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Items: 1 to 50 of 67

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
21.

Mapping the patent landscape of synthetic biology for fine chemical production pathways.

Carbonell P, Gök A, Shapira P, Faulon JL.

Microb Biotechnol. 2016 Sep;9(5):687-95. doi: 10.1111/1751-7915.12401. Epub 2016 Aug 3. Review.

22.

SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals.

Carbonell P, Currin A, Dunstan M, Fellows D, Jervis A, Rattray NJ, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C, Barran P, Breitling R, Chen GG, Faulon JL, Goble C, Goodacre R, Kell DB, Feuvre RL, Micklefield J, Scrutton NS, Shapira P, Takano E, Turner NJ.

Biochem Soc Trans. 2016 Jun 15;44(3):675-7. doi: 10.1042/BST20160009.

23.

SensiPath: computer-aided design of sensing-enabling metabolic pathways.

Delépine B, Libis V, Carbonell P, Faulon JL.

Nucleic Acids Res. 2016 Jul 8;44(W1):W226-31. doi: 10.1093/nar/gkw305. Epub 2016 Apr 22.

24.

Semisupervised Gaussian Process for Automated Enzyme Search.

Mellor J, Grigoras I, Carbonell P, Faulon JL.

ACS Synth Biol. 2016 Jun 17;5(6):518-28. doi: 10.1021/acssynbio.5b00294. Epub 2016 Mar 30.

PMID:
27007080
25.

A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli.

Fehér T, Libis V, Carbonell P, Faulon JL.

Front Bioeng Biotechnol. 2015 Apr 8;3:46. doi: 10.3389/fbioe.2015.00046. eCollection 2015.

26.

Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.

Fehér T, Planson AG, Carbonell P, Fernández-Castané A, Grigoras I, Dariy E, Perret A, Faulon JL.

Biotechnol J. 2014 Nov;9(11):1446-57. doi: 10.1002/biot.201400055. Epub 2014 Oct 15.

PMID:
25224453
27.

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.

Pauthenier C, Faulon JL.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W205-9. doi: 10.1093/nar/gku393. Epub 2014 May 14.

28.

XTMS: pathway design in an eXTended metabolic space.

Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W389-94. doi: 10.1093/nar/gku362. Epub 2014 May 3.

29.

Computer-aided design for metabolic engineering.

Fernández-Castané A, Fehér T, Carbonell P, Pauthenier C, Faulon JL.

J Biotechnol. 2014 Dec 20;192 Pt B:302-13. doi: 10.1016/j.jbiotec.2014.03.029. Epub 2014 Apr 2. Review.

PMID:
24704607
30.

Retropath: automated pipeline for embedded metabolic circuits.

Carbonell P, Parutto P, Baudier C, Junot C, Faulon JL.

ACS Synth Biol. 2014 Aug 15;3(8):565-77. doi: 10.1021/sb4001273. Epub 2013 Oct 16.

PMID:
24131345
31.

Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks.

Joo J, Plimpton SJ, Faulon JL.

BMC Syst Biol. 2013 Jun 7;7:45. doi: 10.1186/1752-0509-7-45.

32.

Stereo signature molecular descriptor.

Carbonell P, Carlsson L, Faulon JL.

J Chem Inf Model. 2013 Apr 22;53(4):887-97. doi: 10.1021/ci300584r. Epub 2013 Apr 5.

PMID:
23527586
33.

Retrosynthetic design of heterologous pathways.

Carbonell P, Planson AG, Faulon JL.

Methods Mol Biol. 2013;985:149-73. doi: 10.1007/978-1-62703-299-5_9.

PMID:
23417804
34.

OMG: Open Molecule Generator.

Peironcely JE, Rojas-Chertó M, Fichera D, Reijmers T, Coulier L, Faulon JL, Hankemeier T.

J Cheminform. 2012 Sep 17;4(1):21. doi: 10.1186/1758-2946-4-21.

35.

A retrosynthetic biology approach to therapeutics: from conception to delivery.

Planson AG, Carbonell P, Grigoras I, Faulon JL.

Curr Opin Biotechnol. 2012 Dec;23(6):948-56. doi: 10.1016/j.copbio.2012.03.009. Epub 2012 Apr 2. Review.

