Difference between revisions of "INF-BIOX121 H15 curriculum"
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− | + | == 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. | 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 == | |
+ | |||
+ | '''''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.''''' | ||
===== Sequencing ===== | ===== Sequencing ===== | ||
− | [https://wiki.uio.no/projects/clsi/images/0/0d/Buermans2014.pdf | + | [https://wiki.uio.no/projects/clsi/images/0/0d/Buermans2014.pdf Buermans ''et al.'', Next generation sequencing technology: Advances and applications ''Biochimica et Biophysica Acta'' 2014] |
+ | |||
===== Assembly ===== | ===== Assembly ===== | ||
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− | Miller | + | [https://wiki.uio.no/projects/clsi/images/7/74/Assembly_algorithms_for_next-generation_sequencing_data.pdf Miller ''et al.'', Assembly algorithms for next-generation sequencing data ''Genomics.'' 2010 ] |
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/a/a9/Amemiya.pdf Amemiya''et al.'', The African coelacanth genome provides insights into tetrapod evolution ''Nature'' 2014] | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/c/cd/Brawand2014.pdf 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] | ||
+ | |||
+ | |||
+ | ===== Variant Calling ===== | ||
− | + | [https://wiki.uio.no/projects/clsi/index.php/File:Genotype_and_SNP_calling_from_next-generation_sequencing_data.pdf Nielsen ''et al.,'' Genotype and SNP calling from next-generation sequencing data. Nature Reviews ''Genetics'' 2011] | |
− | + | [https://wiki.uio.no/projects/clsi/images/7/79/Ng2010.pdf ''Ng et al.'', Exome sequencing identifies the cause of a mendelian disorder. ''Nature Genetics'' 2010] | |
− | + | [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] | |
− | ==== Recommended reading | + | |
+ | ===== Statistical genomics ===== | ||
+ | |||
+ | [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] | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/4/4e/Christiansen2015.pdf Christiansen ''et al.'' Transcriptionally Active Regions Are the Preferred Targets for Chromosomal HPV Integration in Cervical Carcinogenesis ''PLOS One'' 2015] | ||
+ | |||
+ | |||
+ | ===== Reproducibility ===== | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/e/ed/Sandve2013-2.pdf Sandve ''et al.'', Ten Simple Rules for Reproducible Computational Research ''PLOS Computational Biolgoy'' 2013] | ||
+ | |||
+ | == Recommended reading == | ||
===== Sequencing ===== | ===== Sequencing ===== | ||
− | |||
− | + | [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] | |
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013] | ||
+ | |||
+ | [http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide] | ||
+ | |||
+ | |||
+ | ===== Assembly ===== | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf Baker, De novo genome assembly: what every biologist should know ''Nature Methods'' 2012] | ||
+ | |||
+ | [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] | ||
+ | |||
+ | [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] | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ] | ||
+ | |||
+ | |||
+ | ===== RNASeq ===== | ||
− | + | [https://wiki.uio.no/projects/clsi/images/4/45/Hackett_2015_Transcriptional_maturation_mouse.pdf Hackett ''et al.'', Transcriptional maturation of the mouse auditory forebrain. ''BMC Genomics'' 2015] | |
− | + | [https://wiki.uio.no/projects/clsi/images/9/9f/Brown_Goecks_2015_Sample_NextGenDNASequencingInformatics2ed.pdf Brwon ''et al.'', RNA Sequencing with Next-Generation Sequencing. Next-Generation DNA Sequencing Informatics, 2nd edition.] | |
+ | ===== Variant Calling ===== | ||
− | ===== | + | [https://wiki.uio.no/projects/clsi/images/7/75/Sims2014.pdf Sims ''et al.'', Sequencing depth and coverage: key considerations in genomic analyses. ''Nature Reviews 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] | ||
+ | |||
+ | |||
+ | ===== Statistical genomics ===== | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/0/07/Sandve2013.pdf Sandve ''et al.'' The Genomic HyperBrowser: an analysis web server for genome-scale data. ''Nucleic Acids Research'' 2013] | ||
+ | |||
+ | [https://wiki.uio.no/projects/clsi/images/f/fa/Sandve2010.pdf Sandve ''et al.'' The Genomic HyperBrowser: inferential genomics at the sequence level ''Genome Biology'' 2010] | ||
+ | |||
+ | |||
+ | ===== Reproducibility ===== | ||
− | + | [https://wiki.uio.no/projects/clsi/images/8/85/Galaxy_a_comprehensive_approach_for_supporting_accessible_reproducible_and_transparent_computational_research_in_the_life_sciences.pdf Goecks ''et al.'', Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences ''Genome Biology'' 2010] | |
− | + | [https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses ''Biostatistics'' 2015] |
Latest revision as of 14:58, 15 October 2015
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
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.
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
Reproducibility
Recommended reading
Sequencing
Metzker Sequencing technologies — the next generation Nature Reviews Genetics 2010
Ross et al., Characterizing and measuring bias in sequence 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
Variant Calling
Statistical genomics