1. Interoperable and scalable data analysis with microservices: Applications in Metabolomics Kultima, Kim, Emami Khoonsari, Payam, Herman, Stephanie, Gonzalez-Beltran, Alejandra, Johnson, David, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Vliet, Michael, Hankemeier, Thomas, Ruttkies, Christoph, Schober, Daniel, Peters, Kristian, Neumann, Steffen, Zanetti, Gianluigi, Pireddu, Luca, Thévenot, Etienne A, Roger, Pierrick, Sadawi, Noureddin, Salek, Reza M, Haug, Kenneth, Kale, Namrata, Moreno, Pablo, He, Sijin, Steinbeck, Christoph, Rueedi, Rico, Bergmann, Sven, Burman, Joachim, Capuccini, Marco, Carone, Matteo, Spjuth, Ola, Larsson, Anders, Foguet, Carles, Cascante, Marta, Atauri, Pedro, and Selivanov, Vitaly 2019 [Abs]
  2. "Why did you do that?": Explaining black box models with Inductive Synthesis Paçacı, Görkem, Johnson, David, McKeever, Steve, and Hamfelt, Andreas arXiv 2019
  3. COPO: a metadata platform for brokering FAIR data in the life sciences Etuk, Anthony, Shaw, Felix, Gonzalez-Beltran, Alejandra, Johnson, David, Laporte, Marie-Angélique, Rocca-Serra, Philippe, Arnaud, Elizabeth, Devare, Medha, Kersey, Paul J, Sansone, Susanna-Assunta, and others, BioRxiv 2019


  1. PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud Peters, Kristian, Bradbury, James, Bergmann, Sven, Capuccini, Marco, Cascante, Marta, Atauri, Pedro, Ebbels, Tim, Foguet, Carles, Glen, Robert, Gonzalez-Beltran, Alejandra, and others, GigaScience 2018 [Abs]
  2. Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud Moreno, Pablo, Pireddu, Luca, Roger, Pierrick, Goonasekera, Nuwan, Afgan, Enis, Beek, Marius, He, Sijin, Larsson, Anders, Ruttkies, Christoph, Schober, Daniel, and others, bioRxiv 2018


  1. Teaching agile methods to software engineering professionals: 10 years, 1000 release plans Martin, Angela, Anslow, Craig, and Johnson, David In International Conference on Agile Software Development 2017


  1. The role of markup for enabling interoperability in health informatics McKeever, Steve, and Johnson, David Frontiers in physiology 2015
  2. Creating a Chemistry of Sciences with Big Data: Building the Data Science Institute at Imperial College London Guo, Y, and Johnson, D In 2014 ASE BigData Science/Social Computing Conference, Tsinghua University, Beijing, China, August 4-7, 2014 2015
  3. Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes Johnson, David, Osborne, James, Wang, Zhihui, and Marias, Kostas Cancer Informatics 2015


  1. Web-based workflow planning platform supporting the design and execution of complex multiscale cancer models Sakkalis, Vangelis, Sfakianakis, Stelios, Tzamali, Eleftheria, Marias, Kostas, Stamatakos, Georgios, Misichroni, Fay, Ouzounoglou, Eleftherios, Kolokotroni, Eleni, Dionysiou, Dimitra, Johnson, David, and others, IEEE journal of biomedical and health informatics 2014
  2. Optimising parallel R correlation matrix calculations on gene expression data using MapReduce Wang, Shicai, Pandis, Ioannis, Johnson, David, Emam, Ibrahim, Guitton, Florian, Oehmichen, Axel, and Guo, Yike BMC bioinformatics 2014
  3. DSIMBench: A benchmark for microarray data using R Wang, Shicai, Pandis, Ioannis, Emam, Ibrahim, Johnson, David, Guitton, Florian, Oehmichen, Axel, and Guo, Yike In Workshop on Big Data Benchmarks, Performance Optimization, and Emerging Hardware 2014
  4. Semantically Linking In Silico Cancer Models Johnson, D, Connor, AJ, McKeever, S, Deisboeck, TS, Wang, Z, Quasier, T, and Shochat, E Cancer Informatics 2014
  5. High dimensional biological data retrieval optimization with NoSQL technology Wang, Shicai, Pandis, Ioannis, Wu, Chao, He, Sijin, Johnson, David, Emam, Ibrahim, Guitton, Florian, and Guo, Yike BMC genomics 2014


