User:Jarle Pahr/FBA

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