Difference between revisions of "INF-BIOX121 H15 curriculum"
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[https://wiki.uio.no/projects/clsi/images/6/65/Baroy2015.pdf Barøy ''et al.'', A novel type of rhizomelic chondrodysplasia punctata, RCDP5, is caused by loss of the PEX5 long isoform. ''Human Molecular Genetics'' 2015] | [https://wiki.uio.no/projects/clsi/images/6/65/Baroy2015.pdf Barøy ''et al.'', A novel type of rhizomelic chondrodysplasia punctata, RCDP5, is caused by loss of the PEX5 long isoform. ''Human Molecular Genetics'' 2015] | ||
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+ | ===== Statistical genomics ===== | ||
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+ | [https://wiki.uio.no/projects/clsi/images/9/92/The_dilemma_of_choosing_the_ideal_permutation_strategy_while_estimating_statistical_significance_of_genome-wide_enrichment.pdf Subhajyoti ''et al.'' Briefings in Bioinformatics'' 2013] | ||
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+ | [https://wiki.uio.no/projects/clsi/images/4/4e/Christiansen2015.pdf Christiansen ''et al.'' PLOS One 2015] | ||
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+ | ===== Hyperbrowser ===== | ||
==== Recommended reading ==== | ==== Recommended reading ==== | ||
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[https://wiki.uio.no/projects/clsi/images/1/1d/Depristo2011.pdf DePristo ''et al.'' A framework for variation discovery and genotyping using next-generation DNA sequencing data. ''Nature Genetics'' 2011] | [https://wiki.uio.no/projects/clsi/images/1/1d/Depristo2011.pdf DePristo ''et al.'' A framework for variation discovery and genotyping using next-generation DNA sequencing data. ''Nature Genetics'' 2011] | ||
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+ | ===== Statistical genomics ===== | ||
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+ | ===== Hyperbrowser ===== |
Revision as of 16:32, 9 September 2015
Contents
Curriculum for INF-BIO5/9121
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.
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
Martin et al., Next-generation transcriptome assembly Nature 2011
Variant Calling
Ng et al., Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics 2010
Statistical genomics
Subhajyoti et al. Briefings in Bioinformatics 2013
Christiansen et al. PLOS One 2015
Hyperbrowser
Recommended reading
Sequencing
Metzker Sequencing technologies — the next generation Nature Reviews Genetics 2010
Ross et al., Characterizing and measuring bias insequence data Genome Biology 2013
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
Hackett et al., Transcriptional maturation of the mouse auditory forebrain. BMC Genomics 2015