https://wiki.uio.no/projects/clsi/api.php?action=feedcontributions&user=Karinlag%40uio.no&feedformat=atomprojects/clsi - User contributions [en]2024-03-28T09:52:07ZUser contributionsMediaWiki 1.27.4https://wiki.uio.no/projects/clsi/index.php?title=File:Goodwin2016.pdf&diff=1602File:Goodwin2016.pdf2016-09-02T11:58:51Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Fabbro2013.pdf&diff=1601File:Fabbro2013.pdf2016-09-02T11:57:05Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Ekblom2014.pdf&diff=1600File:Ekblom2014.pdf2016-09-02T11:56:05Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Simpson2015.pdf&diff=1599File:Simpson2015.pdf2016-09-02T11:54:55Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Hatem2013.pdf&diff=1598File:Hatem2013.pdf2016-09-02T11:53:48Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Conesa2016.pdf&diff=1597File:Conesa2016.pdf2016-09-02T11:52:34Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Todd2016.pdf&diff=1596File:Todd2016.pdf2016-09-02T11:51:19Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Christiansen2015.pdf&diff=1595File:Christiansen2015.pdf2016-09-02T11:50:03Z<p>Karinlag@uio.no: Karinlag@uio.no uploaded a new version of File:Christiansen2015.pdf</p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:SimovskiPre.pdf&diff=1594File:SimovskiPre.pdf2016-09-02T11:48:52Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Noble_-_2009_-_A_quick_guide_to_organizing_computational_biology_projects.pdf&diff=1593File:Noble - 2009 - A quick guide to organizing computational biology projects.pdf2016-09-02T11:46:31Z<p>Karinlag@uio.no: </p>
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<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1342INF-BIOX121 H15 curriculum2015-10-15T12:58:07Z<p>Karinlag@uio.no: </p>
<hr />
<div>== Curriculum for INF-BIO5/9121 ==<br />
<br />
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.<br />
<br />
== Core curriculum ==<br />
<br />
'''''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.'''''<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
== Recommended reading ==<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf Baker, De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1318INF-BIOX121 H15 curriculum2015-09-11T13:15:39Z<p>Karinlag@uio.no: </p>
<hr />
<div>== Curriculum for INF-BIO5/9121 ==<br />
<br />
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.<br />
<br />
== Core curriculum ==<br />
<br />
'''''NOTE: Questions for the exam will ONLY be based on the core curriculum papers.'''''<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
== Recommended reading ==<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf Baker, De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1317INF-BIOX121 H15 curriculum2015-09-11T13:11:29Z<p>Karinlag@uio.no: </p>
<hr />
<div>== Curriculum for INF-BIO5/9121 ==<br />
<br />
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.<br />
<br />
== Core curriculum ==<br />
<br />
NOTE: '''''Questions for the exam will ONLY be based on the core curriculum papers.'''''<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
== Recommended reading ==<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1316INF-BIOX121 H15 curriculum2015-09-10T14:10:15Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
Questions for the exam will be based on the core curriculum papers.<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1315INF-BIOX121 H15 curriculum2015-09-10T09:30:33Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Reproducibility =====<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1314INF-BIOX121 H15 curriculum2015-09-09T15:09:52Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
[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]<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1313INF-BIOX121 H15 curriculum2015-09-09T15:08:34Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
Assembly<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
===== Hyperbrowser =====<br />
<br />
[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]<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1312INF-BIOX121 H15 curriculum2015-09-09T15:05:18Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
[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]<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1311INF-BIOX121 H15 curriculum2015-09-09T15:02:57Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
[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]<br />
<br />
==== Recommended reading ====<br />
<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/2/22/Nygaard2015.pdf Nygaard ''et al.'' ]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Nygaard2015.pdf&diff=1310File:Nygaard2015.pdf2015-09-09T15:00:49Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Sandve2013-2.pdf&diff=1309File:Sandve2013-2.pdf2015-09-09T14:58:09Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1308INF-BIOX121 H15 curriculum2015-09-09T14:43:08Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias in sequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
<br />
===== Hyperbrowser =====</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Sandve2010.pdf&diff=1307File:Sandve2010.pdf2015-09-09T14:41:50Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Sandve2013.pdf&diff=1306File:Sandve2013.pdf2015-09-09T14:40:26Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1305INF-BIOX121 H15 curriculum2015-09-09T14:32:57Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== Statistical genomics =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/4e/Christiansen2015.pdf Christiansen ''et al.'' PLOS One 2015]<br />
<br />
<br />
===== Hyperbrowser =====<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias insequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== Statistical genomics =====<br />
<br />
