Difference between revisions of "Additional curriculum"
From projects/clsi
Jonkl@uio.no (talk | contribs) |
Jonkl@uio.no (talk | contribs) |
||
| Line 10: | Line 10: | ||
*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/gks1189 Nucleic Acids Res. '''41''', D8 (2013)] | *NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gks1189 Nucleic Acids Res. '''41''', D8 (2013)] | ||
| − | *The UniProt Consortium, "Update on activities at the Universal Protein Resource (UniProt) in 2013", [http://dx.doi.org/10.1093/nar/gks1068 Nucleic Acids Res.''' | + | *The UniProt Consortium, "Update on activities at the Universal Protein Resource (UniProt) in 2013", [http://dx.doi.org/10.1093/nar/gks1068 Nucleic Acids Res. '''41''', D43 (2013)] |
*P. Flicek ''et al.'', "Ensembl 2013", [http://dx.doi.org/10.1093/nar/gks1236 Nucleic Acids Res. '''41''', D48 (2013)] | *P. Flicek ''et al.'', "Ensembl 2013", [http://dx.doi.org/10.1093/nar/gks1236 Nucleic Acids Res. '''41''', D48 (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. '''41''', 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. '''41''', 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 '''25''', 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 '''25''', 1422 (2009)] | ||
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics '''25''', 1189 (2009)] | *A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics '''25''', 1189 (2009)] | ||
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. '''41''', W29 (2013)] | *G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 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", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. '''6''', 1669 (2011)] | *J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. '''6''', 1669 (2011)] | ||
| − | *L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc.''' | + | *L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. '''4''', 1 (2009)] |
*J. Carlsson'' et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. '''7''', 769 (2011)] | *J. Carlsson'' et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. '''7''', 769 (2011)] | ||
| − | *J. Paulsen ''et al.,'' "Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements", | + | *J. Paulsen ''et al.,'' "Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements", [http://dx.doi.org/10.1093/nar/gkt227 Nucleic Acids Res. '''41''', 5164 (2013)] |
| − | *R.M. Kuhn'' | + | *R.M. Kuhn'' et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 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", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. '''11''', R86 (2010)] | *J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. '''11''', R86 (2010)] | ||
| − | *G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", | + | *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)] | ||
| − | *N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. | + | *N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. '''14''', 157 (2013)] |
| − | *... | + | *... |
| − | + | *More articles may still appear on this list! | |
| − | *More articles | ||
Revision as of 14:46, 8 November 2013
Back to main page
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. 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)
- ...
- More articles may still appear on this list!
