Mitinori Saitou

Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

Species-OT uses Gromov-Wasserstein optimal transport to compare transcriptome geometries across species, identifying gene correspondences and transcriptomic discrepancies.

CycloCross: Adversarial single-cell RNA-seq data translation across species

Translating cells between mouse, macaque and human scRNA-seq with a CycleGAN, without ortholog mapping, preserved developmental time structure, imputed missing states and produced more realistic synthetic cells than scGAN.

Atlas of Cynomolgus Macaque Hematopoiesis

The paper develops a single-cell transcriptomic map of cynomolgus macaque hematopoietic stem cells and progenitors, revealing molecular differences from humans and a direct differentiation pathway to megakaryocyte lineages.

scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport

scEGOT is a single-cell trajectory inference framework that identifies cell populations and segregation events in time-series scRNA-seq data, revealing key transcription factors involved in PGCLC differentiation.

Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence

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.

A temporally controlled sequence of X-chromosomeinactivation and reactivation defines female mouse in vitro germ cells with meiotic potential

This study investigates X-chromosome inactivation and reactivation dynamics in female mouse PGCLCs, showing that a precise temporal sequence is critical for meiotic potential.

The developmental origin and the specification of the adrenal cortex in humans and cynomolgus monkeys

The paper identifies the adrenal cortex's origin in adrenogenic coelomic epithelium, distinct from gonadogenesis, in humans and cynomolgus monkeys.

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.

A symmetric toggle switch explains the onset of random X inactivation in different mammals

The paper identifies a symmetric toggle switch as the mechanism for random Xist up-regulation during X-chromosome inactivation in mammals.

Differential epigenetic landscapes and transcription factors explain X-linked gene behaviours during X-chromosome reactivation in the mouse inner cell mass

The paper investigates X-linked gene reactivation in mouse inner cell mass by analyzing epigenetic marks and transcription factors, finding differential reactivation speeds and mechanisms.