  1. Abstraction in physiological modelling languages McKeever, Steve, Gill, Mandeep, Connor, Anthony, and Johnson, David In SCS SpringSim 2013 2013
  2. Mobile support in CSCW applications and groupware development frameworks Johnson, David International Journal of Interactive Mobile Technologies (iJIM) 2013
  3. Dealing with diversity in computational cancer modeling Johnson, David, McKeever, Steve, Stamatakos, Georgios, Dionysiou, Dimitra, Graf, Norbert, Sakkalis, Vangelis, Marias, Konstantinos, Wang, Zhihui, and Deisboeck, Thomas S Cancer informatics 2013
  4. Connecting digital cancer model repositories with markup: introducing TumorML version 1.0 Johnson, David, McKeever, Steve, Deisboeck, Thomas S, and Wang, Zhihui ACM SIGBioinformatics Record 2013


  1. Modular markup for simulating vascular tumour growth Johnson, David, Connor, Anthony J, and McKeever, Steve In 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (5th IARWISOCI) 2012
  2. Pervading collaborative learning with mobile devices Johnson, David, and Bhana, Ismail M 2012
  3. The TUMOR project: integrating cancer model repositories for supporting predictive oncology Sakkalis, Vangelis, Marias, K, Stamatakos, G, Misichroni, F, Dionysiou, D, McKeever, S, Johnson, D, Deisboeck, TS, and Graf, N Abstract Booklet for VPH2012 Integrative Approaches to Computational Biomedicine 2012


  1. TumorML: Concept and requirements of an in silico cancer modelling markup language Johnson, David, Cooper, Jonathan, and McKeever, Steve In Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE 2011
  2. The case for using markup for biomechanical modelling Johnson, David, and McKeever, Steve In XXIII Congress of the International Society of Biomechanics 2011


  1. Markup languages for in silico oncology Johnson, David, Cooper, Jonathan, and McKeever, Steve In 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (4th IARWISOCI) 2010
  2. mico: a framework for developing groupware for a diverse mobile environment Johnson, David 2010


  1. A middleware independent grid workflow builder for scientific applications Johnson, David, Meacham, Ken, and Kornmayer, Harald In 5th IEEE International Conference on e-Science Workshops 2009
  2. A lightweight supercomputing web portal for inferring phylogenetic trees Johnson, David, Meade, Andrew, and Alexandrov, Vassil N In 5th IEEE International Conference on e-Science Workshops 2009
  3. A platform for supporting micro-collaborations in a diverse device environment Johnson, David International Journal of Interactive Mobile Technologies (iJIM) 2009


  1. Creating mobile ePortfolios on mobile web servers Johnson, David In 10th Interactive Computer-aided Learning Conference 2007
  2. kXML- RPC Enables Service- Oriented Mobile Computing Gabhart, Kyle, and Johnson, David 2007


  1. Developing collaborative social software Bhana, Ismail, and Johnson, David Computational Science - ICCS 2006 2006
  2. Next generation e-learning: enabling the creation of effective information technology mediated educational programs Alexandrov, NS, Ramirez, R, Alexandrov, VN, Ramsay, P, Jamieson, R, Haffegee, A, Al-Khalifah, A, Johnson, D, Bhana, IM, Espindola, G, and others, In 9th Interactive Computer-aided Learning Conference 2006
  3. Aiming for ultra-scalable ePortfolio distribution using peer-to-peer networks Johnson, D, and Bhana, I In 4th EIfEL International ePortfolio Conference 2006
  4. Omnipresent ePortfolio activity enabled by a mobile applet and synchronisation service Johnson, D In ePortfolio 2006: Fourth International ePortfolio Conference 2006


  1. A peer-to-peer approach to content dissemination and search in collaborative networks Bhana, Ismail, and Johnson, David Computational Science - ICCS 2005 2005
  2. Knowledge management for collaborative learning Bhana, Ismail M, and Johnson, David In 8th Interactive Computer-aided Learning Conference 2005
  3. The e-learning grid: integrating e-pedagogy with novel technologies Alexandrov, Nia S, Alexandrov, Vassil N, Bhana, Ismail M, and Johnson, David In 8th Interactive Computer-aided Learning Conference 2005
  4. Harnessing mobile technology for classroom learning Johnson, David, Bhana, Ismail M, and Urmetzer, Florian In 8th Interactive Computer-aided Learning Conference 2005


  1. The e-learning grid: peer-to-peer approach Alexandrov, Vassil, Alexandrov, Nia, Bhana, Ismail, and Johnson, David 2004
  2. Supporting ad hoc collaborations in peer-to-peer networks Bhana, Ismail, Johnson, David, and Alexandrov, Nia S. In ISCA 17th International Conference on Parallel and Distributed Computing Systems 2004