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

Department of Biomedical Engineering
Harvard Medical School
Harvard University
University of California, San Diego
University of Iceland

Research output: Contribution to a Journal (Peer & Non Peer) › Article › peer-review

81 Citations (Scopus)

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
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
Publication status	Published - 2009
Externally published	Yes

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10.1038/nmeth.1348

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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

@article{212b83ca02294c3f889e2f53cbf1bdba,

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.\}",

year = "2009",

doi = "10.1038/nmeth.1348",

language = "English",

volume = "6",

pages = "589--592",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

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}

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

TY - JOUR

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.

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.

UR - https://www.scopus.com/pages/publications/68349108021

U2 - 10.1038/nmeth.1348

DO - 10.1038/nmeth.1348

M3 - Article

SN - 1548-7091

VL - 6

SP - 589

EP - 592

JO - Nature Methods

JF - Nature Methods

IS - 8

ER -

Metabolic network analysis integrated with transcript verification for sequenced genomes

Abstract

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