Page CompMethodsWS11

In this seminar, we will focus on two different kinds of high-throughput technologies:

• second-generation DNA sequencing
• liquid chromatography / mass spectrometry.

Written Summary

• Prepare a 2-3 page summary of your article and send it to us as pdf.
• Make sure you send it before Feb 29, 23:59 CET. We will not accept any summaries after Feb 29.
• The written summary will account for 30% of the entire grade.

Alternative Projects

Those of you who have received alternative projects to compensate for attendance issues, are asked to send their reports before Feb 29, 23:59 CET. We will not accept any reports after Feb 29.

Talk Preparation

IMPORTANT:

• Please make an appointment with us about 4 weeks (at least 2 weeks)

prior to your talk, so we can discuss the focus of the talk and you can start preparing.

• Make another appointment/date about 1.5 weeks prior to your talk

(latest on monday before your talk) where you either - send the COMPLETE slides and audience questions (5-10) via mail - or come to us and present your slides and audience questions (5-10). The latter is recommended, as we can iron out small mistakes much more effectively.

• Prepare the talk for ~50-60 minutes. See the guidelines below for good

talks (or start googling yourself - but remember: not everything on YouTube is true).

Talk schedule

Location, location, location

• Takustr.9 , room 005

Time

• saturdays: 10 am - 4 pm
• sundays: 12 am - 6 pm

Talks

name	topic	date	paper url	slides
Matt Huska	GSNAP	12/03/2011	http://bioinformatics.oxfordjournals.org/content/26/7/873.short	MHuska_GSNAP.pdf
Andreas Eckart	RazerS	12/03/2011	http://genome.cshlp.org/content/19/9/1646.full
Christopher Ozdoba	AGE - BreakPoint DP	12/03/2011	http://bioinformatics.oxfordjournals.org/content/27/5/595.short
Yvonne Mayer	SRiC	12/04/2011	http://www.biomedcentral.com/1471-2164/12/375/abstract
Jörgen Brandt	Isobar - iTRAQ	12/04/2011	http://www.ncbi.nlm.nih.gov/pubmed/21526793
Jan M. Josten	SRMA	12/04/2011	http://genomebiology.com/2010/11/10/R99/
Mathias Kuhring	InsPecT	01/21/2012	http://pubs.acs.org/doi/abs/10.1021/ac050102d
Anke Penzlin	ETISEQ	01/21/2012	http://www.ncbi.nlm.nih.gov/pubmed/19664259
Oliver Stolpe	StructuralVariant Framework	01/21/2012	http://bioinformatics.oxfordjournals.org/content/24/13/i59.short
Sabrina Krakau	Variation Hunter	01/22/2012	http://genome.cshlp.org/content/19/7/1270.full
Martin Wettig	BreakSeq	01/22/2012	http://www.nature.com/nbt/journal/v28/n1/full/nbt.1600.html
Jörn Bethune	CancerSequencing & ChimeraScan	01/22/2012	http://www.nature.com/nature/journal/v458/n7234/full/nature07638.html and http://bioinformatics.oxfordjournals.org/content/27/20/2903.short

Material

Introduction slides:

• see attachment table below

Relevant review papers:

• Genome structural variation discovery and genotyping: http://www.nature.com/nrg/journal/v12/n5/abs/nrg2958.html
• Computational methods for structural variant discovery: http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1374.html
• Next-generation sequencing read mapping: http://bib.oxfordjournals.org/content/11/5/473.short
• OVerview of NGS sequencing technologies: http://www.annualreviews.org/doi/abs/10.1146/annurev.genom.9.081307.164359
• Applied SV detection paper, 1000Genomes project: http://www.nature.com/nature/journal/v470/n7332/full/nature09708.html

• Mass Spectrometry (overview): http://bfg.oxfordjournals.org/content/4/4/295.long

Presentation templates:

• Powerpoint slide template: http://www.fu-berlin.de/sites/cd/ppt/index.html
• Tex slide template: http://www.mi.fu-berlin.de/w/Mi/BeamerTemplateCorporateDesign

Two useful guides on how to give a good seminar talk:

• http://page.mi.fu-berlin.de/~huisinga/teaching/guteVortraege.html
• http://www.lsw.uni-heidelberg.de/users/mcamenzi/vortrag.html

Comments

An welchem Ort findet das ganze statt? Im gleichen Raum im Pi-Gebäude wie bisher?

-- Main.jbethune - 02 Dec 2011