Yutaka Suzuki

This study identifies CD55 and CD248 as novel surface markers for tendon stem/progenitor cells using single-cell and single-nucleus sequencing in mouse Achilles tendon.

This study shows that TNF inhibitor infliximab reduces tertiary lymphoid structures and alleviates Crohn's disease inflammation by targeting follicular dendritic cells and macrophages.

The paper introduces SpatialKNife, a toolkit for analyzing single-cell spatial omics data to estimate spatiotemporal pathological mechanisms in microenvironments.

The paper identifies molecular mechanisms driving the divergence of adult neural stem cells and ependymal cells during embryogenesis through single-cell transcriptomic analysis.

ExDyn is a deep generative model that estimates single-cell transcriptome dynamics influenced by extrinsic factors, showing improved accuracy over existing methods.

The paper compares metabolic dysregulation in obese mice during feeding and fasting using multi-omics data, revealing opposite metabolic shifts linked to obesity.

The paper shows that the orientation of the first cleavage in mouse oocytes follows the shorter diameter of the unfertilized oocyte, leading to segregation of animal and vegetal hemispheres and explaining differences in monozygotic twins.

This paper develops a rat-specific deconvolution method to retrieve immune cell trafficking information from toxicogenomics databases, finding species-specific differences and identifying compound clusters based on immune cell profiles.

The paper evaluates a liver-specific deconvolution method on legacy data, showing improved extrapolation when using optimized reference cell sets for liver transcriptome analysis.

The paper investigates dosage compensation in silkworm males by analyzing allele-specific expression and finds both Z chromosomes are transcriptionally downregulated.

This study uses multiomic analysis of skeletal muscle in obese and healthy mice to reveal differences in metabolic regulation by metabolites and genes after glucose administration.

The paper investigates somatic recombination of Alu and L1 repeat elements in human genomes, finding tissue-specific patterns and links to neurodegenerative diseases.

The paper uses multimodal analysis to reveal cardiac neural crest lineage diversity and gene regulatory networks involved in their differentiation.

The paper analyzes single-cell immune data from healthy individuals to reveal cell diversity and daily fluctuations, showing how immune responses vary between individuals and over time.

The paper develops DeepSpaCE, a deep learning model that predicts spatial transcriptomics profiles to improve histological interpretation of breast cancer tissue sections without additional experiments.

This paper introduces OMELET, a method to infer metabolic flux from multi-omic data, and applies it to identify obesity-associated dysregulation in liver glucose metabolism.

This paper presents a high-quality genome assembly and annotation of the California harvester ant Pogonomyrmex californicus, enabling studies on social polymorphism and adaptation to arid environments.

This study develops Dyrec-seq to measure transcription and RNA degradation rates simultaneously, revealing their relationship to gene function and response to stimuli.

The paper identifies a novel class of structural aberrations in lung cancers using long-read sequencing and shows their occurrence in vivo and in cancer-related genes.

The paper integrates multi-omics data to analyze gene expression dynamics in mouse embryos, revealing discrepancies between transcript and protein levels during early development.

The paper analyzes trans-omic data from healthy and obese mice to reveal that glucose-responsive liver metabolism is regulated by rapid changes in metabolites and gene expression in the healthy state, and by slow transcriptional regulation in the obese state.

This paper introduces a method using hybrid organisms to generate high-resolution linkage maps at lower cost and higher density for pufferfish species.