Dr David Johnson
BSc (Hons), MSc (Dist), PhD

Senior Researcher and Research Software Engineer


Dr Johnson is a Senior Researcher in the Oxford e-Research Centre and a Junior Research Fellow at Kellogg College. His work concerns the development of data infrastructure to support data-intensive research in the life, natural, and biomedical sciences, currently working on the ISA metadata framework for describing scientific experiments. From 2013 to 2015 David was a Research Associate in Computing and Data Science at Imperial College, where he was one of the founding members of the Imperial Data Science Institute; from 2010 to 2013 he was a postdoctoral researcher in the Department of Computer Science at Oxford. David was awarded a PhD in Computer Science from the University Reading in 2010 for his work on peer-to-peer (P2P) software in limited capability mobile phones.

David is an award-winning educator having won a University of Oxford MPLS Division Teaching Award in 2016, and provides teaching support for Oxford’s Software Engineering Programme in a number of subject areas.

Read a Q&A with Dr Johnson.

Selected publications

  1. Interoperable and Scalable Metabolomics Data Analysis with Microservices, Payam Emami Khoonsari, Pablo Moreno, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Steffen Neumann, Kristian Peters, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly Selivanov, Etienne A. Thévenot, Michael van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima and Ola Spjuth. In review, preprint on bioRxiv. Get PDF
  2. Teaching Agile Methods to Software Engineering Professionals: 10 Years, 1000 Release Plans, Angela Martin, Craign Anslow and David Johnson. In Proceedings of the International Conference on Agile Software Development (XP2017), 2017. Springer. DOI: 10.1007/978-3-319-57633-6_10.1 Get PDF
  3. COPO - Linked Open Infrastructure for Plant Data, Felix Shaw, Anthony Etuk, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, David Johnson, Paul Kersey, Ruth Bastow, Susanna Sansone, Vicky Schneider and Rob Davey. In Proceeedings of the International Conference on Semantic Web Applications and Tools for the Life Sciences (SWAT4LS), 2015. Get PDF
  4. Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes, David Johnson, James Osborne, Zhihui Wang and Kostas Marias. In Cancer Informatics, 2016. DOI: 10.4137/CIN.S37982 Get PDF
  5. The Role of Markup for Enabling Interoperability, Steve McKeever and David Johnson. In Frontiers in Computational Physiology and Medicine, 2015. DOI: 10.3389/fphys.2015.00152 Get PDF
  6. Optimising Parallel R Correlation Matrix Calculations on Gene Expression Data Using MapReduce, Shicai Wang, Ioannis Pandis, David Johnson, Ibrahim Emam, Florian Guitton, Axel Oehmichen and Yike Guo. In BMC Bioinformatics, 2014. DOI: 10.1186/s12859-014-0351-9 Get PDF
  7. Semantically Linking In Silico Cancer Models, David Johnson, Anthony J. Connor, Steve McKeever, Thomas S. Deisboeck, Zhihui Wang, Tom Quasier and Eliezer Shochat. Invited paper; in Cancer Informatics, 2014. DOI: 10.4137/CIN.S13895 Get PDF
  8. High Dimensional Biological Data Retrieval Optimization with NoSQL Technology, Shicai Wang, Ioannis Pandis, Chao Wu, Sijin He, David Johnson, Ibrahim Emam, Florian Guitton and Yike Guo. Invited paper; In BMC Genomics, 2014. DOI: 10.1186/1471-2164-15-S8-S3 Get PDF
  9. Web-based Workflow Planning Platform Supporting the Design and Execution of Complex Multiscale Cancer Models, Vangelis Sakkalis, Stelios Sfakianakis, Eleftheria Tzamali, Kostas Marias, Georgios Stamatakos, Fay Misichroni, Eleftherios Ouzounoglou, Eleni Kolokotroni, Dimitra Dionysiou,David Johnson, Steve McKeever, and Norbert Graf. In IEEE Journal of Biomedical and Health Informatics, 2014. DOI: 10.1109/JBHI.2013.2297167 Get PDF
  10. Dealing with Diversity in Computational Cancer Modeling, David Johnson, Steve McKeever, Georgios Stamatakos, Dimitra Dionysiou, Norbert Graf, Vangelis Sakkalis, Kostas Marias, Zhihui Wang and Thomas S. Deisboeck. In Cancer Informatics, 2013. DOI: 10.4137/CIN.S11583 Get PDF

Read by some of David's blog posts on ISA at http://www.isa-tools.org/author/djcomlab/