Systems Biology and Bioengineering II:
Network Reconstruction & Functional States
Lecture: Tu/Th 9:30 - 10:50 AM in PFBH 161
Recon1_212.mat Compartmentalized global genome-scale human metabolic network (Recon1)
288 Metabolic Functions - The 288 functions to be tested.
E. coli Model
iAF1260.xml Compartmentalized full genome-scale E. coli model
ecoli.pdf introduction to the E. coli core model
ecoli_core_model.xml COBRA toolbox version of core model
EcoliCoreMap.pdf visual map of the core model
ecoli_core_model.xls spreadsheet detailing the core model
ecoli_core_regulatory.xls spreadsheet detailing the core regulatory network
ecoli_optimization.m MATLAB script to run the core model
Articles That Are Of General Interest To The Class:
Adaptive Evolution Chapter - Applebee (2009)
Extreme Pathway Analysis of Human Red Blood Cell Metabolism - Wiback (2002)
Network-based analysis of metabolic regulation in the human red blood cell - Price (2003)
Metabolic pathways in the post-genome era - Papin (2003)
Systemic Metabolic Reactions are Obtained by Singular Value Decomposition of Genome-Scale Stoichiometric Matrices - Famili (2003)
Understanding human metabolic physiology: a genome-to-systems approach - Mo (2008) TIBTEC (in press)
A genome-scale, constraint-based approach to systems biology of human metabolism - Mo (2007) Mol. BioSyst. 3:598-603
Global reconstruction of the human metabolic network based on genomic and bibliomic data - Duarte (2007) PNAS 104(6):1777-1782
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information - Feist (2007) Molecular Systems Biology 3; Article number 121
Genome-scale metabolic networks - Terzer (2008) Wiley Interdisciplinary Reviews: Systems Biology and Medicine
Reconstruction of biochemical networks in microorganisms - Feist (2008) Nature Reviews Microbiology
Genome-scale models of bacterial metabolism: reconstruction and applications - Durot (2008) FEMS Microbiol Rev 33 164–190
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli - Feist (2008) Nature Biotechnology 26(6)
Reconstruction of cellular signalling networks and analysis of their properties - Papin (2005) Nature Reviews Molecular Cell Biology 6(2):99-111
Towards multidimensional genome annotation - Reed (2006) Nature Reviews 7:130-141
The model organism as a system: integrating 'omics' data sets - Joyce (2006) Nature Reviews 7:198-210
Genome-Scale Models of Microbial Cells: Evaluating the Consequences of Constraints - Price (2004) Nature Reviews 2:886-897
Molecular Systems Biology Editorial on Systems Biology - Church (2005) Mol. Sys. Biol. IC:2-3
Science Viewpoint by Leroy Hood on Systems Biology and Medicine - Hood et al. (2004) Science 306:640-643.
Nature Biotechnology focus on Systems Biology.
2D-genome annotation - Palsson BO. (2004) Nat Biotech 22:1218-1219.
Systems Biology in a historical perspective - Westerhoff & Palsson. (2004) Nat Biotech 22:1249-1252.
Brush Up On Some Basic Biology With These Recommended Resources:
Biochemistry by Lubert Stryer
Molecular Cell Biology by Harvey Lodish, et al.
Molecular Biology of the Cell by Alberts
Brush Up On Some Linear Algebra With These Recommended Resources:
Info On Flux Balance Analysis:
Some Basic Matlab Commands:
Jennie Reed's Lectures: