BiclusterMiner is a biclustering tool written in Java programming language. It provides a fast solution for finding all biclusters within a discretized data matrix. The method is capable of distinguishing oppositely changing values within the data. There are three available formats for input data, allowed values including 1,0 and -1.

We are thankful for the financial support provided by TAMOP-4.2.2/B-10/1-2010-0025 project. The following people have been involved in the development of BiclusterMiner:

  • Andras Kiraly
  • Asta Laiho
  • Janos Abonyi
  • Attila Gyenesei

For citation please use the following reference:

Kiraly A, Laiho A, GYENESEI A. Biclustering of high-throughput gene expression data with BiclusterMiner. IEEE International Conference on Data Mining, Co-clustering and Applications. Brussels, December 2012.

Contact: attila.gyenesei at

Quick Download and running guide

You can download BiclusterMiner, sample data sets and the supplementary data for the related publication from here:

  • BiclusterMiner program package: BiclusterMiner
  • Sample data1 (StemCell data with 9 conditions, containing {0,1}): SampleData1
  • Sample data2 (StemCell data with 9 conditions, containing {-1,0,1}): SampleData2
  • Sample configuration file (running without GUI): IniFile
  • Supplementary data for the related publication: SupplementaryData
  • Additional supplementary data files for the related publication: SupplementaryDataFiles
After downloading and unpacking the program package, the program with a graphical user interface (GUI) can be run by double-clicking on the executable ‘BiclusterMiner.jar’ file, or typing the following command to the command line:

java -Xmx1024M -jar BiclusterMiner.jar

Use the ‘Browse’ buttons to specify the path of the necessary files. After setting the required parameters (default values are appropriate in most cases), the data has to be loaded by clicking the ‘Load data’ button, and the mining process will start by clicking on ‘Run BiclusterMiner’ button.

Please see the tutorial for short usage examples or the user guide for a comprehensive explanation.


1University of Pannonia, Department of Process Engineering, P.O. Box 158 Veszprém H-8200, Hungary
2Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.