INF-BIOX121 H15 curriculum
Contents
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
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
[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
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.