Applications of genome-scale metabolic reconstructions

被引：578

作者：

Oberhardt, Matthew A. ^{[1
]}

Palsson, Bernhard O. ^{[2
]}

Papin, Jason A. ^{[1
]}

机构：

[1] Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22908 USA

[2] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

来源：

MOLECULAR SYSTEMS BIOLOGY | 2009年 / 5卷

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

computational biology; metabolic model; modeling; network; systems biology; FLUX BALANCE ANALYSIS; HAEMOPHILUS-INFLUENZAE RD; CONSTRAINT-BASED ANALYSIS; NETWORK-BASED PREDICTION; SACCHAROMYCES-CEREVISIAE; STAPHYLOCOCCUS-AUREUS; MYCOBACTERIUM-TUBERCULOSIS; SYSTEMS-ANALYSIS; TRANSCRIPTIONAL REGULATION; GEOBACTER-SULFURREDUCENS;

D O I：

10.1038/msb.2009.77

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago. Reconstructions have now been built for a wide variety of organisms, and have been used toward five major ends: (1) contextualization of high-throughput data, (2) guidance of metabolic engineering, (3) directing hypothesis-driven discovery, (4) interrogation of multi-species relationships, and (5) network property discovery. In this review, we examine the many uses and future directions of genome-scale metabolic reconstructions, and we highlight trends and opportunities in the field that will make the greatest impact on many fields of biology. Molecular Systems Biology 5: 320; published online 3 November 2009; doi: 10.1038/msb.2009.77

引用

页数：15

共 162 条

[61] Geobacter sulfurreducens strain engineered for increased rates of respiration [J].

Izallalen, Mounir ;

Mahadevan, Radhakrishnan ;

Burgard, Anthony ;

Postier, Bradley ;

Didonato, Raymond, Jr. ;

Sun, Jun ;

Schilling, Christopher H. ;

Lovley, Derek R. .

METABOLIC ENGINEERING, 2008, 10 (05) :267-275

[62] Formulating genome-scale kinetic models in the post-genome era [J].

Jamshidi, Neema ;

Palsson, Bernhard O. .

MOLECULAR SYSTEMS BIOLOGY, 2008, 4 (1)

[63] Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets [J].

Jamshidi, Neema ;

Palsson, Bernhard O. .

BMC SYSTEMS BIOLOGY, 2007, 1

[64] The large-scale organization of metabolic networks [J].

Jeong, H ;

Tombor, B ;

Albert, R ;

Oltvai, ZN ;

Barabási, AL .

NATURE, 2000, 407 (6804) :651-654

[65] A multiscale model for avascular tumor growth [J].

Jiang, Y ;

Pjesivac-Grbovic, J ;

Cantrell, C ;

Freyer, JP .

BIOPHYSICAL JOURNAL, 2005, 89 (06) :3884-3894

[66] From genomics to chemical genomics: new developments in KEGG [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Hattori, Masahiro ;

Aoki-Kinoshita, Kiyoko F. ;

Itoh, Masumi ;

Kawashima, Shuichi ;

Katayama, Toshiaki ;

Araki, Michihiro ;

Hirakawa, Mika .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D354-D357

[67] In Silico Genome-Scale Reconstruction and Validation of the Corynebacterium glutamicum Metabolic Network [J].

Kieldsen, Kjeld Raunkjaer ;

Nielsen, Jens .

BIOTECHNOLOGY AND BIOENGINEERING, 2009, 102 (02) :583-597

[68] Genome-scale analysis of Mannheimia succiniciproducens metabolism [J].

Kim, Tae Yong ;

Kim, Hyun Uk ;

Park, Jong Myoung ;

Song, Hyohak ;

Kim, Jin Sik ;

Lee, Sang Yup .

BIOTECHNOLOGY AND BIOENGINEERING, 2007, 97 (04) :657-671

[69] Strategies for systems-level metabolic engineering [J].

Department of Chemical and Biomolecular Engineering , Metabolic and Biomolecular Engineering National Research Laboratory, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, 305-701 Daejeon, Korea, Republic of ;

不详 ;

不详 .

Biotechnol. J., 2008, 5 (612-623) :612-623

[70] Integrative model of the response of yeast to osmotic shock [J].

Klipp, E ;

Nordlander, B ;

Krüger, R ;

Gennemark, P ;

Hohmann, S .

NATURE BIOTECHNOLOGY, 2005, 23 (08) :975-982

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