 30.

PMID:
27028723
20.

Sensing new chemicals with bacterial transcription factors.

Libis V, Delépine B, Faulon JL.

Curr Opin Microbiol. 2016 Oct;33:105-112. doi: 10.1016/j.mib.2016.07.006. Epub 2016 Jul 26. Review.

PMID:
27472026

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