Research summary
A high-throughput strategy generated 6,925 S. cerevisiae deletion strains covering 2,026 ORFs (more than one-third of the genome); 17% of the deleted ORFs were essential for viability in rich medium, and parallel phenotyping of more than 500 strains found growth defects in 40% in rich or minimal media [1]. RegulomeDB was developed to annotate functional non-coding variation in personal genomes by integrating regulatory-feature evidence so that GWAS variants outside genes can be interpreted; the tool localises potentially functional variants and supports interpretation of their regulatory effects [2]. The ENCODE project's integrated encyclopedia of DNA elements systematically mapped transcription, transcription-factor association, chromatin structure and histone modification, assigning biochemical function to 80% of the human genome and linking many candidate regulatory elements to expressed genes [3]. RNA-Seq applied to S. cerevisiae produced a high-resolution transcriptome map showing 74.5% of the non-repetitive yeast genome is transcribed, confirming many predicted introns, demonstrating others are unused, and identifying alternative initiation codons and upstream ORFs [4]. ENCODE and modENCODE developed working standards for ChIP-seq quality, scoring and metadata archiving to address inconsistencies across labs in transcription-factor and histone-modification mapping experiments [5]. A yeast proteome microarray of 5,800 cloned and purified ORFs printed on slides at high density screened for protein and phospholipid interactions, identifying many calmodulin- and phospholipid-binding proteins and a common potential binding motif among calmodulin binders, demonstrating that an entire eukaryotic proteome can be assayed in microarray format and used for drug-interaction and post-translational-modification screens [6].
Recent publications
- RNA-Seq: a revolutionary tool for transcriptomicsDOI
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectDOI
- Functional profiling of the Saccharomyces cerevisiae genomeDOI
- Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel AnalysisDOI
- Annotation of functional variation in personal genomes using RegulomeDBDOI
- An integrated encyclopedia of DNA elements in the human genome
- The Transcriptional Landscape of the Yeast Genome Defined by RNA SequencingDOI
- Single-cell chromatin accessibility reveals principles of regulatory variationDOI
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortiaDOI
- Global Analysis of Protein Activities Using Proteome ChipsDOI
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External profiles
- ORCID: https://orcid.org/0000-0003-0784-7987
- OpenAlex: openalex.org
Profile compiled from public sources (Researchmap, OpenAlex, The University of Tokyo faculty directory). Last refreshed 2026-05. Report incorrect information.