| 16.04.2008 |
Student/Studentin: Anton Thomma
Thema: Reverse Engineering Networks through Graphical Models
Paper:
Paper 1
Werhli AV, Grzegorczyk M, Husmeier D.
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks.
Bioinformatics. 2006 Oct 15;22(20):2523-31. Epub 2006 Jul 14.
Paper 2
Friedman N, Linial M, Nachman I, Pe'er D.
Using Bayesian networks to analyze expression data.
J Comput Biol. 2000;7(3-4):601-20.
Betreuer: Tobias Petri
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| 30.04.2008 |
Student/Studentin: Florian Lindemann
Thema: Protein Structure Alignment
Ausarbeitung
Folien
Hand-out
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Paper:
Paper 1
Birzele F, Gewehr JE, Csaba G, Zimmer R.
Vorolign--fast structural alignment using Voronoi contacts.
Bioinformatics. 2007 Jan 15;23(2):e205-11.
Paper 2
Shindyalov IN, Bourne PE.
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
Protein Eng. 1998 Sep;11(9):739-47.
Paper 3
Gergely Csaba, Fabian Birzele and Ralf Zimmer, Protein structure alignment considering phenotypic plasticity, submitted.
Betreuer: Fabian Birzele
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| 14.05.2008 |
Student/Studentin: Stefan Heinisch
Thema: Subnetwork Detection in Molecular Interaction Networks
Ausarbeitung
Folien
Hand-out
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Paper:
Paper 1
Sohler F, Hanisch D, Zimmer R.
New methods for joint analysis of biological networks and expression data.
Bioinformatics. 2004 Jul 10;20(10):1517-21.
Paper 2
Ideker T, Ozier O, Schwikowski B, Siegel AF.
Discovering regulatory and signalling circuits in molecular interaction networks.
Bioinformatics. 2002;18 Suppl 1:S233-40.
Betreuer: Tobias Petri
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| 21.05.2008 |
Student/Studentin: Eva Hoffmann
Thema: The influence of alternative splicing on protein structures
Ausarbeitung
Folien
Hand-out
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Paper:
Paper 1
Birzele F, Csaba G, Zimmer R.
Alternative splicing and protein structure evolution.
Nucleic Acids Res. 2008 Feb;36(2):550-8. Epub 2007 Nov 30.
Paper 2
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PL, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z,
Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.
The implications of alternative splicing in the ENCODE protein complement.
Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500. Epub 2007 Mar 19.
Paper 3
Wang P, Yan B, Guo JT, Hicks C, Xu Y.
Structural genomics analysis of alternative splicing and application to isoform structure modeling.
Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18920-5. Epub 2005 Dec 14.
Betreuer: Fabian Birzele
|
| 28.05.2008 |
Student/Studentin: Anita Winkler
Thema: Modelling of Signal Transduction Pathways
Ausarbeitung
Folien
Hand-out
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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
Lee DY, Zimmer R, Lee SY, Park S.
Colored Petri net modeling and simulation of signal transduction pathways.
Metab Eng. 2006 Mar;8(2):112-22. Epub 2005 Dec 22.
Paper 3
Kofahl B, Klipp E.
Modelling the dynamics of the yeast pheromone pathway.
Yeast. 2004 Jul 30;21(10):831-50.
Betreuer: Lukas Windhager
|
| 04.06.2008 |
Student/Studentin: Barbara Hummel
Thema: Analysis of Metabolic Networks
Ausarbeitung
Folien
Hand-out
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Paper:
Paper 1
Schuster S, Fell DA, Dandekar T.
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.
Nat Biotechnol. 2000 Mar;18(3):326-32.
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
Voss K, Heiner M, Koch I.
Steady state analysis of metabolic pathways using Petri nets.
In Silico Biol. 2003;3(3):367-87.
Betreuer: Lukas Windhager
|
| 11.06.2008 |
Student/Studentin: Janine Arloth
Thema: Network Topology
Ausarbeitung
Folien
Hand-out
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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
|
| 18.06.2008 |
Student/Studentin: Tatyana Goldberg
Thema: Identification of Protein Complexes
Ausarbeitung
Folien
Hand-out
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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
|
| 25.06.2008 |
Student/Studentin: Niko Gross
Thema: The protein structure fold space
Ausarbeitung
Folien
Hand-out
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Paper:
Paper 1
Hadley C, Jones DT.
A systematic comparison of protein structure classifications: SCOP, CATH and FSSP.
Structure. 1999 Sep 15;7(9):1099-112.
Paper 2
Gergely Csaba, Fabian Birzele and Ralf Zimmer, Systematic comparison of SCOP and CATH: A new Gold Standard for Protein structure analysis, submitted
Paper 3
Day R, Beck DA, Armen RS, Daggett V.
A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.
Protein Sci. 2003 Oct;12(10):2150-60.
Betreuer: Fabian Birzele
|
| 02.07.2008 |
Student/Studentin: Riku Louhimo
Thema: Degree Correlations in PPI Networks
Ausarbeitung
Folien
Hand-out
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Paper:
Paper 1
Maslov, S., Sneppen, K. Specificity and stability in topology of protein networks. Science, 2002, 296, 910-3
Paper 2
Friedel, C. C., Zimmer, R. Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics, 2007, 8, 29.
Betreuer: Caroline Friedel
|
| 09.07.2008 |
Student/Studentin: Thomas Engleitner
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
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| 16.07.2008 |
Student/Studentin: Juuso Parkkinen
Thema:Extraction of molecular interactions from the biomedical literature
Ausarbeitung
Folien
Hand-out
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Paper:
Paper1
Divoli,A. and Attwood,T.K. (2005) BioIE: extracting informative sentences from the
biomedical literature. Bioinformatics, 21, 2138-2139.
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
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