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.
NOTE: Questions for the exam will ONLY be based on the core curriculum papers and the lecture material, and not from papers from the recommended reading list.
Buermans et al., Next generation sequencing technology: Advances and applications Biochimica et Biophysica Acta 2014
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
Martin et al., Next-generation transcriptome assembly Nature 2011
Verbruggen et al., De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways Genomics 2015
Nielsen et al., Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 2011
Ng et al., Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics 2010
Barøy et al., A novel type of rhizomelic chondrodysplasia punctata, RCDP5, is caused by loss of the PEX5 long isoform. Human Molecular Genetics 2015
Subhajyoti et al. Briefings in Bioinformatics 2013
Christiansen et al. Transcriptionally Active Regions Are the Preferred Targets for Chromosomal HPV Integration in Cervical Carcinogenesis PLOS One 2015
Sandve et al., Ten Simple Rules for Reproducible Computational Research PLOS Computational Biolgoy 2013
Metzker Sequencing technologies — the next generation Nature Reviews Genetics 2010
Ross et al., Characterizing and measuring bias in sequence data Genome Biology 2013
NGS Field Guide
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
Nygaard et al.
Hackett et al., Transcriptional maturation of the mouse auditory forebrain. BMC Genomics 2015
Brwon et al., RNA Sequencing with Next-Generation Sequencing. Next-Generation DNA Sequencing Informatics, 2nd edition.
Sims et al., Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics 2011
DePristo et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 2011
Sandve et al. The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research 2013
Sandve et al. The Genomic HyperBrowser: inferential genomics at the sequence level Genome Biology 2010
Goecks et al., Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biology 2010
Nygaard et al. Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses Biostatistics 2015