| Datum:entfällt |
Vortragende/r: --
Ko-Referat: --
Thema: Anwendungsbereiche und Algorithmen.
Paper:
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Sharan, R.; Ulitsky, I. & Shamir, R.
Network-based prediction of protein function.
Mol Syst Biol, School of Computer Science, Tel Aviv University, Tel Aviv, Israel., 2007, 3, 88
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Hart, G. T.; Ramani, A. K. & Marcotte, E. M.
How complete are current yeast and human protein-interaction networks
Genome Biol, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712, USA., 2006, 7, 120
Betreuer: Tobias Petri
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| Datum: 26.10.2009 |
Vortragende/r: Martin Lechner
Ko-Referat: Andreas Kolberg
Thema: Netzwerk-Inferenz aus Zeitreihen
Paper:
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Bar-Joseph, Z.
Analyzing time series gene expression data.
Bioinformatics, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15217, USA. zivbj * at * cs.cmu.edu, 2004, 20, 2493-2503
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Hirose, O.; Yoshida, R.; Imoto, S.; Yamaguchi, R.; Higuchi, T.; Charnock-Jones, D. S.; Print, C. & Miyano, S.
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
Bioinformatics, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan., 2008, 24, 932-942
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Zhao, W.; Serpedin, E. & Dougherty, E. R.
Inferring gene regulatory networks from time series data using the minimum description length principle.
Bioinformatics, M University, College Station, TX 77843-3128, USA. wtzhao * at * ece.tamu.edu, 2006, 22, 2129-2135
Betreuer: Tobias Petri
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| Datum: 02.11.2009 |
Vortragende/r: Sasha Badbanchi
Ko-Referat: Anke Regner
Thema: Modul-Detektion in Netzwerken
Paper:
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Grafahrend-Belau, E.; Schreiber, F.; Heiner, M.; Sackmann, A.; Junker, B. H.; Grunwald, S.; Speer, A.; Winder, K. & Koch, I.
Modularization of biochemical networks based on classification of Petri net t-invariants.
MC Bioinformatics, Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr, 64, 13347 Berlin, Germany. grafahr * at * ipk-gatersleben.de, 2008, 9, 90
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Ulitsky, I. & Shamir, R.
Identification of functional modules using network topology and high-throughput data.
BMC Syst Biol, School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel. ulitskyi * at * tau.ac.il, 2007, 1, 8
Betreuer: Tobias Petri
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| Datum: 9.11.2009 |
Vortragende/r: Markus Meier
Ko-Referat: Martin Lechner
Thema: Influence of Alternative Splicing on Protein Structure
Paper:
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Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, 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, Ramírez 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.
PNAS, 2007 Vol. 104(13), pp. 5494-5500
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Birzele, F., Csaba, G. & Zimmer, R.
Alternative splicing and protein structure evolution.
Nucleic Acids Res, 2008 Vol. 36(2), pp. 550-558
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Melamud, E. & Moult, J.
Structural implication of splicing stochastics.
Nucleic Acids Res, 2009 (June 22)
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Melamud, E. & Moult, J.
Stochastic noise in splicing machinery.
Nucleic Acids Res, 2009 (June 22)
Betreuer: Konrad Schreiber
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| Datum: 16.11.2009 |
Vortragende/r: Andreas Kolberg
Ko-Referat: Sasha Badbanchi
Thema: The Regulatory Code of Alternative Splicing
Paper:
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Wang, Z.; Burge, C.
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code.
RNA, 2008, Vol. 14(5), pp. 802-813
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Friedman, B.A., Stadler, M.B., Shomron, N., Ding, Y. & Burge, C.B.
Ab initio identification of functionally interacting pairs of cis-regulatory elements.
Genome Res, 2008, Vol. 18(10), pp. 1643-1651
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Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B.J. & Darnell, R.B.
An RNA map predicting Nova-dependent splicing regulation.
Nature, 2006, Vol. 444(7119), pp. 580-586
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Voelker, R.B. & Berglund, J.A.
A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing.
Genome Res, 2007, Vol. 17(7), pp. 1023-10331
Betreuer: Konrad Schreiber
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| Datum: 23.11.2009 |
Vortragende/r: Anke Regner
Ko-Referat: Cedric Landerer
Thema: Tissue Specific Splicing
Paper:
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Wang; Sandberg; Luo; Khrebtukova; Zhang; Mayr; Kingsmore; Schroth; Burge
Alternative isoform regulation in human tissue transcriptomes
Nature 456, 470-476 (November 2008)
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Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ.
