Metabolic network analysis integrated with transcript verification for sequenced genomes

Ani Manichaikul; Lila Ghamsari; Erik F.Y. Hom; Chenwei Lin; Ryan R. Murray; Roger L. Chang; S. Balaji; Tong Hao; Yun Shen; Arvind K. Chavali; Ines Thiele; Xinping Yang; Changyu Fan; Elizabeth Mello; David E. Hill; Marc Vidal; Kourosh Salehi-Ashtiani; Jason A. Papin

doi:10.1038/nmeth.1348

Metabolic network analysis integrated with transcript verification for sequenced genomes

Ani Manichaikul, Lila Ghamsari, Erik F.Y. Hom, Chenwei Lin, Ryan R. Murray, Roger L. Chang, S. Balaji, Tong Hao, Yun Shen, Arvind K. Chavali, Ines Thiele, Xinping Yang, Changyu Fan, Elizabeth Mello, David E. Hill, Marc Vidal, Kourosh Salehi-Ashtiani, Jason A. Papin

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

77 Scopus citations

Abstract

With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames. Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.

Original language	English (US)
Pages (from-to)	589-592
Number of pages	4
Journal	Nature Methods
Volume	6
Issue number	8
DOIs	https://doi.org/10.1038/nmeth.1348
State	Published - 2009
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Manichaikul, A., Ghamsari, L., Hom, E. F. Y., Lin, C., Murray, R. R., Chang, R. L., Balaji, S., Hao, T., Shen, Y., Chavali, A. K., Thiele, I., Yang, X., Fan, C., Mello, E., Hill, D. E., Vidal, M., Salehi-Ashtiani, K., & Papin, J. A. (2009). Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods, 6(8), 589-592. https://doi.org/10.1038/nmeth.1348

Manichaikul, A, Ghamsari, L, Hom, EFY, Lin, C, Murray, RR, Chang, RL, Balaji, S, Hao, T, Shen, Y, Chavali, AK, Thiele, I, Yang, X, Fan, C, Mello, E, Hill, DE, Vidal, M, Salehi-Ashtiani, K & Papin, JA 2009, 'Metabolic network analysis integrated with transcript verification for sequenced genomes', Nature Methods, vol. 6, no. 8, pp. 589-592. https://doi.org/10.1038/nmeth.1348

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title = "Metabolic network analysis integrated with transcript verification for sequenced genomes",

abstract = "With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames. Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.",

author = "Ani Manichaikul and Lila Ghamsari and Hom, {Erik F.Y.} and Chenwei Lin and Murray, {Ryan R.} and Chang, {Roger L.} and S. Balaji and Tong Hao and Yun Shen and Chavali, {Arvind K.} and Ines Thiele and Xinping Yang and Changyu Fan and Elizabeth Mello and Hill, {David E.} and Marc Vidal and Kourosh Salehi-Ashtiani and Papin, {Jason A.}",

note = "Funding Information: This research was supported by the Office of Science (Biological and Environmental Research), US Department of Energy, grant DE-FG02-07ER64496 (to J.A.P. and K.S.-A.), the Jane Coffin Childs Memorial Fund for Medical Research (to E.F.Y.H.) and by National Science Foundation IGERT training grant DGE0504645 (to R.L.C.).",

year = "2009",

doi = "10.1038/nmeth.1348",

language = "English (US)",

volume = "6",

pages = "589--592",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "8",

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T1 - Metabolic network analysis integrated with transcript verification for sequenced genomes

AU - Manichaikul, Ani

AU - Ghamsari, Lila

AU - Hom, Erik F.Y.

AU - Lin, Chenwei

AU - Murray, Ryan R.

AU - Chang, Roger L.

AU - Balaji, S.

AU - Hao, Tong

AU - Shen, Yun

AU - Chavali, Arvind K.

AU - Thiele, Ines

AU - Yang, Xinping

AU - Fan, Changyu

AU - Mello, Elizabeth

AU - Hill, David E.

AU - Vidal, Marc

AU - Salehi-Ashtiani, Kourosh

AU - Papin, Jason A.

N1 - Funding Information: This research was supported by the Office of Science (Biological and Environmental Research), US Department of Energy, grant DE-FG02-07ER64496 (to J.A.P. and K.S.-A.), the Jane Coffin Childs Memorial Fund for Medical Research (to E.F.Y.H.) and by National Science Foundation IGERT training grant DGE0504645 (to R.L.C.).

PY - 2009

Y1 - 2009

N2 - With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames. Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.

AB - With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames. Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.

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JO - Nature Methods

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IS - 8

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Metabolic network analysis integrated with transcript verification for sequenced genomes

Abstract

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