Takuya Yamamoto

Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes

PRCGAP provides a haplotype-resolved analysis of cancer genomes, detecting variants missed by standard references and revealing new insights into structural variants and fusion events in leukemia.

Human club cells derived from pluripotent stem cells reveal new insights into epithelial lineage plasticity through structural and functional validation

This study generates human club cells from pluripotent stem cells, revealing epithelial plasticity and new differentiation trajectories.

Towards On-Site Paleogenomics: Application and Perspective of Nanopore Sequencing with Ancient DNA

This study applies nanopore sequencing to ancient DNA from the Early Jomon period, demonstrating its ability to generate genome-wide data and enable rapid, on-site paleogenomic analysis.

In vivo xenogenic reconstitution of human alveolar epithelial architecture and function

This paper develops a chimeric mouse model to replicate human alveolar epithelial architecture and function using hiPSC-derived lung progenitors.

Non-linear gene sets for digital biomarkers of amyotrophic lateral sclerosis

The paper identifies non-linear gene sets from blood cells to classify ALS with high accuracy using machine learning and validates findings in lab samples and iPSC-derived motor neurons.

Transient let-7/miR-98 reprograms primed pluripotency to induce naivehuman PSCs

This paper identifies miR-98-5p as a let-7 family microRNA that enhances naive human PSC induction by repressing NR6A1 and activating BMP2/4 signaling, improving resetting efficiency to ~80%.

Distinct dermal fibroblasts direct mechano-chemical signaling to the epidermis during pregnancy

The paper identifies Cdh4+ dermal fibroblasts in pregnant mice that convert mechanical signals to chemical signals to promote epidermal stem cell proliferation during skin expansion.

Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations

This paper uses rare k-mers to identify centromere haplogroups in human populations and cancer translocations, revealing structural diversity and translocation mechanisms.

Turbulence orchestrates actin-mitochondria dynamics to preserve GPIbα and support iPSC-derived platelet biogenesis

This study develops a turbulence-assisted system to enhance iPSC-platelet production by regulating actin dynamics and mitochondrial inheritance.

The reciprocal regulation between mitochondrial-associated membranes and Notch signaling in skeletal muscle atrophy

This study shows that loss of Mfn2 reduces MAM and activates Notch signaling in muscle atrophy, and DAPT treatment improves mitochondrial function and regeneration.

Histology-associated transcriptomic heterogeneity in ovarian folliculogenesis revealed by quantitative single-cell RNA-sequencing for tissue sections with DRaqL

The paper develops DRaqL, a method for efficient single-cell RNA-seq from fixed tissue sections, revealing transcriptomic heterogeneity in ovarian folliculogenesis.

Reconstituting human somitogenesis in vitro

This paper introduces a 3D in vitro model of human somitogenesis using pluripotent stem cells, showing accurate segmentation dynamics and disease relevance.

Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis

This paper introduces RECODE, a noise reduction method for scRNA-seq data that eliminates the curse of dimensionality, improves cell clustering, and recovers gene expression for all genes.

Post-transcriptionally regulated genes are essential for pluripotent stem cell survival

The paper identifies 20 post-transcriptionally regulated genes essential for pluripotent stem cell survival, showing their protein upregulation and nuclear-to-cytoplasmic mRNA localization.

Capturing Human Trophoblast Development with Naive Pluripotent Stem Cells In Vitro

This study shows that naive human pluripotent stem cells can recapitulate trophoblast development in vitro, producing cells that resemble human placental trophoblasts.

Modeling the Human Segmentation Clock with Pluripotent Stem Cells

This study models the human segmentation clock using iPSC-derived presomitic mesoderm, identifying oscillatory genes and validating disease-related gene effects.