The University of Tokyo · Biochemistry, Genetics and Molecular Biology
Professor Kenta Nakai's research lab specializes in computational biology and bioinformatics, focusing on the molecular mechanisms underlying gene regulation, protein subcellular localization, and transcriptional control. The lab develops and maintains key biological databases such as DBTSS and DBKERO, which provide high-resolution transcriptional start site data and functional genomics context for human genome variations, particularly in regulatory regions. Their work integrates experimental genomics with computational modeling to interpret disease-associated mutations and evolutionary conservation in regulatory elements. The lab also investigates physicochemical properties of amino acids and their implications for protein structure and function.
Figures are computed from collected data and may differ slightly.
The relationship among 222 published indices representing various physicochemical and biochemical properties of amino acid residues has been investigated by hierarchical cluster analysis. The clustering result is illustrated by the minimum spanning tree, which is conveniently divided into four regions: alpha and turn propensities, beta propensity, hydrophobicity and other physicochemical properties including, among others, bulkiness of amino acid residues. In addition, several subclasses of hydr
DBTSS is a database of transcriptional start sites, based on our unique collection of precise, experimentally determined 5'-end sequences of full-length cDNAs. Since its first release in 2002, several major updates have been made. In this update, we expanded the human transcriptional start site dataset by 19 million uniquely mapped, and RefSeq-associated, 5'-end sequences, which were generated by a newly introduced Solexa sequencer. Moreover, in order to provide means for interpreting those mass
Since the proposal of the signal hypothesis on protein subcellular sorting, a number of computational analyses have been performed in this field. A typical example is the development of prediction algorithms for the subcellular localization sites of input protein sequences. In this review, we mainly focus on the biological grounds of the prediction methods rather than the algorithmic issues because we believe the former will be more fruitful for future development. Recent advances on the study o
Supplementary data are available at Bioinformatics online.
VCAM-1 expression is higher in the human aorta in patients with atheromatous changes. Furthermore, concentrations of soluble VCAM-1 may provide important information about endothelial activation or in-vivo damage.
DBTSS (Database of Transcriptional Start Sites)/DBKERO (Database of Kashiwa Encyclopedia for human genome mutations in Regulatory regions and their Omics contexts) is the database originally initiated with the information of transcriptional start sites and their upstream transcriptional regulatory regions. In recent years, we updated the database to assist users to elucidate biological relevance of the human genome variations or somatic mutations in cancers which may affect the transcriptional r
Microangioarchitecture of the rat parietal cortex was studied by means of scanning electron microscopy and dark field microscopy. The richest supply of blood vessels in the parietal cortex was found in layer III + IV and layer V, where 2 isolated plexuses of microvessels were prominent. The appearance of the plexuses was quite different between motor and sensory areas. In the motor area the capillary plexuses were narrow and compact, while in sensory area the plexuses were wide and diffuse. Char
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