Additional curriculum

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THIS IS THE LIST FOR 2013. IT WILL BE UPDATED IN 2014!

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. 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. 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)

This is the final list. No articles will be added to the list now.

Other good articles (not curriculum)

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