Classical papers in bioinformatics
Ph.D. course, Fall 2012,
Scilifelab, Stockholm. Arne Elofsson, 5 ECTS
The subject of the course is a set of classical articles that contain fundamental contributions to bioinformatics. This includes papers describing results or novel approaches that have influenced the thinking in bioinformatics, or recent papers that are considered particularly important.
All students must read the given articles before the meeting. Two students will be responsible for presenting the articles, in order to start the discussion about them. These two students are supposed to meet and prepare the presentation together. The two students should be responsible for a subject that is different from the field of their Ph.D. projects.
All students must prepare at least one question about the articles for the presenting students to consider. Send this question to the course organizer (Arne Elofsson ), at the latest the Moday before the meeting, who will forward it to the presenting students.
All students must attend every meeting. If for some reason a student is unable to attend a meeting the student will have to write a one-page summary (A4, own words) of the articles and send it to Arne Elofsson (arne(at)bioinfo.se) by the latest three weeks after the session that was missed. A maximum number of three sessions could be missed.
The senior scientist(s) will not lead the discussion, only participate. That’s why the senior scientist is called ‘sponsor’, not teacher. The presenting students are encouraged to contact the sponsor well in advance of the meeting to discuss the paper(s).
You will have to get copies of the articles yourself. In a few cases (some very old papers), we may provide paper copies or pdfs.
Format of the discussion
Here is a list of questions to discuss.
- What was novel about these papers ?
- How has they changed the field ?
- What has happened with the field since they were published ?
The email list is accessible by sending an email to firstname.lastname@example.org
The meetings are held weekly, Wednesdays, 15:00-18:00, in the Kilsbergen at floor 4 at Scilifelab. There will be 14 meetings during the fall of 2012. Starting from the 19th of Sept until Christmas.
- Arne Elofsson
- Bengt Persson
- Erik Lindahl
- Gunnar von Heijne
- Jens Carlsson
- Jens Lagergren
- Lars Arvestad
- Lukas Käll
- Lukasz Humaniecki
- Sara Light
- Auwn Muhammad
- Carlos Talavera-Lopez
- Frances Vega
- Ikram Ullah
- Joel Sjöstrand
- Karolis Uziela
- Konstantinos Tsirigos
- Linus Östberg
- Luisa Hugerth
- M Owais Mahmudi
- Özge Yoluk
- Oxana Sachenkova
- Per Warholm
- Raja Hashim
- Ranganathan Anirudh
- Valentine Svensson
- Viktor Granholm
- Walter Basile
- Viveca Lindahl
Location: Kilsbergen, Floor 4 Scilifelab.
NOTE THAT PAPERS IN ITALICS ARE ONLY PRELIMINARY SUGGESTIONS AND THAT THEY WILL CHANGE
|120919||Alignments and Homology detection||
||Carlos Talavera-Lopez, Frances Vega||Arne
||Linus Östberg, Luisa Hugerth, Valentine Svensson||Lars Arvestad|
|121003||Signal peptides and TM proteins||
||Ikram Ullah, Joel Sjöstrand, Oxana Sachenkova||Gunnar von Heijne|
|121010||Networks, function predictions and interactions||
||Karolis Uziela, Per Warholm, Raja Hashim||Bengt Persson|
|121017||Secondary structure predictions||
||Viveca Lindahl , Ranganathan Anirudh, Viktor Granholm||Arne Elofsson|
|121024||Hidden Markov Models||
||Raja Hashim, Walter Basile, Auwn Mohammed||Lukas Käll|
||Ranganathan Anirudh , Auwn Muhammad, Frances
|121107||Genome Assembly and gene annotation||
||Oxana Sachenkova, Özge Yoluk, Carlos Talavera-Lopez||Arne Elofsson|
||Konstantinos Tsirigos, Walter Basile, Per Warholm||Jens Lagergren|
||Joel Sjöstrand,Ikram Ullah||Erik Lindahl|
|121128||Protein Structure prediction||
||Luisa Hugerth, M Owais Mahmudi||Arne Elofsson|
|121205||Molecular docking: Methods for fast scoring of protein-ligand complexes||
||Valentine Svensson,, Viktor Granholm, Konstantinos Tsirigos||Jens Carlsson|
||Linus Östberg, Özge Yoluk||Sara Light|
|121219||Molecular Dynamics and computational chemistry||
||M Owais Mahmudi, Karolis Uziela||Erik Lindahl|