Additional curriculum

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THIS IS NOT THE FINAL LIST AND IT IS NOT YET UPDATED IN 2015. THERE WILL BE CHANGES!

Required reading material for the course

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. 43, D6 (2015)
• The UniProt Consortium, "UniProt: a hub for protein information", Nucleic Acids Res. 43, D204 (2015)
• P. Flicek et al., "Ensembl 2015", Nucleic Acids Res. 43, D662 (2015)
• 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)
• 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)
• M.L. Mertzker, "Sequencing technologies - the next generation", Nat. Rev. Genet. 11, 31 (2010)
• A. Altmann et al., "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)

Other good articles (not curriculum)

• Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", Nat. Rev. Genet. 13, 303 (2012)