Difference between revisions of "INF-BIOX121 H14 curriculum"
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The curriculum consists of these papers: | The curriculum consists of these papers: | ||
| − | [ | + | [https://wiki.uio.no/projects/clsi/images/a/a5/Sequencing_technologies_the_next_generation.pdf '''Sequencing technologies - the next generation.''']<br/>Metzker ML.<br/>Nat Rev Genet. 2010 Jan;11(1):31-46 |
| − | [ | + | [https://wiki.uio.no/projects/clsi/images/1/17/Tools_for_mapping_high-throughput_sequencing_data.pdf '''Tools for mapping high-throughput sequencing data.''']<br/>Fonseca NA, Rung J, Brazma A, Marioni JC.<br/>Bioinformatics. 2012 Dec 15;28(24):3169-77. |
'''[https://wiki.uio.no/projects/clsi/images/b/be/A_scaling_normalization_method_for_differential_expression_analysis_of_RNA-seq_data.pdf A scaling normalization method for differential expression analysis of RNA-seq data]. '''<br/>Robinson MD, Oshlack A.<br/>Genome Biol. 2010;11(3):R25. | '''[https://wiki.uio.no/projects/clsi/images/b/be/A_scaling_normalization_method_for_differential_expression_analysis_of_RNA-seq_data.pdf A scaling normalization method for differential expression analysis of RNA-seq data]. '''<br/>Robinson MD, Oshlack A.<br/>Genome Biol. 2010;11(3):R25. | ||
| − | '''Assembly algorithms for next-generation sequencing data.'''<br/>Miller JR, Koren S, Sutton G.<br/>Genomics. 2010 Jun;95(6):315-27 | + | [https://wiki.uio.no/projects/clsi/images/7/74/Assembly_algorithms_for_next-generation_sequencing_data.pdf '''Assembly algorithms for next-generation sequencing data.''']<br/>Miller JR, Koren S, Sutton G.<br/>Genomics. 2010 Jun;95(6):315-27 |
| − | '''ChIP-seq: advantages and challenges of a maturing technology.'''<br/>Park PJ.<br/>Nat Rev Genet. 2009 Oct;10(10):669-80. | + | [https://wiki.uio.no/projects/clsi/images/9/97/ChIP-Seq_advantages_and_challenges_of_a_maturing_technology.pdf '''ChIP-seq: advantages and challenges of a maturing technology.''']<br/>Park PJ.<br/>Nat Rev Genet. 2009 Oct;10(10):669-80. |
| − | '''Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. '''<br/>Goecks J, Nekrutenko A, Taylor J; Galaxy Team.<br/>Genome Biol. 2010;11(8):R86. | + | [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 '''Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.''']<br/>Goecks J, Nekrutenko A, Taylor J; Galaxy Team.<br/>Genome Biol. 2010;11(8):R86. |
| − | '''The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.'''<br/>De S, Pedersen BS, Kechris K.<br/>Brief Bioinform. 2013 Aug 16. | + | [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 '''The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.''']<br/>De S, Pedersen BS, Kechris K.<br/>Brief Bioinform. 2013 Aug 16. |
| − | '''RNA-Seq: a revolutionary tool for transcriptomics. '''<br/>Wang Z, Gerstein M, Snyder M.<br/>Nat Rev Genet. 2009 Jan;10(1):57-63 | + | [https://wiki.uio.no/projects/clsi/images/2/29/RNA-Seq_a_revolutionary_tool_for_transcriptomics.pdf '''RNA-Seq: a revolutionary tool for transcriptomics.''']<br/>Wang Z, Gerstein M, Snyder M.<br/>Nat Rev Genet. 2009 Jan;10(1):57-63 |
| − | '''Genotype and SNP calling from next-generation sequencing data.'''<br/>Nielsen R, Paul JS, Albrechtsen A, Song YS.<br/>Nat Rev Genet. 2011 Jun;12(6):443-51. | + | [https://wiki.uio.no/projects/clsi/images/3/33/Genotype_and_SNP_calling_from_next-generation_sequencing_data.pdf '''Genotype and SNP calling from next-generation sequencing data.''']<br/>Nielsen R, Paul JS, Albrechtsen A, Song YS.<br/>Nat Rev Genet. 2011 Jun;12(6):443-51. |
Revision as of 09:43, 1 October 2014
Required curriculum for credit students
The curriculum consists of these papers:
Sequencing technologies - the next generation.
Metzker ML.
Nat Rev Genet. 2010 Jan;11(1):31-46
Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics. 2012 Dec 15;28(24):3169-77.
A scaling normalization method for differential expression analysis of RNA-seq data.
Robinson MD, Oshlack A.
Genome Biol. 2010;11(3):R25.
Assembly algorithms for next-generation sequencing data.
Miller JR, Koren S, Sutton G.
Genomics. 2010 Jun;95(6):315-27
ChIP-seq: advantages and challenges of a maturing technology.
Park PJ.
Nat Rev Genet. 2009 Oct;10(10):669-80.
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.
Goecks J, Nekrutenko A, Taylor J; Galaxy Team.
Genome Biol. 2010;11(8):R86.
The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.
De S, Pedersen BS, Kechris K.
Brief Bioinform. 2013 Aug 16.
RNA-Seq: a revolutionary tool for transcriptomics.
Wang Z, Gerstein M, Snyder M.
Nat Rev Genet. 2009 Jan;10(1):57-63
Genotype and SNP calling from next-generation sequencing data.
Nielsen R, Paul JS, Albrechtsen A, Song YS.
Nat Rev Genet. 2011 Jun;12(6):443-51.
SAM (and BAM): "Sequence Alignment/Map Format Specification" by "The SAM/BAM Format Specification Working Group"
FASTQ: Peter J. A. Cock et al
Nucleic Acids Res. 2010 April; 38(6): 1767–1771
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
