The University of Tokyo · Biochemistry, Genetics and Molecular Biology
Professor Shinichi Morishita's research lab specializes in computational biology and bioinformatics, focusing on the analysis of genomic variation and its functional implications. The lab investigates the relationship between DNA sequence variation, chromatin structure, and gene regulation, particularly through long-read sequencing and population genomic approaches. Key research directions include understanding centromeric repeat diversity, identifying structural variants in complex genomic regions, and exploring the evolutionary dynamics of higher-order repeats across human populations. The lab also applies statistical and algorithmic methods to mine biological data, such as association rules in genomics and the functional effects of pharmacological agents on cardiac and respiratory systems.
Figures are computed from collected data and may differ slightly.
We study how to efficiently compute significant association rules according to common statistical measures such as a chi-squared value or correlation coefficient. For this purpose, one might consider to use of the Apriori algorithm, but the algorithm needs major conversion, because none of these statistical metrics are anti-monotone, and the use of higher support for reducing the search space cannot guarantee solutions in its the search space. We here present a method of estimating a tight upper
Might DNA sequence variation reflect germline genetic activity and underlying chromatin structure? We investigated this question using medaka (Japanese killifish, Oryzias latipes), by comparing the genomic sequences of two strains (Hd-rR and HNI) and by mapping approximately 37.3 million nucleosome cores from Hd-rR blastulae and 11,654 representative transcription start sites from six embryonic stages. We observed a distinctive approximately 200-base pair (bp) periodic pattern of genetic variati
The cardiotonic and arrhythmogenic effects, and the excitatory effect on respiration of "Kyushin," a drug containing toad venom, were studied in comparison with those of digoxin. In anesthetized rabbits, the maximum rate of rise of left ventricular systolic pressure (max dP/dt) was measured as an index of cardiotonic effect, and the respiratory flow was measured as an index of respiratory function. Intraduodenal (i.d.) administration of 80 mg/kg "Kyushin" produced a cardiotonic effect and an exc
Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations including a Han Chinese trio and 21 Japanese. We revealed substantial structural diversity with many previously unidentified variant higher-order repeats specific to individuals charac
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