Difference between revisions of "INF-BIOX121 H15 curriculum"

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Revision as of 10:05, 9 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


RNASeq

Text


[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin et al., Next-generation transcriptome assembly Nature 2011]

[https://wiki.uio.no/projects/clsi/images/1/13/Verbuggen2015.pdf Verbruggen et al., De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways Genomics 2015]


Recommended reading

Sequencing

Suggested Reading for Sequencing in general

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

[https://wiki.uio.no/projects/clsi/index.php/File:Sequencing_technologies_the_next_generation.pdf Metzker Sequencing technologies — the next generation Nature Reviews Genetics 2010]

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

RNASeq

Tillegg: Referanse basert: Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus. Generelt RNAseq [1](http://www.cshlpress.org/pdf/sample/2015/nextgen2/NGS2Chap13.pdf) - This is a free sample of content from Next-Generation DNA Sequencing Informatics, 2nd edition.