In bioinformatics, I am developing tools for studying microarray data (in the context of toxicogenomics) and RNA-seq data, as well as tools for de novo genome assembly and NGS data processing (in the context of wheat genomics).

In computer science, I am interested in programming languages (virtual machines, modular static analysis, code synthesis).

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)
Johan Nyström-Persson and Shinichi Honiden.
Poplar: A Java Extension for Evolvable Component Integration.
Available on the ArXiv. June 2011. Unreviewed.
Levent Gürgen, Johan Nyström-Persson, Amin Cherbal, Cyril Labbé, Claudia Roncancio, Shinichi Honiden.
Service-oriented Middleware for Dynamic Management of Heterogeneous Sensing Devices.
In proceedings of the 7th ACM International Conference on Pervasive Services (ICPS 2010). July 13-15 2010.
Levent Gürgen, Johan Nyström-Persson, Amin Cherbal, Cyril Labbé, Claudia Roncancio, Shinichi Honiden.
Plug&Manage Heterogeneous Sensing Devices.
(Demonstration) In proceedings of the 6th International Workshop on Data Management for Sensor Networks (DMSN 2009), in conjunction with VLDB 2009. August 2009. Lyon, France.
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


Tritigate - an 'omics platform for wheat data. In beta, not currently under active development.

Toxygates - an interactive data viewer and analysis framework for Open TG-GATEs, a massive toxicogenomics microarray dataset collected by the Japanese Toxicogenomics Project at NIBIO.

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.

JTronic - a game designed for programming competitions. I was part of a team that developed this for the ACM/ICPC regional Asia contest 2011.