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| - | ====== Reviews in Computational Biology: Assimilate, Write, and Evaluate Reviews====== | + | ====== Assimilate, Write, and Evaluate Reviews====== |
| ~~NOTOC~~ | ~~NOTOC~~ | ||
| - | Welcome to the course homepage of //Review in Computational Biology//, which will take place at DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge during **Lent Term 2012**. | + | Welcome to the course homepage of //Review in Computational Biology//, which will take place at Cambridge Computational Biology Institute, Centre for Mathematical Sciences, Wilberforce Road, Cambridge during **Lent Term 2013**. |
| - | + | The aim of this course is to develop two critical skills for research: the ability to identify relevant questions from the scientific literature and effective scientific writing. In addition, it introduces students to the process of publishing and peer reviewing of manuscripts. Every week, the course reviews a current research topic in computational biology. Each student will write one review, and provide two reports on colleagues' written work. | |
| - | This course mainly aims at developing two critical skills for research: the ability to identify relevant questions from the scientific literature and effective scientific writing. In addition, it introduces students to the process of peer reviewing. Every week, the course reviews a current computational biology research topic. Each student will write one review, and provide two reports on colleagues' written work. | + | |
| ^Lecturers | [[http://christophe.dessimoz.org/research|Christophe Dessimoz]] and [[mailto:js252@cam.ac.uk|James Smith]] | | ^Lecturers | [[http://christophe.dessimoz.org/research|Christophe Dessimoz]] and [[mailto:js252@cam.ac.uk|James Smith]] | | ||
| - | ^Target Group | 1st and 2nd-year PhD Students (and interested Masters, Part III and 4th-year undergraduates) | | + | ^Students | 1st and 2nd-year PhD Students | |
| - | ^Lecture Room & Time | Wednesdays during Lent Term, 2pm CCBI Seminar Room, 3pm MR15 (tbc) | | + | ^Lecture Rooms & Times | Every Wednesday Lent Term (Weeks 0 - 9), 14:00 - 15:00 CCBI Seminar in MR4, 15:30 - 16:30 Lecture in MR15 | |
| - | ^Office Hours| Mondays, 9 - 11am and 12 - 2pm (tbc) | | + | ^Supervisions (Tutorials)| **Supervision B** Wednesdays 13:00 – 14:00, **Supervision A** Wednesdays 16:30 – 17:30 | |
| - | ^Course | Pilot Doctoral Training Course | | + | ^Course | Doctoral Training Course Module | |
| ====== Sections ====== | ====== Sections ====== | ||
| * [[Course Details|Course details and policy]] | * [[Course Details|Course details and policy]] | ||
| - | * [[Schedule 2012|Schedule, slides, and assignments]] | + | * [[Schedule 2013|Schedule, slides, and assignments]] |
| * [[http://journals.cbrg.ethz.ch/revcompbiol|Article Management System]] | * [[http://journals.cbrg.ethz.ch/revcompbiol|Article Management System]] | ||
| * [[Instructions for authors]] | * [[Instructions for authors]] | ||
| Line 21: | Line 20: | ||
| * [[Resources| Other Resources & Links]] | * [[Resources| Other Resources & Links]] | ||
| - | ====== News ====== | + | ====== Published reviews initiated in this course ====== |
| - | + | ||
| - | Three reviews from last year (at ETH Zurich, Switzerland) have been submitted (after additional work during the summer) and accepted for publication in [[http://bib.oxfordjournals.org|Briefings in Bioinformatics]] (Oxford Journals): | + | |
| - | * Adam Szalkowski and Christoph Schmid, //Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts//, ([[http://bib.oxfordjournals.org/content/early/2010/11/08/bib.bbq068.full.html?ijkey=JiyuBmNw42pQXxj&keytype=ref|Link]]) | + | |
| - | * Christian Ledergerber and Christophe Dessimoz, //Base-calling for next-generation sequencing platforms//, ([[http://dx.doi.org/10.1093/bib/bbq077|Link]]) | + | |
| - | * Louis du Plessis et al., //The What, Where, How, and Why of Gene Ontology -- A Primer for Bioinformaticians//, ([[http://dx.doi.org/10.1093/bib/bbr002|Link]]) | + | |
| + | The following publications started as student assignment in this course, either at ETH Zurich (2010-2011) or University of Cambridge (2012-2013): | ||
| + | - A Szalkowski and C Schmid, //Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts//, Brief Bioinform (2011) 12 (6): 626-633. ([[http://bib.oxfordjournals.org/content/early/2010/11/08/bib.bbq068.full.html?ijkey=JiyuBmNw42pQXxj&keytype=ref|Link]]) | ||
| + | - C Ledergerber and C Dessimoz, //Base-calling for next-generation sequencing platforms//, Brief Bioinform (2011) 12 (5): 489-497 ([[http://bib.oxfordjournals.org/content/12/5/489.full|Link]]) | ||
| + | - L du Plessis et al., //The What, Where, How, and Why of Gene Ontology -- A Primer for Bioinformaticians//, Brief Bioinform (2011) 12 (6): 723-735 ([[http://dx.doi.org/10.1093/bib/bbr002|Link]]) | ||
| + | - A Altenhoff and C Dessimoz, //Inferring Orthology and Paralogy//, Evolutionary Genomics: Statistical and Computational methods (M Anisimova, Editor), 2012, Springer Humana, Vol. 855, ([[http://www.springerlink.com/content/q7845n48142v8250/?MUD=MP|Link]]) | ||
| + | - F Iorio et al., //Transcriptional data: a new gateway to drug repositioning?//, Drug Discovery Today (2013), 18:7/8, pp350-357, ([[http://www.sciencedirect.com/science/article/pii/S1359644612002735|Link]]) | ||
| + | - D Reker and L Malmström, //Bioinformatic challenges in targeted proteomics//, Journal of Proteome Research (2012), J. Proteome Res., 2012, 11 (9), pp 4393–4402, ([[http://pubs.acs.org/doi/pdf/10.1021/pr300276f|Link]]) | ||
| + | - M Sunnåker et al., //Topic Page: Approximate Bayesian computation//, PLoS Comput Biol (2013), 9:1, e1002803 ([[http://dx.doi.org/10.1371/journal.pcbi.1002803|Link]]) | ||
| + | - S Iantorno, K Gori, et al., //Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment//, Multiple Sequence Alignment Methods (D Russell, Editor), Methods in Molecular Biology, 2014, Springer Humana, Vol. 1079 ([[http://arxiv.org/abs/1211.2160|arXiv]], [[http://dx.doi.org/10.1007/978-1-62703-646-7_4|journal]]) | ||
| + | - Q Ul Ain, A Aleksandrova, FD Roessler and PJ Ballester, //Machine-learning scoring functions to improve structure-based binding affinity | ||
| + | prediction and virtual screening//, WIREs Comput Mol Sci (2015). ([[http://onlinelibrary.wiley.com/doi/10.1002/wcms.1225/pdf|link]]) | ||
| + | - M Ravenhall, N Škunca, F Lasalle, C Dessimoz, //Inferring horizontal gene transfer//, PLOS Computational Biology (2015), 11:5, e1004095 ([[http://dx.doi.org/10.1371/journal.pcbi.1004095]]) | ||