Difference between revisions of "Additional curriculum"

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Back to [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2013 main page]
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Back to [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2015 main page]
  
=== Required reading material for the course  ===
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'''''THIS IS THE FINAL LIST. THERE WILL BE NO CHANGES!'''''
  
'''''This list is not yet finished!'''''
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=== 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:  
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The following articles/reviews/written material '''''is part of the curriculum''''' for MBV-INF4410 and MBV-INF9410:
  
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science '''342''', 186 (2013)]  
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*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]  
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*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)]  
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*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, "Update on activities at the Universal Protein Resource (UniProt) in 2013", [http://dx.doi.org/10.1093/nar/gks1068 Nucleic Acids Res.'''&nbsp;41''', D43 (2013)]
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*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 2013", [http://dx.doi.org/10.1093/nar/gks1236 Nucleic Acids Res. '''41''', D48 (2013)]  
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*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. '''41''', D475 (2013)]
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*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 '''25''', 1422 (2009)]  
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*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)]
*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)]  
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*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 <b>25</b>, 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)]  
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*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, 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)]  
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*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. <b>6</b>, 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.'''&nbsp;4''', 1 (2009)]&nbsp;
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*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]
*J. Carlsson''&nbsp;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)]
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*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. <b>7</b>, 769 (2011)]
*J. Paulsen&nbsp;''et al.,'' "Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements",&nbsp;[http://dx.doi.org/10.1093/nar/gkt227 Nucleic Acids Res.&nbsp;'''41''', 5164 (2013)]  
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*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]
*R.M. Kuhn''&nbsp; et al.'', "The&nbsp;UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform.&nbsp;'''14''', 144 (2013)]&nbsp;
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*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. <b>11</b>, 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)]  
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*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research",&nbsp; [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. '''9''', e1003285 (2013)]  
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*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. <b>41</b>, 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)]  
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*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]
*N. Nagarajan &amp; M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet.&nbsp;'''14''', 157 (2013)]&nbsp;
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*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]
*...  
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*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]
*CASP10 report
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*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]
*More articles will appear on this list!
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=== Other good articles (''not ''curriculum) ===
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*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]

Latest revision as of 14:01, 2 December 2015

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THIS IS THE FINAL LIST. THERE WILL BE NO CHANGES!

Required reading material for the course

The following articles/reviews/written material is part of the curriculum for MBV-INF4410 and MBV-INF9410:

Other good articles (not curriculum)