Bioinformatics is the information technology to deal with biological data. Recently emerging systems biology has drawn great interest inspired by world-wide efforts for modeling and analyzing biological processes with a systems perspective. Bioinformatics, which has analyzed multi-omics data such as genomics, transcriptomics, and proteomics, and explored novel biological patterns embedded within the data, now has a transition to its application to systems biology, called systems bioinformatics. Systems bioinformatics includes various research areas: system modeling, system structure and dynamics analysis, causality analysis, and multi-omics data fusion. In this review, we introduce bioinformatics for genomics, transcriptomics, proteomics, and systems biology according to the different aspects of biological processes.