Difference between revisions of "INF-BIOX121 H15 curriculum"

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=== Curriculum for INF-BIO5/9121 ===
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== Curriculum for INF-BIO5/9121 ==
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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 ====
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== Core curriculum ==
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'''''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 '''Buermans ''et al.'',''' Next generation sequencing technology: Advances and applications ''Biochimica et Biophysica Acta'' 2014]
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[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]
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===== Assembly =====
 
===== Assembly =====
  
[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 ]
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[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]
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[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]
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[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 =====
 
===== RNASeq =====
  
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Text]
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[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]
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[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]
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===== Variant Calling =====
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[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]
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[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]
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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]
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===== Statistical genomics =====
  
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin et al., Next-generation transcriptome
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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]
assembly Nature 2011]
 
  
[https://wiki.uio.no/projects/clsi/images/1/13/Verbuggen2015.pdf Verbruggen et al., De novo assembly of the Carcinus maenas
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[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]
transcriptome and characterization of innate immune system pathways Genomics 2015]
 
  
  
==== Recommended reading ====
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===== Reproducibility =====
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[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]
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== Recommended reading ==
  
 
===== Sequencing =====
 
===== Sequencing =====
Suggested Reading for Sequencing in general
 
  
Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)
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[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/index.php/File:Sequencing_technologies_the_next_generation.pdf Metzker  Sequencing technologies —
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[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]
the next generation Nature Reviews Genetics 2010]
 
  
http://www.genomebiology.com/2013/14/5/R51
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[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]
  
website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/
 
  
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===== Assembly =====
  
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[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf Baker,  De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]
  
===== Assembly =====
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[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/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]
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[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/4/45/Star2011.pdf '''Star ''et al.'',''' The genome sequence of Atlantic cod reveals a unique immune system ''Nature'' 2011]
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[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]
  
[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]
 
  
 
===== RNASeq =====
 
===== RNASeq =====
  
Tillegg:
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[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]
Referanse basert:
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Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus.  
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[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.]
Generelt RNAseq
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[http://www.cshlpress.org/pdf/sample/2015/nextgen2/NGS2Chap13.pdf](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.
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===== Variant Calling =====
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 +
[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]
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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]
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 +
 
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===== Statistical genomics =====
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 +
[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]
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 +
[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]
 +
 
 +
 
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===== Reproducibility =====
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 +
[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]
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 +
[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 13:58, 15 October 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

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

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

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


Variant Calling

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


Statistical genomics

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


Reproducibility

Sandve et al., Ten Simple Rules for Reproducible Computational Research PLOS Computational Biolgoy 2013

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

NGS Field Guide


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

Nygaard et al.


RNASeq

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.


Variant Calling

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


Statistical genomics

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


Reproducibility

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