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Problem Based Learning SoSe 2018
| Type | 5S (1 year module, 2 SWS/Summer, 3 SWS/Winter) |
| ECTS | 9 |
| Lecturer | Burkhard Rost |
| Time | Monday, 12:30 - 14:00 |
| Room | MI 01.09.034 |
| Language | English |
News
The timeplan for the winter term is up. Attendance to all meetings is mandatory.
If you cannot make it to a meeting, please let us know in advance.
Kick-off Meeting
Apr. 16th, 12:00, Room MI 01.09.034
Timeplan for WiSe 18/19
| Date | Student Groups | Supervisors | |
|---|---|---|---|
|
29.10.18 |
Intermediate Student Presentation |
Haucke/Born, Kiefl/Riess, Bock/Dvoretskii |
Jonas Reeb, Maria Schelling |
|
5.11.18 |
Intermediate Student Presentation |
Meyer/Yuan, Pelz/Andrusca, Marsoner, Orfandis/Henke |
Michael Bernhofer, Michael Heinzinger |
|
12.11.18 |
Rostlab presentation (1. How to evaluate Machine Learning, 2. Tips on scientific writing) |
|
Maria Schelling |
|
|
|
|
|
|
21.1.19 |
Final student presentations |
Marsoner, Kiefl, Riess, Born |
Jonas Reeb, Maria Schelling, Michael Bernhofer |
|
28.1.19 |
Final student presentations |
Bock, Dvoretskii, Andrusca |
Jonas Reeb, Michael Heinzinger |
|
4.2.19 |
Final student presentations |
Meyer, Yuan, Pelz |
Michael Heinzinger |
Topics for SoSe 18
| Topic | Intermediate talk topic | Supervisor | Student ANN | Student SVM | Date for intermediate talk |
|---|---|---|---|---|---|
|
Secondary structure, 8 states |
Secondary Structure (DSSP) |
Michael Heinzinger |
Matthias Meyer |
Kevin Yuan |
11.06 |
|
Secondary structure, 3 states |
ML introduction |
Michael Heinzinger |
Konstantin Pelz |
Sandra Andrusca |
11.06 |
|
|
|
|
|
|
|
|
Nuclear traveler proteins |
Subnuclear localization, concept of multi-class localization |
Maria Schelling |
|
Kilian Born | 18.06 |
|
Transmembrane Proteins/Helices |
Transmembrane proteins (general overview) |
Michael Bernhofer |
Laura Marsoner |
|
18.06 |
|
Sarcoma (Radiomics) |
Radiomics (general overview), Soft tissue sarcoma |
Michael Bernhofer |
Georgios Orfandis |
Adrian Henke |
11.06 |
|
Transmembrane protein expression |
(Transmembrane) protein structure determination |
Jonas Reeb |
Yannick Kiefl |
Christopher Riess |
18.06 |
|
Protein interaction |
Protein interaction and networks |
Jonas Reeb |
Oliver Bock |
Stefan Dvoretskii |
18.06 |
Meeting slides
14.05.2018 - How to give a good presentation
25.06.2018 - Machine Learning Introduction
02.07.2018 - ProtVec What's next?
12.11.2018 - Evaluation of Machine Learning and Tips on Scientific Paper Writing
Material
For your final report, please use the Bioinformatics template
Literature
Also check the literature mentioned in slides from the kick-off meeting. When in doubt, contact your supervisor.
Secondary structure prediction
- Kabsch, Wolfgang, and Christian Sander. "Dictionary of protein secondary structure: pattern recognition of hydrogen‐bonded and geometrical features." Biopolymers 22.12 (1983): 2577-2637.
- Rost, Burkhard, and Chris Sander. "Prediction of protein secondary structure at better than 70% accuracy." Journal of molecular biology 232.2 (1993): 584-599.
- Heffernan, Rhys, et al. "Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning." Scientific reports 5 (2015): 11476.
- DSSP Github
- DSSP Maintainer
Radiomics
Transmembrane proteins/helices
- Käll L, Krogh A, Sonnhammer EL (2005). An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics, 21 Suppl 1:i251-7.
- Nugent T, Jones DT (2009). Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics, 10:159.
- Bernhofer M, Kloppmann E, Reeb J, Rost B (2016). TMSEG: Novel prediction of transmembrane helices. Proteins, 84, 11:1706-1716.
Transmembrane protein expression
- Kloppmann, E., Punta, M., & Rost, B. (2012). Structural genomics plucks high-hanging membrane proteins. Current Opinion in Structural Biology, 22(3), 326–32. http://doi.org/10.1016/j.sbi.2012.05.002
- Mancia, F., & Love, J. (2011). High throughput platforms for structural genomics of integral membrane proteins. Current Opinion in Structural Biology, 21(4), 517–522. http://doi.org/10.1016/j.sbi.2011.07.001.High
- Moraes, I., Evans, G., Sanchez-Weatherby, J., Newstead, S., & Stewart, P. D. S. (2014). Membrane protein structure determination — The next generation. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1838(1), 78–87. http://doi.org/10.1016/j.bbamem.2013.07.010
- Jonas Reeb Master thesis excerpt
-
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2008). Molecular biology of the cell. Figure (5th ed.). New York: Garland Science. (Section "Protein Structure Can Be Determined Using X-Ray Diffraction" and following. Can be obtained at the library, or contact Jonas)
Protein interaction
- Keskin, O., Tuncbag, N., & Gursoy, A. (2016). Predicting Protein-Protein Interactions from the Molecular to the Proteome Level. Chemical Reviews, 116(8), 4884–4909. http://doi.org/10.1021/acs.chemrev.5b00683
- Hamp, T., & Rost, B. (2015). Evolutionary profiles improve protein-protein interaction prediction from sequence. Bioinformatics, 31(February), 1945–1950. http://doi.org/10.1093/bioinformatics/btv077
- Barabási, A.-L., & Oltvai, Z. N. (2004). Network biology: understanding the cell’s functional organization. Nature Reviews. Genetics, 5(2), 101–13. http://doi.org/10.1038/nrg1272
- Barabási, A.-L. (2009). Scale-free networks: a decade and beyond. Science (New York, N.Y.), 325(5939), 412–3. http://doi.org/10.1126/science.1173299
Subcellular localization
- Goldberg T, Hamp T, Rost B (2012). LocTree2 predicts localization for all domains of life. Bioinformatics 28: i458-i465
- Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Nielsen H, Rost B et al. (2014). LocTree3 prediction of localization. Nucleic Acids Research. pii: gku396
- Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2008). Molecular biology of the cell. Figure (5th ed.). New York: Garland Science. (Section "Intracellular Compartments and Protein Sorting" and following. Can be obtained at the library, or contact Maria)
Subnuclear localization
- Goldberg T, Next Generation Machine Learning Prediction of Protein Cellular Sorting
- Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2008). Molecular biology of the cell. Figure (5th ed.). New York: Garland Science. (Section "Intracellular Compartments and Protein Sorting" and following. Can be obtained at the library, or contact Maria)
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