===== Hyperbrowser =====</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Christiansen2015.pdf&diff=1304File:Christiansen2015.pdf2015-09-09T14:29:00Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:The_dilemma_of_choosing_the_ideal_permutation_strategy_while_estimating_statistical_significance_of_genome-wide_enrichment.pdf&diff=1303File:The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.pdf2015-09-09T14:27:01Z<p>Karinlag@uio.no: Karinlag@uio.no uploaded a new version of File:The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.pdf</p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:The_dilemma_of_choosing_the_ideal_permutation_strategy_while_estimating_statistical_significance_of_genome-wide_enrichment.pdf&diff=1302File:The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.pdf2015-09-09T14:25:10Z<p>Karinlag@uio.no: Karinlag@uio.no uploaded a new version of File:The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.pdf</p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1301INF-BIOX121 H15 curriculum2015-09-09T13:56:02Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias insequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Depristo2011.pdf&diff=1300File:Depristo2011.pdf2015-09-09T13:54:59Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Sims2014.pdf&diff=1299File:Sims2014.pdf2015-09-09T13:53:27Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1298INF-BIOX121 H15 curriculum2015-09-09T13:53:01Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias insequence data ''Genome Biology'' 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
===== Variant Calling =====</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1297INF-BIOX121 H15 curriculum2015-09-09T13:51:49Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
===== Variant Calling =====<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias insequence data Genome Biology 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]<br />
<br />
===== Variant Calling =====</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Baroy2015.pdf&diff=1296File:Baroy2015.pdf2015-09-09T13:49:51Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Ng2010.pdf&diff=1295File:Ng2010.pdf2015-09-09T13:48:19Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1294INF-BIOX121 H15 curriculum2015-09-09T13:39:33Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin ''et al.,'' Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross ''et al.'', Characterizing and measuring bias insequence data Genome Biology 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1293INF-BIOX121 H15 curriculum2015-09-09T13:38:25Z<p>Karinlag@uio.no: added rnaseq</p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin et al Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross et al., Characterizing and measuring bias insequence data Genome Biology 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
[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]<br />
<br />
[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.]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Brown_Goecks_2015_Sample_NextGenDNASequencingInformatics2ed.pdf&diff=1292File:Brown Goecks 2015 Sample NextGenDNASequencingInformatics2ed.pdf2015-09-09T13:36:08Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Hackett_2015_Transcriptional_maturation_mouse.pdf&diff=1291File:Hackett 2015 Transcriptional maturation mouse.pdf2015-09-09T13:33:25Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1289INF-BIOX121 H15 curriculum2015-09-09T09:23:16Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
<br />
Work in progress!! Everything that is already here will be in the curriculum, but we are currently adding papers to the list.<br />
<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin et al Next-generation transcriptome assembly Nature 2011]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
<br />
[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]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/0/00/Ross2013.pdf Ross et al., Characterizing and measuring bias insequence data Genome Biology 2013]<br />
<br />
[http://www.molecularecologist.com/next-gen-fieldguide-2014/ NGS Field Guide]<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
Tillegg:<br />
Referanse basert:<br />
Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus. <br />
Generelt RNAseq<br />
[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.</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Ross2013.pdf&diff=1288File:Ross2013.pdf2015-09-09T09:20:00Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1287INF-BIOX121 H15 curriculum2015-09-09T09:16:13Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf What about a long text]<br />
<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf |Martin et al., Next-generation transcriptome<br />
assembly Nature 2011]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/1/13/Verbuggen2015.pdf Verbruggen et al., De novo assembly of the Carcinus maenas<br />
transcriptome and characterization of innate immune system pathways Genomics 2015]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
Suggested Reading for Sequencing in general<br />
<br />
Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)<br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/File:Sequencing_technologies_the_next_generation.pdf Metzker Sequencing technologies —<br />
the next generation Nature Reviews Genetics 2010]<br />
<br />
http://www.genomebiology.com/2013/14/5/R51<br />
<br />
website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/<br />
<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
Tillegg:<br />
Referanse basert:<br />
Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus. <br />
Generelt RNAseq<br />
[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.</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1286INF-BIOX121 H15 curriculum2015-09-09T09:06:52Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Text]<br />
<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Martin et al., Next-generation transcriptome<br />
assembly Nature 2011]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/1/13/Verbuggen2015.pdf Verbruggen et al., De novo assembly of the Carcinus maenas<br />
transcriptome and characterization of innate immune system pathways Genomics 2015]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
Suggested Reading for Sequencing in general<br />
<br />
Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)<br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/File:Sequencing_technologies_the_next_generation.pdf Metzker Sequencing technologies —<br />
the next generation Nature Reviews Genetics 2010]<br />
<br />
http://www.genomebiology.com/2013/14/5/R51<br />
<br />
