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This shows you the differences between two versions of the page.

--- home [2012/12/24 20:37]
James Smith
+++ home [2015/08/28 12:21] (current)
Christophe Dessimoz
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-====== Reviews in Computational Biology: Assimilate, Write, and Evaluate Reviews======
+====== Assimilate, Write, and Evaluate Reviews======
 ~~NOTOC~~
 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.
@@ Line 23: / Line 22: @@
 ====== Published reviews initiated in this course ======
-The following publications started as student assignment in this course, either at ETH Zurich (2010-2011) or University of Cambridge (2012):
+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]])
@@ Line 29: / Line 28: @@
   -  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 (2012), //in press//, ([[http://www.sciencedirect.com/science/article/pii/S1359644612002735|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), //in press//, ([[http://pubs.acs.org/doi/pdf/10.1021/pr300276f|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, accepted ([[http://topicpages.ploscompbiol.org/wiki/Approximate_Bayesian_computation|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, Springer Humana, to appear ([[http://arxiv.org/abs/1211.2160|arXiv]])
+  - 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]])