Kazumitsu Maehara

spSheaf: sheaf-theoretic spatial domain inference from raw molecules without cell segmentation

spSheaf infers spatial domains from raw molecular data without cell segmentation, outperforming existing methods on benchmark datasets.

Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge

The paper introduces ddHodge, a method for reconstructing vector fields from scRNA-seq data to analyze cell-state dynamics, revealing gene expression follows a gradient system during mouse embryogenesis.

Histone H2B isoform H2bc27 is expressed in the developing brain of mouse embryos

The paper investigates the role of H2bc27, an H2B isoform, in mouse brain development through gene expression analysis and knockout studies, finding it regulates gene expression in brain development.

Discriminative feature of cells characterizes cell populations of interest by a small subset of genes

The paper introduces DFC, a method using adaptive LASSO logistic regression to identify a small subset of genes that distinguish cell populations, addressing issues with P-value inflation in single-cell transcriptomics.

Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections

The paper introduces tsChIL, a method to analyze tissue-level epigenomic data from single-thin sections, enabling independent evaluation of cell population changes and gene activation in regenerating skeletal muscle.

High resolution spatial transcriptome analysis by photo-isolation chemistry

This paper introduces PIC, a method for high-resolution spatial transcriptome analysis, and shows it detects gene expression in small regions of mouse embryos.

Tracking H3K27me3 and H4K20me1 during XCI reveals similarities in enrichment dynamics

The paper tracks H3K27me3 and H4K20me1 dynamics during XCI and finds they accumulate concurrently but have distinct genomic distributions, with H4K20me1 possibly contributing to chromatin compaction.

Calcineurin broadly regulates the initiation of skeletal muscle-specific gene expression by binding target promoters and facilitating the interaction of the SWI/SNF chromatin remodeling enzyme

This study identifies four temporal patterns of calcineurin-dependent gene expression during skeletal muscle differentiation and shows Cn promotes gene expression by facilitating chromatin remodeling and transcription factor interactions.

Modeling latent flows on single-cell data using the Hodge decomposition

This paper introduces ddhodge, a method using Hodge decomposition to model latent flows in single-cell data, enabling visualization and interpretation of complex biological processes.

SraTailor: GUI software for visualizing high-throughput sequence read archives

SraTailor converts SRA files into BigWig format and allows graphical visualization, making SRAs accessible to biologists without command-line expertise.

Identification of five patterns of nucleosome positioning that globally describe transcription factor function

The paper identifies five nucleosome positioning patterns around transcription factor binding sites that predict transcriptional regulation function in mouse cells.