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author:("ransom, Clare")
1.  2010 ISCB Overton Prize Awarded to Steven E. Brenner 
PLoS Computational Biology  2010;6(6):e1000831.
doi:10.1371/journal.pcbi.1000831
PMCID: PMC2891695  PMID: 20585610
3.  ISCB Honors David Haussler and Aviv Regev 
PLoS Computational Biology  2008;4(7):e1000101.
doi:10.1371/journal.pcbi.1000101
PMCID: PMC2536508  PMID: 18795145
4.  A Fugu–Human Genome Synteny Viewer: web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genes 
Nucleic Acids Research  2004;32(8):2618-2622.
A web server has been developed to access annotation and graphical reports of synteny and gene order between the Fugu genome and human genes. In this system, the assembled Fugu genomic sequences (also known as scaffolds) are annotated. The annotations for each Fugu scaffold are computed, stored and made publicly available. The annotations describe matches to human homologous genes. For each significant human gene match on the Fugu scaffold, the corresponding human chromosome map and measures of the significance of each match are given. The web-based server provides public access to these annotations and graphical displays of the results. The user is provided with a selection of views including a chromosome-colour-coded image and a table containing the details of the matches. The Fugu–Human Genome Synteny Viewer has been tested by comparing results with examples from a paper that includes a study of transcription factors, Fos and Jun encoding regions. The Fugu–human genome synteny views are available for each Fugu scaffold through the clonesearch web page located at the Fugu Genomics website (http://fugu.rfcgr.mrc.ac.uk/).
doi:10.1093/nar/gkh573
PMCID: PMC419461  PMID: 15141032
5.  The European Conference on Computational Biology 2002 
doi:10.1002/cfg.256
PMCID: PMC2447376  PMID: 18629090
6.  A Novel Predictive Technique for the MHC Class II Peptide–Binding Interaction 
Molecular Medicine  2003;9(9-12):220-225.
Antigenic peptide is presented to a T-cell receptor through the formation of a stable complex with a Major Histocompatibility Complex (MHC) molecule. Various predictive algorithms have been developed to estimate a peptide’s capacity to form a stable complex with a given MHC Class II allele, a technique integral to the strategy of vaccine design. These have previously incorporated such computational techniques as quantitative matrices and neural networks. We have developed a novel predictive technique that uses molecular modeling of predetermined crystal structures to estimate the stability of an MHC Class II peptide complex. This is the 1st structure-based technique, as previous methods have been based on binding data. ROC curves are used to quantify the accuracy of the molecular modeling technique. The novel predictive technique is found to be comparable with the best predictive software currently available.
PMCID: PMC1430983  PMID: 15208743
7.  CCP11 Group Meeting—Towards the Functional Analysis of Microarrays 
The CCP11 project [2] aims to foster bioinformatics in the UK through conferences, workshops and the provision of Web resources. In March 2002, CCP11 held a meeting in Manchester, UK, on the functional analysis of microarrays. This was part of Manchester BioinformaticsWeek—three consecutive short bioinformatics meetings held in the attractive setting of the Chancellor's Conference Centre at the University of Manchester. The other meetings in the series were a workshop on ontologies and the 12th Annual MASAMB (Mathematical and Statistical Aspects of Molecular Biology) Conference. Many delegates were able to attend more than one meeting, which led to a useful cross-fertilization of ideas across the bioinformatics community. The CCP11 meeting shared with MASAMB a strong emphasis on the statistical analysis and interpretation of data—most often image intensity data.
doi:10.1002/cfg.201
PMCID: PMC2447340  PMID: 18629056

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