Genome Informatics Journal has been publishing the accepted papers on International Conference on Genome Informatics (GIW) and International Workshop on Bioinformatics and Systems Biology (IBSB), and it is an official publication of the Japanese Society for Bioinformatics (JSBi). The Board Members of JSBi solicited contributions from all oral presenters in The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010) to this special issue of Genome Informatics. We invited expanded papers based upon the 13 accepted oral presentations in the JSBi2010 Sessions. 6 papers were submitted and peer reviewed. Among them, 5 papers were accepted and published in this special issue of Genome Informatics.