In bioinformatics, I am developing tools for managing and studying various kinds of 'omics data, as well as tools for de novo genome assembly and NGS data processing. I have worked with mRNA and microRNA microarray data, RNA-seq data, and de novo DNA assembly.

In computer science, I am interested in programming languages (virtual machines, modular static analysis, code synthesis), type systems, semantic web/linked data, low-level systems programming.

I am curious about the tension at the boundaries of formal models (including but not limited to software), which arises as a result of the models' interaction with, and anchoring in, the outside world. I believe that ideas from continental philosophy might be fruitfully applied to this area.

Selected publications

Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits et al. Optical and Physical Mapping with Local Finishing Enables Megabase-Scale Resolution of Agronomically Important Regions in the Wheat Genome. Genome Biology 2018 (19:112), accepted 9 July 2018.
Johan Nyström-Persson, Yayoi Natsume-Kitatani, Yoshinobu Igarashi, Daisuke Satoh and Kenji Mizuguchi. Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates. Sci Rep. 2017 May 3;7(1):1390. May 2017.
Rudi Appels, Johan Nyström-Persson, Hollie Webster and Gabriel Keeble-Gagnère. Discoveries and Advances in Plant and Animal Genomics. In Functional and Integrative Genomics 15(2), published March 2015.
Yi-An Chen, Lokesh P. Tripathi, Benoit H. Desailly, Johan Nyström-Persson, Shandar Ahmad and Kenji Mizuguchi. Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation. In PLOS ONE, published June 11, 2014.
Johan Nyström-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, and Kenji Mizuguchi.
Toxygates: Interactive Toxicity Analysis on a Hybrid Microrray and Linked Data Platform
In Bioinformatics, accepted 9 Sep 2013.
Gabriel Keeble-Gagnère, Johan Nyström-Persson, Matthew I Bellgard, and Kenji Mizuguchi.
An Open Framework for Extensible Multi-Stage Bioinformatics Software
In proceedings of the 7th International Conference on Pattern Recognition in Bioinformatics (PRIB) 2012, Tokyo, Japan. (This paper is about the Friedrich framework). (Slides)
Johan Nyström-Persson.
Extending the Java Programming Language for Evolvable Component Integration.
Ph.D. Thesis. University of Tokyo, Japan. March 2012. (Slides)
Johan Nyström-Persson and Shinichi Honiden.
Poplar: Java Composition with Labels and AI Planning.
In proceedings of the workshop on Free Composition (FREECO) at Onward! 2011. October 2011, Portland, Oregon. (This is a shorter, revised version of the paper below). (Slides)
Andrew M. Cheadle, A. J. Field, J. W. Ayres, N. Dunn, R. A. Hayden, J. Nyström-Persson.
Visualising dynamic memory allocators.
ACM International Symposium of Memory Management 2006: 115-125


Hypercut - an experimental tool for indexing and analysing short read NGS data.

Panomicon/Toxygates - an interactive data viewer and analysis framework for Open TG-GATEs, a large toxicogenomics microarray dataset collected by the Japanese Toxicogenomics Project at NIBIO. Now also applicable for general-purpose multi-omics data analysis.

Friedrich - a software framework for experimental, data intensive bioinformatics.

Poplar - an extended version of the Java language with support for automated component integration using partial order planning. This is mostly of interest to researchers and PL enthusiasts and not ready for general use.

I have made minor contributions to Bioscala but don't have as much time as I'd like for working on it these days.