Proseminar 'Proteins and Disease' SoSe 2016

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

News

~~~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

  • students from both groups (Group 1 and 2) meet at the same time, at 12:00, in MI 01.09.034

Presentations

  • students assigned the same topic can present it either in a common presentation of 30 minutes or in two separate presentations, 20 mins each
  • if students give two separate presentations, then they are held after each other and the audience for both presentations remains the same
  • if students share one presentation, then they need to make sure that they speak an equal amount of time

Final report

  • if a presentation is made by two students, then it is sufficient if they submit together one common report
  • otherwise, if a topic is presented in two talks by two different students, then two reports need to be submitted
  • each student (or  two students) need to update one wikipedia article on a bioinformatics topic - preferably - an article about presented topic
  • each report needs to contain the name and the URL to the edited article as well as the edited text
  • reports are due one week after the presentation

Report review

  • On July 4th, after the last report is submitted, the students will peer-review each other reports
  • For review, the group presenting first sends its report to the group presenting second. The group presenting second sends the report to the group presenting third and so on
  • Groups will have one week to review the reports, until July 11, which will need to be sent to supervisors of the corresponding group. For example, the group presenting first sends its report of the group that presented on June 27th to Dr. Richter
  • For guidelines on how to write a report, please see Bioinformatics reviewer guidelines (section: Completing the Referee Report)

Application / Registration

Application is organised centrally for all bioinformatics seminars. After you have been assigned to our seminar, we will distribute the topics.

Content

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.

Pre-meeting

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. 

Schedule for SoSe 16

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

 

 

  

Topics

Sequence alignment: local and global

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:

 

Sequence alignment and searches: heuristic methods

Dr. Lothar Richter

This talk shall explain the heuristic approximations made to speed up sequence alignment and sequence searches (BLAST, FASTA).

Literature:

  • Korf, Ian et al. BLAST. O'Reilly Media, Inc. 2003
  • David Mount, Bioinformatics: Sequence and Genome Analysis, Second Edition, CSH Laboratory Press

The human proteome

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:

 

PolyPhobius: Prediction of transmembrane in protein sequences

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:

  • Alberts
  • Bioinformatics
  • Lukas Käll, Anders Krogh and Erik Sonnhammer. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics, 21 (Suppl 1):i251-i257, June 2005.

 

SignalP 4: Prediction of signal peptides in protein sequences

Jonas Reeb

 

Literature:

  • Alberts
  • Bioinformatics
  • Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods8:785-786, 2011

 

PiNat: Assessment of protein networks

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:

  •  

Protein disorder--a breakthrough invention of evolution?

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

  • ...

 

Biological Databases

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.

  • Arthur M. Lesk. Introduction to bioinformatics (Third Edition) Oxford University Press

 

  •