Difference between revisions of "INF-BIOX121 H15 curriculum"

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===== Assembly =====
 
===== Assembly =====
http://www.ncbi.nlm.nih.gov/pubmed/25553065
 
  
http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html
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[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]
  
http://www.nature.com/nature/journal/v477/n7363/full/nature10342.html
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[https://wiki.uio.no/projects/clsi/images/4/45/Star2011.pdf '''Star ''et al.'',''' The genome sequence of Atlantic cod reveals a unique immune system ''Nature'' 2011]
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[https://wiki.uio.no/projects/clsi/images/a/a4/Ekblom_et_al-2014-Evolutionary_Applications.pdf '''Ekblom ''et al.'',''' A field guide to whole-genome sequencing, assembly and annotation ''Evolutionary Applications'' 2014]

Revision as of 19:27, 26 August 2015

Work in progress, expected to be complete no later than 1st of September, 2015.

Curriculum for INF-BIO5/9121

The fields of bioinformatics and genomics are in rapid development. Hence, the curriculum for this course is not a book, but a set of articles. We have put together two sets of articles for this course. The first comprises the core curriculum, these are articles from which questions for the exam might be pulled. The second set is a list of articles that will give more in-depth information. These articles will not be used for the exam, but still represent highly useful and relevant knowledge that we highly recommend reading.

Core curriculum

Sequencing

Buermans et al., Next generation sequencing technology: Advances and applications Biochimica et Biophysica Acta 2014

Assembly

Miller et al., Assembly algorithms for next-generation sequencing data Genomics. 2010

Amemiyaet al., The African coelacanth genome provides insights into tetrapod evolution Nature 2014

Brawand et al., The genomic substrate for adaptive radiation in African cichlid fish Nature 2014


Recommended reading

Sequencing

Suggested Reading for Sequencing in general

Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)

http://www.genomebiology.com/2013/14/5/R51

website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/


Assembly

Baker, De novo genome assembly: what every biologist should know Nature Methods 2012

Star et al., The genome sequence of Atlantic cod reveals a unique immune system Nature 2011

Ekblom et al., A field guide to whole-genome sequencing, assembly and annotation Evolutionary Applications 2014