Difference between revisions of "Additional curriculum"
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*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. '''9''', e1003285 (2013)] | *G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. '''9''', e1003285 (2013)] | ||
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. '''41''', W133 (2013)] | *G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. '''41''', W133 (2013)] | ||
− | *A. Altmann ''et al.'',l "A beginners guide to SNP calling from high-throughput DNA-sequencing data", Hum. Genet. '''131''', 1541 (2012) | + | *A. Altmann ''et al.'',l "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. '''131''', 1541 (2012)] |
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. '''14''', 157 (2013)] | *N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. '''14''', 157 (2013)] | ||
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. '''4''', 44 (2009)] | *D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. '''4''', 44 (2009)] | ||
*... | *... | ||
*More articles may still appear on this list! | *More articles may still appear on this list! |
Revision as of 17:23, 14 November 2013
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Required reading material for the course
This list is not yet finished!
The following articles/reviews/written material is part of the curriculum for MBV-INF4410, MBV-INF9410, and MBV-INF9410A:
- R.F. Service, "Biology's dry future", Science 342, 186 (2013)
- EMBnet, A Quick Guide to UNIX
- NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", Nucleic Acids Res. 41, D8 (2013)
- The UniProt Consortium, "Update on activities at the Universal Protein Resource (UniProt) in 2013", Nucleic Acids Res. 41, D43 (2013)
- P. Flicek et al., "Ensembl 2013", Nucleic Acids Res. 41, D48 (2013)
- P.W. Rose et al., "The RCSB Protein Data Bank: new resources for research and education", Nucleic Acids Res. 41, D475 (2013)
- P.J.A. Cock et al., "Biopython: freely available Python tools for computational molecular biology and bioinformatics", Bioinformatics 25, 1422 (2009)
- A.M. Waterhouse et al., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", Bioinformatics 25, 1189 (2009)
- G.M. Boratyn et al., "BLAST: a more efficient report with usability improvements", Nucleic Acids Res. 41, W29 (2013)
- J.-F. Taly et al., "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", Nat. Protoc. 6, 1669 (2011)
- L. Bordoli et al., "Protein structure homology modeling using SWISS-MODEL workspace", Nat. Protoc. 4, 1 (2009)
- J. Carlsson et al., "Ligand discovery from a dopamine D3 receptor homology model and crystal structure", Nat. Chem. Biol. 7, 769 (2011)
- J. Paulsen et al., "Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements", Nucleic Acids Res. 41, 5164 (2013)
- R.M. Kuhnet al., "The UCSC genome browser and associated tools", Brief. Bioinform. 14, 144 (2013)
- J. Goecks et al., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", Genome Biol. 11, R86 (2010)
- G.K. Sandve et al., "Ten Simple Rules for reproducible computational Research", PLoS Comput. Biol. 9, e1003285 (2013)
- G.K. Sandve et al., "The Genomic HyperBrowser: an analysis web server for genome-scale data", Nucleic Acids Res. 41, W133 (2013)
- A. Altmann et al.,l "A beginners guide to SNP calling from high-throughput DNA-sequencing data", Hum. Genet. 131, 1541 (2012)
- N. Nagarajan & M. Pop, "Sequence assembly demystified", Nat. Rev. Genet. 14, 157 (2013)
- D.W. Huang et al., "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", Nat. Protoc. 4, 44 (2009)
- ...
- More articles may still appear on this list!