Peer-reviewed papers, reviews & articles

• Karamanis et al (2018) Designing an intuitive web application for drug discovery scientists Drug Discovery Today https://doi.org/10.1016/j.drudis.2018.01.032
• 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
• Karamanis et al (2017) Designing an intuitive scientific web resource using lean user experience methods Pre-print paper at http://www.biorxiv.org/content/early/2017/07/27/169193 doi: https://doi.org/10.1101/169193
• Koscielny G et al. (2016) Open Targets: a platform for therapeutic target identification and validation, Nucleic Acids Research. DOI: 10.1093/nar/gkw1055
• Squizzato S et al (2015) The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI Nucleic Acids Research DOI: 10.1093/nar/gkv316
• Pavelin K, Pundir S and Cham JA (2014) Ten Simple Rules for Running Interactive Workshops. PLoS Computational Biology DOI: 10.1371/journal.pcbi.1003485
• 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 et al (2012) The EBI Enzyme Portal Nucleic Acids Research 41(Database issue):D773-80
• Pavelin K, Cham JA, de Matos P, Brooksbank C, Cameron G and Steinbeck C (2012) Bioinformatics meets user-centred design: a perspective PLoS Computational Biology 8(7): e1002554

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