M. Hamada

Landscape of Evolutionary Arms Races between Transposable Elements and KRAB-ZFP Family

The paper investigates the evolutionary arms race between transposable elements and KRAB-ZFP proteins using ChIP-seq data, revealing new instances and regulatory impacts.

Intraplacental injection of human iPSC-derived PDX1+ pancreatic progenitors prolongs Pdx1-deficient mice survival

This study transplants human iPSC-derived pancreatic progenitors into Pdx1-deficient mice, extending their lifespan and demonstrating functional engraftment of human pancreatic cells.

Hidden Challenges in Evaluating Spillover Risk of Zoonotic Viruses using Machine Learning Models

This study improves machine learning models for predicting zoonotic virus infectivity by expanding datasets and using large language models, showing better performance for segmented RNA viruses and post-2018 emerging viruses.

Willingness of Japanese people in their 20s, 30s and 40s to pay for genetically modified foods

This study compares willingness-to-pay for GM foods among Japanese adults aged 20-40, finding lower WTP for animal-derived GM products compared to plant and ornamental GM items.

The evolution of RNA interference among Metazoa

This study investigates the evolution of RNA interference mechanisms in Metazoa, finding that the endo-siRNA pathway is lost in Lophotrochozoa while miRNAs remain conserved.

Transfer learning of an in vivo-derived senescence signature identifies conserved and tissue-specific senescence across species and diverse pathologies

The paper develops a transfer learning approach to identify senescent cells across species and tissues using an in vivo-derived gene expression signature, revealing conserved and tissue-specific senescence features.

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model

Umibato estimates time-varying microbial interactions using a Bayesian model and Gaussian process regression, outperforming existing methods on synthetic data and providing insights into diet-gut microbiota relationships.

Revisiting the gastrin-releasing peptide/bombesin system: A reverse-evolutionary study considering Xenopus

This study investigates the evolutionary relationships of the gastrin-releasing peptide (GRP) and bombesin systems in vertebrates using Xenopus tropicalis, showing GRP is not a mammalian counterpart of bombesin and that the NMB/bombesin system has diversified in frogs.

Revealing microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation

This study uses latent Dirichlet allocation to detect microbial assemblages in the human gut microbiome, revealing four assemblages with distinct compositions and relationships to enterotypes.

Metabolic co-dependence drives the evolutionary ancient Hydra-Chlorella symbiosis

The paper identifies metabolic co-dependence as the driving force behind the ancient Hydra-Chlorella symbiosis, showing nutrient exchange between host and symbiont.