Papers

Peer-reviewed articles & research

User Experience Design

  • Cham JA & Costa K (2017) UX design: maximising the value of scientific software in life science R&D Drug Discovery World July 2017 Issue, page 58
  • Koscielny G, et al. (2016) Open Targets: a platform for therapeutic target identification and validation, Nucleic Acids ResearchDOI: 10.1093/nar/gkw1055
  • de Matos P, Cham JA, Cao H, Alcántara R, Rowland F, Lopez R and Steinbeck C (2013) Enzyme Portal: a case study in applying user-centred design methods in bioinformatics BMC Bioinformatics 14:103
  • Alcántara R, Onwubiko J, Cao H, de Matos P, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O’Donovan C, Martín M, Thornton JM and Steinbeck C (2012) The EBI Enzyme Portal Nucleic Acids Research 41(Database issue):D773-80

Me, Katrina Pavelin and Paula de Matos (main co-authors of the Plos Computational Biology article on user-centred design in bioinformatics)

Bioinformatics (aka computing for life science research)

  • [Provided sketchnotes in:] Brazas et al (2014) A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences PLoS Computational Biology DOI: 10.1371/journal.pcbi.1003510
  • Cham (Mead) JA, Bianco L and Bessant C (2010) Free computational resources for designing selected reaction monitoring (SRM) transitions. Proteomics 10(6):1106-26
  • Cham (Mead) JA, Bianco L and Bessant C (2010) Mining proteomic MS/MS data for MRM transitions. Methods in Mol. Biol. 2010;604:187-99
  • Cham JA, Bianco, L, Barton C and Bessant C (2010) MRMaid-DB: a public repository for published SRM transitions. Journal of Proteome Research 9(1):620-5
  • Bianco L, Mead JA and Bessant C (2009) Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS datasets. Journal of Proteome Research 8:1782-1791
  • Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond N and Bessant C (2009) MRMaid: the web-based tool for design of multiple reaction monitoring (MRM) transitions , Mol Cell Proteomics 8(4):696-705
  • Mead JA, Bianco L and Bessant C (2009) Recent developments in public proteomic MS repositories and pipelines. Proteomics 9(4):861-881
  • Mead JA, Shadforth IP and Bessant C (2007) Public proteomic MS repositories and pipelines: available tools and biological applications Proteomics 7(16): 2769-86
  • Mead JA and Shadforth IP (2007) Bringing protein identifications to the masses. Institute of Biology, Biologist 54:200-206[links to PDF]
  • In Conference Proceedings: Mead JA, Bianco L and Bessant C (2008) Using Bioinformatics to Increase Speed and Reduce Uncertainty in Protein Biomarker Discovery. Cranfield Multi-Strand Conference Proceedings (6-7th May, 2008), 35, Cranfield University Press
  • Ernst, W., Trummer, E., Mead, J.., Bessant, C., Strelec, H., Katinger, H. And Hesse, F. (2006) Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant CHO cells. Biotechnology Journal 1: 639–650 

 

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