Kyoto University · Medicine
Professor Ryo Yamada's research lab specializes in systems biology and functional genomics, focusing on the genetic and molecular mechanisms underlying human disease susceptibility. The lab investigates expression quantitative trait loci (eQTLs) and post-translational modifications—particularly citrullination mediated by PADI4—to uncover how genetic variants and protein modifications contribute to complex diseases like rheumatoid arthritis. By integrating high-throughput omics data with statistical and computational approaches, the lab aims to decode the regulatory networks linking genetic variation to phenotypic outcomes. Their work bridges population genetics, molecular pathology, and systems-level data analysis to identify disease mechanisms and potential therapeutic targets.
Figures are computed from collected data and may differ slightly.
Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQ
Omics studies attempt to extract meaningful messages from large-scale and high-dimensional data sets by treating the data sets as a whole. The concept of treating data sets as a whole is important in every step of the data-handling procedures: the pre-processing step of data records, the step of statistical analyses and machine learning, translation of the outputs into human natural perceptions, and acceptance of the messages with uncertainty. In the pre-processing, the method by which to contro
Citrullinated proteins that are produced by enzymatic deimination of arginine residues in proteins by peptidylarginine deiminases (PADIs) are of particular interest in the pathogenesis of rheumatoid arthritis (RA). First, peptidylarginine deiminase type 4 (PADI4) gene, which codes one of the PADI enzyme isotypes, has a genetic variant that increases susceptibility to RA. The RA-susceptible variant of PADI4 seems to increase the risk of RA by increasing its enzymatic activity. Second, this post-t
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