SensiPath: computer-aided design of Sensing-enabling metabolic PathwaysCitation formats

  • Authors:
  • Baudoin Delépine
  • Vincent Libis
  • Pablo Carbonell
  • Jean-Loup Faulon

Standard

SensiPath: computer-aided design of Sensing-enabling metabolic Pathways. / Delépine, Baudoin; Libis, Vincent; Carbonell, Pablo; Faulon, Jean-Loup.

In: Nucleic acids research, Vol. 44, No. W1, 22.04.2016, p. 226-231.

Research output: Contribution to journalArticlepeer-review

Harvard

Delépine, B, Libis, V, Carbonell, P & Faulon, J-L 2016, 'SensiPath: computer-aided design of Sensing-enabling metabolic Pathways', Nucleic acids research, vol. 44, no. W1, pp. 226-231. https://doi.org/10.1093/nar/gkw305

APA

Delépine, B., Libis, V., Carbonell, P., & Faulon, J-L. (2016). SensiPath: computer-aided design of Sensing-enabling metabolic Pathways. Nucleic acids research, 44(W1), 226-231. https://doi.org/10.1093/nar/gkw305

Vancouver

Delépine B, Libis V, Carbonell P, Faulon J-L. SensiPath: computer-aided design of Sensing-enabling metabolic Pathways. Nucleic acids research. 2016 Apr 22;44(W1):226-231. https://doi.org/10.1093/nar/gkw305

Author

Delépine, Baudoin ; Libis, Vincent ; Carbonell, Pablo ; Faulon, Jean-Loup. / SensiPath: computer-aided design of Sensing-enabling metabolic Pathways. In: Nucleic acids research. 2016 ; Vol. 44, No. W1. pp. 226-231.

Bibtex

@article{80c9db811e0c473d9d442d95fb9b2e8b,
title = "SensiPath: computer-aided design of Sensing-enabling metabolic Pathways",
abstract = "Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr. SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications.",
author = "Baudoin Del{\'e}pine and Vincent Libis and Pablo Carbonell and Jean-Loup Faulon",
year = "2016",
month = apr,
day = "22",
doi = "10.1093/nar/gkw305",
language = "English",
volume = "44",
pages = "226--231",
journal = "Nucleic acids research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "W1",

}

RIS

TY - JOUR

T1 - SensiPath: computer-aided design of Sensing-enabling metabolic Pathways

AU - Delépine, Baudoin

AU - Libis, Vincent

AU - Carbonell, Pablo

AU - Faulon, Jean-Loup

PY - 2016/4/22

Y1 - 2016/4/22

N2 - Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr. SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications.

AB - Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability of detecting and quantifying intracellular amounts of a compound of interest are central to whole-cell biosensors design for medical and environmental applications, and they also constitute essential parts for the selection and regulation of high-producer strains in metabolic engineering. However, the number of compounds that can be detected through natural mechanisms, like allosteric transcription factors, is limited; expanding the set of detectable compounds is therefore highly desirable. Here, we present the SensiPath web server, accessible at http://sensipath.micalis.fr. SensiPath implements a strategy to enlarge the set of detectable compounds by screening for multi-step enzymatic transformations converting non-detectable compounds into detectable ones. The SensiPath approach is based on the encoding of reactions through signature descriptors to explore sensing-enabling metabolic pathways, which are putative biochemical transformations of the target compound leading to known effectors of transcription factors. In that way, SensiPath enlarges the design space by broadening the potential use of biosensors in synthetic biology applications.

U2 - 10.1093/nar/gkw305

DO - 10.1093/nar/gkw305

M3 - Article

VL - 44

SP - 226

EP - 231

JO - Nucleic acids research

JF - Nucleic acids research

SN - 0305-1048

IS - W1

ER -