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Notes on Flux Balance Analysis and related methods: | |||
http://systemsbiology.ucsd.edu/Downloads/FluxBalanceAnalysis | |||
=Research groups/persons= | |||
Reed lab: http://reedlab.che.wisc.edu/Downloads/downloads.html | |||
Palsson lab: http://gcrg.ucsd.edu/Researchers/Palsson | |||
http://covertlab.stanford.edu/projects/ScienceGenealogy/viewScientist.php?ScientistID=21319 | |||
Jeffrey Orth: http://gcrg.ucsd.edu/Researchers/Orth | |||
Thiele lab: http://thielelab.eu/ | |||
Tomer Schlomi: http://www.cs.technion.ac.il/~tomersh/ | |||
Costas D Maranas: http://maranas.che.psu.edu/index.htm | |||
Adam Feist: http://systemsbiology.ucsd.edu/Researchers/Feist | |||
Anthony Burgard: http://www.biomedexperts.com/Profile.bme/172456/Anthony_P_Burgard | |||
Markus Covert: http://bioengineering.stanford.edu/faculty/covert.html | |||
Jeremy S Edwards: https://sites.google.com/site/edwardsunmlab/people/edwards | |||
David Fell: http://scholar.google.com/citations?user=KiFdFGQAAAAJ&hl=en | |||
Nicola Zamboni: http://www.imsb.ethz.ch/researchgroup/nzamboni | |||
Uwe Sauer: http://www.imsb.ethz.ch/researchgroup/sauer | |||
Lars Kuepfer: http://www.frontiersin.org/people/26593/larskuepfer/publications | |||
Nathan D Price: http://price.systemsbiology.net/ | |||
Markus J Herrgård: http://covertlab.stanford.edu/projects/ScienceGenealogy/viewScientist.php?ScientistID=19957 | |||
Prof. Matthias Heinemann: http://www.rug.nl/research/molecular-systems-biology/ | |||
Prof. Jens Nielsen: http://www.sysbio.se/ | |||
Nathan E Lewis: http://sbcg.wikidot.com/n | |||
Jason Papin: http://bme.virginia.edu/people/papin.html | |||
Jan Schellenberger: http://scholar.google.no/citations?user=h00uG8UAAAAJ&hl=no | |||
Stephan Shuster: http://scholar.google.no/citations?user=HMtRbrkAAAAJ&hl=no | |||
Jorg Stelling: http://www.csb.ethz.ch/people/joergs | |||
=Extensions/Related methods= | |||
GF-FBA: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572438/ | |||
Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis | |||
=Network metrics= | |||
Synthetic accessibility: | |||
*"the total number of reactions needed to transform a given set of input metabolites into a set of output metabolites" | |||
*http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557581/ | |||
*Used to predict gene essentiality. | |||
=Bibliography= | |||
Integration of expression data in genome-scale metabolic network reconstructions: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429070/ | |||
RELATCH: http://genomebiology.com/2012/13/9/R78/ | |||
The geometry of the Pareto front in biological phenotype space | |||
H Sheftel, O Shoval, A Mayo, U Alon | |||
Ecology and Evolution | |||
MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0051511 | |||
A method for accounting for maintenance costs: http://onlinelibrary.wiley.com/doi/10.1111/tpj.12252/abstract | |||
http://www.biomedcentral.com/bmcbioinformatics/ | |||
'''Books:''' | |||
http://gcrg.ucsd.edu/Publications/Books | |||
=Online tools= | |||
FAME: http://f-a-m-e.org/ajax/page1.php | |||
=Software= | |||
GAMS: http://www.gams.com/ | |||
OpenCOBRA: | |||
OptFlux: http://www.optflux.org/ | |||
SurreyFBA: http://sysbio3.fhms.surrey.ac.uk/sfba/index.html | |||
Sybil: http://www.cs.hhu.de/en/research-groups/bioinformatics/software/sybil.html |
Latest revision as of 14:45, 7 February 2014
Notes on Flux Balance Analysis and related methods:
http://systemsbiology.ucsd.edu/Downloads/FluxBalanceAnalysis
Research groups/persons
Reed lab: http://reedlab.che.wisc.edu/Downloads/downloads.html
Palsson lab: http://gcrg.ucsd.edu/Researchers/Palsson
http://covertlab.stanford.edu/projects/ScienceGenealogy/viewScientist.php?ScientistID=21319
Jeffrey Orth: http://gcrg.ucsd.edu/Researchers/Orth
Thiele lab: http://thielelab.eu/
Tomer Schlomi: http://www.cs.technion.ac.il/~tomersh/
Costas D Maranas: http://maranas.che.psu.edu/index.htm
Adam Feist: http://systemsbiology.ucsd.edu/Researchers/Feist
Anthony Burgard: http://www.biomedexperts.com/Profile.bme/172456/Anthony_P_Burgard
Markus Covert: http://bioengineering.stanford.edu/faculty/covert.html
Jeremy S Edwards: https://sites.google.com/site/edwardsunmlab/people/edwards
David Fell: http://scholar.google.com/citations?user=KiFdFGQAAAAJ&hl=en
Nicola Zamboni: http://www.imsb.ethz.ch/researchgroup/nzamboni
Uwe Sauer: http://www.imsb.ethz.ch/researchgroup/sauer
Lars Kuepfer: http://www.frontiersin.org/people/26593/larskuepfer/publications
Nathan D Price: http://price.systemsbiology.net/
Markus J Herrgård: http://covertlab.stanford.edu/projects/ScienceGenealogy/viewScientist.php?ScientistID=19957
Prof. Matthias Heinemann: http://www.rug.nl/research/molecular-systems-biology/
Prof. Jens Nielsen: http://www.sysbio.se/
Nathan E Lewis: http://sbcg.wikidot.com/n
Jason Papin: http://bme.virginia.edu/people/papin.html
Jan Schellenberger: http://scholar.google.no/citations?user=h00uG8UAAAAJ&hl=no
Stephan Shuster: http://scholar.google.no/citations?user=HMtRbrkAAAAJ&hl=no
Jorg Stelling: http://www.csb.ethz.ch/people/joergs
Extensions/Related methods
GF-FBA: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572438/
Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis
Network metrics
Synthetic accessibility:
- "the total number of reactions needed to transform a given set of input metabolites into a set of output metabolites"
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557581/
- Used to predict gene essentiality.
Bibliography
Integration of expression data in genome-scale metabolic network reconstructions: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429070/
RELATCH: http://genomebiology.com/2012/13/9/R78/
The geometry of the Pareto front in biological phenotype space H Sheftel, O Shoval, A Mayo, U Alon Ecology and Evolution
MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0051511
A method for accounting for maintenance costs: http://onlinelibrary.wiley.com/doi/10.1111/tpj.12252/abstract
http://www.biomedcentral.com/bmcbioinformatics/
Books:
http://gcrg.ucsd.edu/Publications/Books
Online tools
FAME: http://f-a-m-e.org/ajax/page1.php
Software
GAMS: http://www.gams.com/
OpenCOBRA:
OptFlux: http://www.optflux.org/
SurreyFBA: http://sysbio3.fhms.surrey.ac.uk/sfba/index.html
Sybil: http://www.cs.hhu.de/en/research-groups/bioinformatics/software/sybil.html