PMID:
22475981
36.

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms.

Carbonell P, Fichera D, Pandit SB, Faulon JL.

BMC Syst Biol. 2012 Feb 6;6:10. doi: 10.1186/1752-0509-6-10.

37.

Origins of specificity and promiscuity in metabolic networks.

Carbonell P, Lecointre G, Faulon JL.

J Biol Chem. 2011 Dec 23;286(51):43994-4004. doi: 10.1074/jbc.M111.274050. Epub 2011 Nov 3.

38.

Compound toxicity screening and structure-activity relationship modeling in Escherichia coli.

Planson AG, Carbonell P, Paillard E, Pollet N, Faulon JL.

Biotechnol Bioeng. 2012 Mar;109(3):846-50. doi: 10.1002/bit.24356. Epub 2011 Nov 9.

PMID:
22038678
39.

A retrosynthetic biology approach to metabolic pathway design for therapeutic production.

Carbonell P, Planson AG, Fichera D, Faulon JL.

BMC Syst Biol. 2011 Aug 5;5:122. doi: 10.1186/1752-0509-5-122.

40.

Toward Quantitative Structure-Property Relationships for Charge Transfer Rates of Polycyclic Aromatic Hydrocarbons.

Misra M, Andrienko D, Baumeier B, Faulon JL, von Lilienfeld OA.

J Chem Theory Comput. 2011 Aug 9;7(8):2549-55. doi: 10.1021/ct200231z. Epub 2011 Jul 25.

PMID:
26606628
41.

Editorial: Synthetic Biology - applying new paradigms at the interface of fundamental research and innovation.

Jaramillo A, Faulon JL.

Biotechnol J. 2011 Jul;6(7):766-7. doi: 10.1002/biot.201100254. No abstract available.

PMID:
21728241
42.

Engineering antibiotic production and overcoming bacterial resistance.

Planson AG, Carbonell P, Grigoras I, Faulon JL.

Biotechnol J. 2011 Jul;6(7):812-25. doi: 10.1002/biot.201100085. Epub 2011 Jun 10. Review.

PMID:
21661120
43.

Molecular signatures-based prediction of enzyme promiscuity.

Carbonell P, Faulon JL.

Bioinformatics. 2010 Aug 15;26(16):2012-9. doi: 10.1093/bioinformatics/btq317. Epub 2010 Jun 15.

PMID:
20551137
44.

Understanding virulence mechanisms in M. tuberculosis infection via a circuit-based simulation framework.

May E, Leitao A, Faulon JL, Joo J, Misra M, Oprea TI.

Conf Proc IEEE Eng Med Biol Soc. 2008;2008:4953-5. doi: 10.1109/IEMBS.2008.4650325.

PMID:
19163828
45.

Data mining PubChem using a support vector machine with the Signature molecular descriptor: classification of factor XIa inhibitors.

Weis DC, Visco DP Jr, Faulon JL.

J Mol Graph Model. 2008 Nov;27(4):466-75. doi: 10.1016/j.jmgm.2008.08.004. Epub 2008 Aug 27.

PMID:
18829357
46.

Identification of expression patterns of IL-2-responsive genes in the murine T cell line CTLL-2.

Zhang Z, Martino A, Faulon JL.

J Interferon Cytokine Res. 2007 Dec;27(12):991-5. doi: 10.1089/jir.2006.0169.

PMID:
18184039
47.

Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor.

Faulon JL, Misra M, Martin S, Sale K, Sapra R.

Bioinformatics. 2008 Jan 15;24(2):225-33. Epub 2007 Nov 23.

PMID:
18037612
48.

Sensitivity analysis of a computational model of the IKK NF-kappaB IkappaBalpha A20 signal transduction network.

Joo J, Plimpton S, Martin S, Swiler L, Faulon JL.

Ann N Y Acad Sci. 2007 Dec;1115:221-39. Epub 2007 Oct 12.

PMID:
17934057
49.

Using product kernels to predict protein interactions.

Martin S, Brown WM, Faulon JL.

Adv Biochem Eng Biotechnol. 2008;110:215-45. Review.

PMID:
17922100
50.

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