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.

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

A more complete list may be available at Google Scholar.
Johan Nyström-Persson, Gabriel Keeble-Gagnère, and Niamat Zawad. Compact and evenly distributed k-mer binning for genomic sequences. Bioinformatics, accepted 3 March 2021.
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.
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)
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

Software

Discount - a tool for k-mer counting on Spark.

Panomicon/Toxygates - an interactive data viewer and analysis framework for Open TG-GATEs, and for general multi-omics and network data analysis. Developed jointly by a team at Lifematics and NIBIOHN.

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