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Type | Seminar (2 SWS) |
ECTS | 3 (FPO 2007) 4 (FPO 2013) |
Lecturer | Burkhard Rost |
Time | Monday, 12:00 - 14:00 |
Room | MI 01.09.034 |
Language | English |
~~~Meeting CANCELLED on Monday, May 23rd!~~~
~~~Meeting CANCELLED on Monday, May 2nd!~~~
As disussed on Monday, April 18th, the new rules for this seminar include:
Meeting time
Presentations
Final report
Report review
Application is organised centrally for all bioinformatics seminars. After you have been assigned to our seminar, we will distribute the topics.
Topics related to the research interests of the group: protein sequence analysis, sequence based predictions, protein structure prediction and analysis and commonly used tools. The list below shows topics from proseminars of the last years and might still be subject to change.
Wednesday, Feb 3rd, 15.00-16.00 o'clock, Room MI 01.09.034
The rules and hints for preparation of the seminar discussed in the pre-meeting are also summarised in our Checklist and on these slides.
Slides from the pre-meeting. Topics and schedule have been moved to the table below. Timetable last updated on Mar 7th, 2016.
Date | Topic | Supervisor | Group 1 | Group 2 |
---|---|---|---|---|
Apr 18th | Pairwise Alignment: Global / Local | Richter | Hilger | Hoffmann |
Apr 25th | Sequence Alignment: Heuristic Methods | Richter | Kraft-Blank | Resch |
May 2nd | The Human Proteome - CANCELLED | Kloppmann | Njah | Seif |
May 9th | Protein Disorder | Goldberg | Müller | Weiß |
May 23rd | PolyPhobius - CANCELLED | Reeb | Lungala | Spier |
May 30th | PiNat: Assessment of Protein Networks | Goldberg | Schwarze | Altschäffel |
Jun 6th | SignalP 4 | Reeb | Dietrich | Raykov |
Jun 13th | Biological Databases | Cejuela | Beer | Heinemann |
June 20th | The Human Proteome | Kloppmann | Njah | - |
June 27th | PolyPhobius | Reeb | Lungala | Spier |
Dr. Lothar Richter
Finding an alignment of two protein sequences is the basis of all techniques to infer knowledge by homology. This talk shall review well-known local and global alignment methods (Smith-Waterman, Needleman-Wunsch).
Literature:
Dr. Lothar Richter
This talk shall explain the heuristic approximations made to speed up sequence alignment and sequence searches (BLAST, FASTA).
Literature:
Dr. Edda Kloppmann
The talk shall give an introduction to the human proteome. The Human Genome Project shall be briefly introduced, the change in the number of postulated proteins over time and definitions of "proteome". The main focus shall be on the "mass-spectrometry-based draft of the human proteome": Using mass-spectrometry, researchers from TUM have produced an almost complete inventory of the human proteome on the protein level. This information is now freely available in the ProteomicsDB database, which is a joint development of TUM and software company SAP. The database includes information for example on the types, distribution, and abundance of proteins in various cells and tissues as well as in body fluids. The talk may briefly explain mass-spectrometry and, in more detail, the results of the publication.
Literature:
Jonas Reeb
PolyPhobius uses hidden markov models (HMMs) to predict transmembrane helices in protein sequences. This talk shall introduce transmembrane proteins, HMMs and sequence-based transmembrane helix prediction at the example of PolyPhobius.
Literature:
Jonas Reeb
Literature:
Tatyana Goldberg
A platform for data integration shall be presented in this talk. The platform generates networks on the macro system-level, analyzes the molecular characteristics of each protein on the micro level, and then combines the two levels by using the molecular characteristics to assess networks. It also annotates the function and subcellular localization of each protein and displays the process on an image of a cell, rendering each protein in its respective cellular compartment.
Literature:
Ofran Y, Rost B, et al. (2006). Create and assess protein networks through molecular characteristics of individual proteins. Bioinformatics; 22(14):e402-7. http://www.ncbi.nlm.nih.gov/pubmed/16873500
Barabási AL & Oltvai ZN (2004). Network biology: understanding the cell's functional organization. Nature Reviews Genetics 5, 101-113. http://www.ncbi.nlm.nih.gov/pubmed/14735121
Tatyana Goldberg
The regions in proteins that do not adopt regular three-dimensional structures in isolation are called disordered regions. In this seminar the functional and structural aspects of disordered proteins shall be discussed. Though only one literature source is provided, the student is expected to use and refer to in his presentation to additional sources for a detailed understanding of protein disorder.
Literature:
Schlessinger A, Schaefer C, Vicedo E, Schmidberger M, Punta M, Rost B (2011). Protein disorder--a breakthrough invention of evolution? Curr Opin Struct Biol. Jun;21(3):412-8 http://www.ncbi.nlm.nih.gov/pubmed/21514145
...
Juan Miguel Cejuela
Huge volumes of primary data are archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories. This seminar shall give an overview of different Databases, how to access them and problems associated.