Rintaro Saito's Information Centre
University of California, San Diego, School of Medicine

• Pubmed
• Journal Citation Reports
• citeulike

• NCBI Gene
• UCSC Genome Data
• UniProt
• Inparanoid Eukaryotic Ortholog Groups
• BioGRID Interaction Datasets
• YEASTRACT, hPDI, TRED Transcription Regulatory Networks

• Cytoscape
• R, Rpy2
• NumPy, SciPy
• NetworkX
• DAVID
• Galaxy
• CLUSTER
• Treeview
• Matplotlib
• Maxima
• Sage Mathematics software system
• Enthought Python Distribution

Welcome

Recent development of experimental technologies for molecular biology enabled us to obtain huge amount of information inside a cell. However without proper analyses and interpretation, such information is just a huge mess. Computer can greatly assist us to analyze such information to obtain new insights into life. The research field which aims to understand biological phenomenon throught computational analyses is called bioinformatics. In our bioinformatics researches, our main focuses are DNA Sequences, i.e. Genomic sequences which carry genetic information, RNA sequences, which are shown to have important role in gene regulations, and protein sequences, which have main role in cellular reactions. We are further interested in interactions among them in order to understand how cellular components are organized.

One of our missions is to develop a method to discover novel biological knowledge from these data.

Focus

In a cell, there are huge amount of molecules such as RNAs, proteins and metabolites. They will play a functional role in the cell through interactions with other molecules. To understand a life at molecular level, it is important to understand how the molecules are organized through these interactions. Nowadays, high-throughput experimental methods to comprehensively screen these interactions in the cell (ex. yeast two hybrid, tandem affinity purification, etc.) are available and huge amount of interaction data are produced. The biology focusing on molecular interaction networks inside the cell is called network biology. We conduct researches on network biology to analyze these data in efficient ways to discover novel biological knowledge.

Our laboratory has been developing a software Cytoscape (Cline MS et al. 2007), which is generic platform to integrate, visualize and analyze various types of biological data in terms of networks.

We make the best use of Cytoscape to explore molecular networks in the cell.

Click here to see overview of my research.