Accelerated discovery via a whole-cell model

Jayodita C. Sanghvi; Sergi Regot; Silvia Carrasco; Jonathan R. Karr; Miriam V. Gutschow; Benjamin Bolival; Markus W. Covert

doi:10.1038/nmeth.2724

Accelerated discovery via a whole-cell model

Jayodita C. Sanghvi
, Sergi Regot
, Silvia Carrasco
, Jonathan R. Karr
, Miriam V. Gutschow
, Benjamin Bolival
, Markus W. Covert

Research output: Contribution to journal › Article › peer-review

60 Scopus citations

Abstract

To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimental measurements for all viable single-gene disruption Mycoplasma genitalium strains. Discrepancies between simulations and experiments led to predictions about kinetic parameters of specific enzymes that we subsequently validated. These findings represent, to our knowledge, the first application of whole-cell modeling to accelerate biological discovery.

Original language	English
Pages (from-to)	1192-1195
Number of pages	4
Journal	Nature Methods
Volume	10
Issue number	12
DOIs	https://doi.org/10.1038/nmeth.2724
State	Published - Dec 2013
Externally published	Yes

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title = "Accelerated discovery via a whole-cell model",

abstract = "To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimental measurements for all viable single-gene disruption Mycoplasma genitalium strains. Discrepancies between simulations and experiments led to predictions about kinetic parameters of specific enzymes that we subsequently validated. These findings represent, to our knowledge, the first application of whole-cell modeling to accelerate biological discovery.",

author = "Sanghvi, \{Jayodita C.\} and Sergi Regot and Silvia Carrasco and Karr, \{Jonathan R.\} and Gutschow, \{Miriam V.\} and Benjamin Bolival and Covert, \{Markus W.\}",

note = "Funding Information: We acknowledge support from: an US National Institutes of Health Pioneer Award (5DP1LM01150-05) and an Allen Distinguished Investigator Award to M.W.C.; Siebel Scholars, US National Science Foundation and Stanford University Bio-X Fellowships to J.C.S.; an European Molecular Biology Organization Fellowship (ALTF1371-2011) to S.R.; US National Defense Science and Engineering Graduate Fellowship, US National Science Foundation fellowship, and Stanford Graduate Fellowship to J.R.K.; and Weiland and Rensselaer Engineering Fellowships to M.V.G.",

year = "2013",

month = dec,

doi = "10.1038/nmeth.2724",

language = "English",

volume = "10",

pages = "1192--1195",

journal = "Nature Methods",

issn = "1548-7091",

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T1 - Accelerated discovery via a whole-cell model

AU - Sanghvi, Jayodita C.

AU - Regot, Sergi

AU - Carrasco, Silvia

AU - Karr, Jonathan R.

AU - Gutschow, Miriam V.

AU - Bolival, Benjamin

AU - Covert, Markus W.

N1 - Funding Information: We acknowledge support from: an US National Institutes of Health Pioneer Award (5DP1LM01150-05) and an Allen Distinguished Investigator Award to M.W.C.; Siebel Scholars, US National Science Foundation and Stanford University Bio-X Fellowships to J.C.S.; an European Molecular Biology Organization Fellowship (ALTF1371-2011) to S.R.; US National Defense Science and Engineering Graduate Fellowship, US National Science Foundation fellowship, and Stanford Graduate Fellowship to J.R.K.; and Weiland and Rensselaer Engineering Fellowships to M.V.G.

PY - 2013/12

Y1 - 2013/12

N2 - To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimental measurements for all viable single-gene disruption Mycoplasma genitalium strains. Discrepancies between simulations and experiments led to predictions about kinetic parameters of specific enzymes that we subsequently validated. These findings represent, to our knowledge, the first application of whole-cell modeling to accelerate biological discovery.

AB - To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimental measurements for all viable single-gene disruption Mycoplasma genitalium strains. Discrepancies between simulations and experiments led to predictions about kinetic parameters of specific enzymes that we subsequently validated. These findings represent, to our knowledge, the first application of whole-cell modeling to accelerate biological discovery.

UR - https://www.scopus.com/pages/publications/84888883268

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DO - 10.1038/nmeth.2724

M3 - Article

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SN - 1548-7091

VL - 10

SP - 1192

EP - 1195

JO - Nature Methods

JF - Nature Methods

IS - 12

ER -

Accelerated discovery via a whole-cell model

Abstract

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