| Datum: 27. 10. |
Student/Studentin: Zhou
Thema: PPI Network Topology
Paper: Paper 1
Han, J. J.; Dupuy, D.; Bertin, N.; Cusick, M. E., Vidal, M. Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol, 2005, 23, 839-44
Paper 2
Friedel, C. C., Zimmer, R. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics, 2006, 7, 519
Betreuer: Caroline Friedel
|
| Datum: 3. 11. |
Student/Studentin: Badbanchi
Thema: Protein Complexes
Paper:
Paper 1
Pu, S.; Vlasblom, J.; Emili, A.; Greenblatt, J., Wodak, S. J. Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics, 2007, 7, 944-960
Paper 2
Friedel, C.C.; Krumsiek, J.; Zimmer, R.. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB 2008, LNBI 4955.
Betreuer: Caroline Friedel
|
| Datum: 10. 11. |
Diskussion: Complex Networks
Paper:
Paper 1
Royer, L., Reimann, M., Andreopoulos, B., Schroeder, M. Unraveling protein networks with power graph analysis.
PLoS Comput. Biol., 2008, 4, e1000108
Paper 2
Bandyopadhyay, S., Kelley, R., Krogan, N. J., Ideker, T. Functional maps of protein complexes from quantitative genetic interaction data.
PLoS Comput Biol, 2008, 4, e1000065.
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| Datum: 17. 11. |
Student/Studentin: Nissen
Thema: The influence of alternative splicing on protein structures
Paper:
Paper 1
Birzele F, Csaba G, Zimmer R. Alternative splicing and protein structure evolution.
Nucleic Acids Res. 2008 Feb;36(2):550-8
Paper 2
Michael L. Tress et al. The implications of alternative splicing in the ENCODE protein complement.
Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500.
Betreuer: Fabian Birzele
|
| Datum: 24. 11. |
Student/Studentin: Kaufmann
Thema: The regulatory code of alternative splicing
Paper:
Paper 1
Matthew Fagnani et al. Functional coordination of alternative splicing in the mammalian central nervous system
Genome Biology 2007, 8:R108
Paper 2
Zefeng Wang and Christophar B. Burge, Splicing regulation: From a parts list of regulatory elements to an integrated splicing code
RNA 2008, 14:802-813
Betreuer: Fabian Birzele
|
| Datum: 1. 12. |
Diskussion: Novel developments in the analysis of alternative splicing: Splicing and Disease
Paper:
Paper 1
Mariano Garcia-Blanco et al., Alternative Splicing in disease and therapy, Nature Biotechnology, 2004, Volume 22, Number 5, 535-546
Paper 2
Eric T. Wang et al., Alternative Isoform regulation in human tissue transcriptomes, 2008, Nature
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| Datum: 8. 12. |
Student/Studentin: Bräuer
(Handout,
Folien)
Thema:Extraction of molecular interactions from the biomedical literature
Paper:
Paper1
Kim, S., Yoon, J. and Yang, J. (2008) Kernel approaches for genic interaction extraction. Bioinformatics 24(1):118-126
Paper2
Fundel K, Küffner R, Zimmer R (2007) RelEx--relation extraction using dependency parse trees.
Bioinformatics. Feb 1;23(3):365-71.
Betreuer: Robert Küffner
|
| Datum: 15. 12. |
Student/Studentin: Strache
(Handout,
Folien)
Thema:Analyzing large scale expression data with biological processes
Paper:
Paper1
Lee HK, Braynen W, Keshav K, Pavlidis P. (2005) ErmineJ: Tool for functional analysis of gene expression data sets.
BMC Bioinformatics 6(1):269.
Paper2
Küffner R, Fundel K, Zimmer R. (2005) Expert knowledge without the expert: integrated analysis of gene expression and literature to
Bioinformatics. Sep 1;21 Suppl 2:ii259-67
Betreuer: Robert Küffner
|
| Datum: 15. 12. |
Diskussion: (Combined
Expression data and Network analysis)
Paper:
Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Biol. 2007;3:88. Epub 2007 Mar 13
|
| Datum: 12. 1. |
Student/Studentin: Achten (Ausarbeitung)
Thema: Analysis of Metabolic Networks
Paper:
Paper 1
Klamt S, Stelling J.
Two approaches for metabolic pathway analysis?
Trends Biotechnol. 2003 Feb;21(2):64-9.
Paper 2
Zevedei-Oancea I, Schuster S.
Topological analysis of metabolic networks based on Petri net theory.
In Silico Biol. 2003;3(3):323-45.
Paper 3
Koch I, Junker BH, Heiner M.
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.
Bioinformatics. 2005 Apr 1;21(7):1219-26. Epub 2004 Nov 16.
Betreuer: Lukas Windhager
|
| Datum: 19. 1. |
Student/Studentin: Hecht (Ausarbeitung, Folien, Handout)
Thema: Modelling of Signal Transduction Pathways
Paper:
Paper 1
Li C, Ge QW, Nakata M, Matsuno H, Miyano S.
Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets.
J Biosci. 2007 Jan;32(1):113-27. Erratum in: J Biosci. 2007 Jun;32(4):805.
Paper 2
Breitling R, Gilbert D, Heiner M, Orton R.
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways.
Brief Bioinform. 2008 Sep;9(5):404-21. Epub 2008 Jun 23.
Paper 3
Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK.
Physicochemical modelling of cell signalling pathways.
Nat Cell Biol. 2006 Nov;8(11):1195-203.
Betreuer: Lukas Windhager
|
| Datum: 26. 1. |
Diskussion: Systems Biology
Paper:
Paper 1
Schlitt T, Brazma A.
Current approaches to gene regulatory network modelling.
BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S9.
Paper 2
Feist AM, Palsson BO.
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.
Nat Biotechnol. 2008 Jun;26(6):659-67.
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