Literature DB >> 19769971

Metabolic systems biology.

Bernhard Palsson1.   

Abstract

The first full genome sequences were established in the mid-1990s. Shortly thereafter, genome-scale metabolic network reconstructions appeared. Since that time, we have witnessed an exponential growth in their number and uses. Here I discuss, from a personal point of view, four topics: (1) the placement of metabolic systems biology in the context of broader scientific developments, (2) its foundational concepts, (3) some of its current uses, and (4) some of the expected future developments in the field.

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Year:  2009        PMID： 19769971      PMCID： PMC3119668          DOI： 10.1016/j.febslet.2009.09.031

Source DB:  PubMed          Journal:  FEBS Lett        ISSN： 0014-5793            Impact factor:   4.124


  42 in total

Review 1.  New surveyor tools for charting microbial metabolic maps.

Authors:  Rainer Breitling; Dennis Vitkup; Michael P Barrett
Journal:  Nat Rev Microbiol       Date:  2008-02       Impact factor: 60.633

Review 2.  Insights from site-specific phosphoproteomics in bacteria.

Authors:  Boumediene Soufi; Carsten Jers; Mette Erichsen Hansen; Dina Petranovic; Ivan Mijakovic
Journal:  Biochim Biophys Acta       Date:  2007-08-15

Review 3.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.

Authors:  Adam M Feist; Bernhard Ø Palsson
Journal:  Nat Biotechnol       Date:  2008-06       Impact factor: 54.908

Review 4.  Towards systems metabolic engineering of microorganisms for amino acid production.

Authors:  Jin Hwan Park; Sang Yup Lee
Journal:  Curr Opin Biotechnol       Date:  2008-09-06       Impact factor: 9.740

5.  Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.

Authors:  Christopher D Herring; Anu Raghunathan; Christiane Honisch; Trina Patel; M Kenyon Applebee; Andrew R Joyce; Thomas J Albert; Frederick R Blattner; Dirk van den Boom; Charles R Cantor; Bernhard Ø Palsson
Journal:  Nat Genet       Date:  2006-11-05       Impact factor: 38.330

6.  Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli.

Authors:  Tobias Fuhrer; Lifeng Chen; Uwe Sauer; Dennis Vitkup
Journal:  J Bacteriol       Date:  2007-09-14       Impact factor: 3.490

7.  A protocol for generating a high-quality genome-scale metabolic reconstruction.

Authors:  Ines Thiele; Bernhard Ø Palsson
Journal:  Nat Protoc       Date:  2010-01-07       Impact factor: 13.491

8.  Network-based prediction of human tissue-specific metabolism.

Authors:  Tomer Shlomi; Moran N Cabili; Markus J Herrgård; Bernhard Ø Palsson; Eytan Ruppin
Journal:  Nat Biotechnol       Date:  2008-09       Impact factor: 54.908

9.  Formulating genome-scale kinetic models in the post-genome era.

Authors:  Neema Jamshidi; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2008-03-04       Impact factor: 11.429

10.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Authors:  Adam M Feist; Christopher S Henry; Jennifer L Reed; Markus Krummenacker; Andrew R Joyce; Peter D Karp; Linda J Broadbelt; Vassily Hatzimanikatis; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2007-06-26       Impact factor: 11.429
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  40 in total

Review 1.  A road map for the development of community systems (CoSy) biology.

Authors:  Karsten Zengler; Bernhard O Palsson
Journal:  Nat Rev Microbiol       Date:  2012-03-27       Impact factor: 60.633

2.  The challenges of integrating multi-omic data sets.

Authors:  Bernhard Palsson; Karsten Zengler
Journal:  Nat Chem Biol       Date:  2010-11       Impact factor: 15.040

Review 3.  Systematizing the generation of missing metabolic knowledge.

Authors:  Jeffrey D Orth; Bernhard Ø Palsson
Journal:  Biotechnol Bioeng       Date:  2010-10-15       Impact factor: 4.530

Review 4.  High-Dimensional Immunology for Schizophrenia Research: A Short Perspective.

Authors:  George K Lewis
Journal:  Schizophr Bull       Date:  2018-08-20       Impact factor: 9.306

5.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

Authors:  Jan Schellenberger; Richard Que; Ronan M T Fleming; Ines Thiele; Jeffrey D Orth; Adam M Feist; Daniel C Zielinski; Aarash Bordbar; Nathan E Lewis; Sorena Rahmanian; Joseph Kang; Daniel R Hyduke; Bernhard Ø Palsson
Journal:  Nat Protoc       Date:  2011-08-04       Impact factor: 13.491

6.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.

Authors:  Jan Schellenberger; Nathan E Lewis; Bernhard Ø Palsson
Journal:  Biophys J       Date:  2011-02-02       Impact factor: 4.033

Review 7.  A systems approach to drug discovery in Alzheimer's disease.

Authors:  Michael Shelanski; William Shin; Soline Aubry; Peter Sims; Mariano J Alvarez; Andrea Califano
Journal:  Neurotherapeutics       Date:  2015-01       Impact factor: 7.620

8.  LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine.

Authors:  Michelle F Clasquin; Eugene Melamud; Joshua D Rabinowitz
Journal:  Curr Protoc Bioinformatics       Date:  2012-03

9.  Application of metabolomics technology in the research of Chinese medicine.

Authors:  Ping Liu; Ping Wang
Journal:  Chin J Integr Med       Date:  2014-04-03       Impact factor: 1.978

Review 10.  Analysis of omics data with genome-scale models of metabolism.

Authors:  Daniel R Hyduke; Nathan E Lewis; Bernhard Ø Palsson
Journal:  Mol Biosyst       Date:  2012-12-18
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