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.
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.
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.
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.