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
Science 31(5891), 956-960
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Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML.
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.
Nature Genetics 40(12), 1413-15
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Tress, M.L., Bodenmiller, B., Aebersold, R. & Valencia, A.
Proteomics studies confirm the presence of alternative protein isoforms on a large scale.
Genome Biol, 2008, Vol. 9(11), pp. R162
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Birzele, F., Zimmer, R.
Alternative Splicing and Proteome Complexity in Mass Spectrometry Data
submitted. (Paper gibt's auf Anfrage)
Betreuer: Konrad Schreiber
|
| Datum: 30.11.2009 |
Vortragende/r: Jakob Betke
Ko-Referat: Florian Seifert
Thema: Massenspektrometrie, MaxQuant
Paper:
Betreuer: Florian Erhard
|
| Datum: 7.12.2009 |
Vortragende/r: Kerstin Lahr
Ko-Referat: Max Liebkies
Thema: miRNA target prediction: Einfuehrung, RNAhybrid
Paper:
Betreuer: Florian Erhard
|
| Datum: 14.12.2009 |
Vortragende/r: Battal Ates
Ko-Referat: Rupert
Hofmarksrichter
Thema: miRNA target prediction: PITA und Kritiken
Paper:
- Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul, Eran
Segal: The role of site accessibility in microRNA target recognition,
Nature Genetics 39, 1278 - 1284 (2007)
- Kevin Chen, Jonas Maaskola, Mark L. Siegal, Nikolaus Rajewsky:
Reexamining microRNA Site Accessibility in Drosophila: A Population
Genomics Study, PLoS ONE 4(5): e5681. doi:10.1371/journal.pone.0005681
- Matthias Selbach, Bjoern Schwanhaeusser, Nadine Thierfelder, Zhuo Fang,
Raya Khanin & Nikolaus Rajewsky: Widespread changes in protein synthesis
induced by microRNAs, Nature, 2008, 455, 58 - 63
Betreuer: Florian Erhard
|
| Datum: 21.12.2009 |
Vortragende/r: Cedric Landerer
Ko-Referat: Jakob Betke
Thema: Deterministic Modeling of Biological Systems
Paper:
- Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK. Physicochemical modelling of cell signalling pathways. Nat Cell Biol. 2006;8(11):1195-1203. (REVIEW)
- Klipp E, Herwig R, Kowald A, Wierling C, Lehrach H. Systems Biology in Practice. Wiley-VCH; 2005:225-256 (BUCH)
- Gershenfeld N. The Nature of Mathematical Modeling. Cambridge University Press; 1999:67-77 (BUCH)
Betreuer: Lukas Windhager
|
| Datum: 18.1.2010 |
Vortragende/r: Florian Seifert
Ko-Referat: Kerstin Lahr
Thema: Boolean Network Models and Robustness
Paper:
Betreuer: Lukas Windhager
|
| Datum: 25.1.2010 |
Vortragende/r: Max Liebkies
Ko-Referat: Battal Ates
Thema: Fuzzy Logic Based Models
Paper:
- Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA. Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. PLoS Comput Biol. 2009;5(4):e1000340.
- Windhager L, Zimmer R. Intuitive Modeling of Dynamic Systems with Petri Nets and Fuzzy Logic. Lecture Notes in Informatics, vol P-136, pp. 106-115, Gesellschaft für Informatik, 2008.
- Michels K, Klawonn F, Kruse R, Nürnberger A. Fuzzy-Regelung. Springer; 2002:420. (BUCH)
Betreuer: Lukas Windhager
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| Datum: 1.2.2010 |
Vortragende/r: Rupert Hofmarksrichter
Ko-Referat: Christian Lang
Thema: Petri Net Models and Timed Simulation
Paper:
- Chen L, Qi-Wei G, Nakata M, Matsuno H, Miyano S. Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. Journal of Biosciences. 2007;32(1):113-127.
- Junker BH, Schreiber F. Analysis of Biological Networks. Wiley-Interscience; 2008:139-179. (BUCH))
Betreuer: Lukas Windhager
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