Difference between revisions of "Additional curriculum"
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*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX] | *EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX] | ||
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)] | *NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)] | ||
| − | *The UniProt Consortium, " | + | *The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)] |
| − | *P. Flicek ''et al.'', "Ensembl | + | *P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)] |
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)] | *P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)] | ||
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)] | *P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)] | ||
Revision as of 15:02, 28 October 2015
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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)
