Additional curriculum

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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)
• P. Flicek et al., "Ensembl 2013", Nucleic Acids Res. 41, D48 (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. Kuhn  et 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)
• N. Nagarajan & M. Pop, "Sequence assembly demystified", Nat. Rev. Genet. 14, 157 (2013) 
• ...
• CASP10 report
• More articles will appear on this list!