Welcome to the lecture wiki Molekulare Netzwerke (B) SS 2013
News
Deadline for extended abstracts: 30 September 2013
SWS/credit hrs: 2, credits: 4/5 ECTS
Lecturer: Alexander Bockmayr
Language: English/German
Audience: Master students in bioinformatics or mathematics
Content
Mathematical and computational modeling/analysis of molecular networks.
The focus in this semester is on metabolic networks.
Dates
| Thursday 12:00-13:30 |
Arnimallee 6 SR 108/109 |
Seminar Schedule
Topics A1-D4 refer to literature list below.
| Date |
Topic |
Lecturer |
|
|
| 11. Apr |
Introduction and assignment of talks |
A. Bockmayr |
|
|
| 18. Apr |
A1 |
A. Grigore |
|
|
| 25. Apr |
A2 |
J. Ibn-Salem |
|
|
| 02. Mai |
A3 |
M. Schroeder |
|
|
| 09. Mai |
Himmelfahrt/Holiday |
|
|
|
| 16. Mai |
A4 |
G. Fürstenheim |
|
|
| 23. Mai |
B1 |
S. Appelt |
|
|
| 30. Mai |
B2 |
K. Schmid |
|
|
| 06. Juni |
No seminar |
C. Matzig (canceled) |
|
|
| 13. Juni |
C2 |
M. Günther |
|
|
| 20. Juni |
C4 |
B. Schelling |
|
|
| 27. Juni |
No seminar |
|
|
|
| 04. Juli |
10.15 -11.45: D2
12.00 -13.30: D4 |
B. Hillmer
P. Germann |
SR 108/109
SR 108/109 |
|
| 11. Juli |
10.15 -11.45: C3
12.00 -13.30: D1
14-16: D3 |
N. Loginova
M. Pawletta
M. Mokroß |
SR 108/109
SR 108/109
SR 025/026 |
|
Literature
A) Metabolic pathway analysis
1) Optimal flux spaces of genome-scale stoichiometric models are
determined by a few subnetworks.
Kelk SM, Olivier BG, Stougie L, Bruggeman FJ.
Sci Rep. 2012;2:580.
http://dx.doi.org/10.1038/srep00580.
2) Designing optimal cell factories: integer programming couples
elementary mode analysis with regulation.
Jungreuthmayer C, Zanghellini J.
BMC Syst Biol. 2012 Aug 16;6:103.
http://dx.doi.org/10.1186/1752-0509-6-103
3) Optimal regulatory strategies for metabolic pathways in Escherichia
coli depending on protein costs.
Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C.
Mol Syst Biol. 2011 Jul 19;7:515.
http://dx.doi.org/10.1038/msb.2011.46
4) Computing complex metabolic intervention strategies using constrained
minimal cut sets.
Hädicke O, Klamt S.
Metab Eng. 2011 Mar;13(2):204-13.
http://dx.doi.org/10.1016/j.ymben.2010.12.004
B) Thermodynamical constraints
1) Elimination of thermodynamically infeasible loops in steady-state
metabolic models.
Schellenberger J, Lewis NE, Palsson BØ.
Biophys J. 2011 Feb 2;100(3):544-53.
Erratum in: Biophys J. 2011 Mar 2;100(5):1381.
http://dx.doi.org/10.1016/j.bpj.2010.12.3707
2) Thermodynamic constraints for biochemical networks.
Beard DA, Babson E, Curtis E, Qian H.
J Theor Biol. 2004 Jun 7;228(3):327-33.
http://dx.doi.org/10.1016/j.jtbi.2004.01.008
A proof for loop-law constraints in stoichiometric metabolic networks.
Noor E, Lewis NE, Milo R.
BMC Syst Biol. 2012 Nov 12;6:140.
http://dx.doi.org/10.1186/1752-0509-6-140
C) Control
1) Prediction of temporal gene expression. Metabolic optimization by
re-distribution of enzyme activities.
Klipp E, Heinrich R, Holzhütter HG.
Eur J Biochem. 2002 Nov;269(22):5406-13.
http://dx.doi.org/10.1046/j.1432-1033.2002.03223.x
2) Dynamic flux balance analysis of diauxic growth in Escherichia coli.
Mahadevan R, Edwards JS, Doyle FJ 3rd.
Biophys J. 2002 Sep;83(3):1331-40.
http://dx.doi.org/10.1016/S0006-3495(02)73903-9
3) Sequential activation of metabolic pathways: a dynamic optimization approach.
Oyarzún DA, Ingalls BP, Middleton RH, Kalamatianos D.
Bull Math Biol. 2009 Nov;71(8):1851-72.
http://dx.doi.org/10.1007/s11538-009-9427-5
4) Cell design in bacteria as a convex optimization problem.
Goelzer A, Fromion V, Scorletti G.
Automatica. 2011 Jun; 47(6):1210-18.
http://dx.doi.org/10.1016/j.automatica.2011.02.038
D) Applications
1) Detailing the optimality of photosynthesis in cyanobacteria through
systems biology analysis.
Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I.
Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2678-83.
http://dx.doi.org/10.1073/pnas.1117907109
2) Redirector: designing cell factories by reconstructing the metabolic
objective.
Rockwell G, Guido NJ, Church GM.
PLoS Comput Biol. 2013 Jan;9(1):e1002882.
http://dx.doi.org/10.1371/journal.pcbi.1002882
3) Regulatory architecture determines optimal regulation of gene
expression in metabolic pathways.
Chubukov V, Zuleta IA, Li H.
Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):5127-32.
http://dx.doi.org/10.1073/pnas.1114235109
4) Manipulating redox and ATP balancing for improved production of
succinate in E. coli.
Singh A, Cher Soh K, Hatzimanikatis V, Gill RT.
Metab Eng. 2011 Jan;13(1):76-81.
http://dx.doi.org/10.1016/j.ymben.2010.10.006
Credit requirements
Slides of talk (pdf) or handout
Extended abstract (3-4 pages,
Springer LNCS style, Deadline: 30 September 2013)
Alternatively: Poster (to be discussed)