website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/<br />
<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
Tillegg:<br />
Referanse basert:<br />
Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus. <br />
Generelt RNAseq<br />
[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.</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1285INF-BIOX121 H15 curriculum2015-09-09T09:05:08Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf Text]<br />
<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf '''Martin ''et al.'',''' Next-generation transcriptome<br />
assembly ''Nature'' 2011]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/1/13/Verbuggen2015.pdf '''Verbruggen ''et al.'',''' De novo assembly of the Carcinus maenas<br />
transcriptome and characterization of innate immune system pathways ''Genomics'' 2015]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
Suggested Reading for Sequencing in general<br />
<br />
Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)<br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/File:Sequencing_technologies_the_next_generation.pdf '''Metzker ''' Sequencing technologies —<br />
the next generation ''Nature Reviews Genetics'' 2010]<br />
<br />
http://www.genomebiology.com/2013/14/5/R51<br />
<br />
website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/<br />
<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
Tillegg:<br />
Referanse basert:<br />
Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus. <br />
Generelt RNAseq<br />
[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.</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1284INF-BIOX121 H15 curriculum2015-09-09T09:04:33Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
[[Text]]<br />
<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf '''Martin ''et al.'',''' Next-generation transcriptome<br />
assembly ''Nature'' 2011]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/1/13/Verbuggen2015.pdf '''Verbruggen ''et al.'',''' De novo assembly of the Carcinus maenas<br />
transcriptome and characterization of innate immune system pathways ''Genomics'' 2015]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
Suggested Reading for Sequencing in general<br />
<br />
Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)<br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/File:Sequencing_technologies_the_next_generation.pdf '''Metzker ''' Sequencing technologies —<br />
the next generation ''Nature Reviews Genetics'' 2010]<br />
<br />
http://www.genomebiology.com/2013/14/5/R51<br />
<br />
website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/<br />
<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
Tillegg:<br />
Referanse basert:<br />
Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus. <br />
Generelt RNAseq<br />
[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.</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1283INF-BIOX121 H15 curriculum2015-09-09T09:01:09Z<p>Karinlag@uio.no: </p>
<hr />
<div>=== Curriculum for INF-BIO5/9121 ===<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
===== RNASeq =====<br />
<br />
<br />
[https://wiki.uio.no/projects/clsi/images/4/47/Martin2011.pdf '''Martin ''et al.'',''' Next-generation transcriptome<br />
assembly ''Nature'' 2011]<br />
<br />
[https://wiki.uio.no/projects/clsi/images/1/13/Verbuggen2015.pdf '''Verbruggen ''et al.'',''' De novo assembly of the Carcinus maenas<br />
transcriptome and characterization of innate immune system pathways ''Genomics'' 2015]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
Suggested Reading for Sequencing in general<br />
<br />
Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)<br />
<br />
[https://wiki.uio.no/projects/clsi/index.php/File:Sequencing_technologies_the_next_generation.pdf '''Metzker ''' Sequencing technologies —<br />
the next generation ''Nature Reviews Genetics'' 2010]<br />
<br />
http://www.genomebiology.com/2013/14/5/R51<br />
<br />
website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/<br />
<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
===== RNASeq =====<br />
<br />
Tillegg:<br />
Referanse basert:<br />
Hackett 2015 - 29 sider! En særdeles godt lagt opp analyse i mus. <br />
Generelt RNAseq<br />
[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.</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Verbuggen2015.pdf&diff=1282File:Verbuggen2015.pdf2015-09-09T08:51:44Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Martin2011.pdf&diff=1281File:Martin2011.pdf2015-09-09T08:51:04Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=INF-BIOX121_H15_curriculum&diff=1280INF-BIOX121 H15 curriculum2015-08-26T18:27:22Z<p>Karinlag@uio.no: </p>
<hr />
<div>Work in progress, expected to be complete no later than 1st of September, 2015.<br />
<br />
=== Curriculum for INF-BIO5/9121 ===<br />
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.<br />
<br />
==== Core curriculum ====<br />
<br />
===== Sequencing =====<br />
[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]<br />
<br />
===== Assembly =====<br />
<br />
<br />
[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 ]<br />
<br />
[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]<br />
<br />
[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]<br />
<br />
<br />
==== Recommended reading ====<br />
<br />
===== Sequencing =====<br />
Suggested Reading for Sequencing in general<br />
<br />
Metzker http://dx.doi.org/10.1038/nrg2626 (står nevnt på 2014 wiki)<br />
<br />
http://www.genomebiology.com/2013/14/5/R51<br />
<br />
website: NGS Field Guide http://www.molecularecologist.com/next-gen-fieldguide-2014/<br />
<br />
<br />
<br />
===== Assembly =====<br />
<br />
[https://wiki.uio.no/projects/clsi/images/a/ab/Baker2012.pdf '''Baker, ''' De novo genome assembly: what every biologist should know ''Nature Methods'' 2012]<br />
<br />
[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]<br />
<br />
[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]</div>Karinlag@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:Ekblom_et_al-2014-Evolutionary_Applications.pdf&diff=1279File:Ekblom et al-2014-Evolutionary Applications.pdf2015-08-26T17:16:19Z<p>Karinlag@uio.no: </p>
<hr />
<div></div>Karinlag@uio.no