S. Miura

Fragility of ER homeostatic regulation underlies haploid instability in human somatic cells

This study identifies ER stress-induced proteotoxicity as a key factor causing haploid instability in human somatic cells, showing that haploids are more prone to apoptosis due to inefficient proteostasis.

Variability in radiocesium activity concentration in growing hardwood shoots in Fukushima, Japan

The paper models radiocesium activity concentration variability in hardwood shoots to determine an optimal sample size for accurate estimation.

Anemonefish are better taxonomists than humans.

The paper uses transcriptomic data to reveal cryptic lineages within the bubble-tip sea anemone and shows that anemonefish species are associated with specific lineages.

Transcription factor-mediated direct cellular reprogramming yields cell-type specific DNA methylation signature

This study investigates DNA methylation changes during direct reprogramming of mouse embryonic fibroblasts to induced intestinal stem cells, showing similar methylation states between organoid-forming cells and minimal impact on gene expression.

Phylomedicine of mutational processes in somatic cancer cell populations

This study integrates cancer cell phylogeny with mutational signature deconvolution to track mutational process changes in lung cancer patients over time.

An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic

The paper reconstructs the progenitor SARS-CoV-2 genome and traces its evolution and spread globally, showing multiple dominant strains and lineage replacements in different regions.

CREB-binding protein gene, HAC701, negatively regulates WRKY45-dependent immunity in rice

This study shows that HAC701 negatively regulates WRKY45-dependent immunity in rice, enhancing disease resistance against Pseudomonas syringae pv. oryzae.

Generation of nanometer-size aggregates using Solubility Controlling Peptide tags and their ability to increase a proteins immunogenicity in vivo

This study shows that nanometer-scale protein aggregates can increase immunogenicity in vivo, using BPTI-19A as a model.

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

This study evaluates seven computational methods for inferring clone phylogenies from bulk sequencing data, finding significant variation in their accuracy for mutation order and clone grouping.

A new method for inferring timetrees from temporally sampled molecular sequences

This paper introduces RTDT, a new method for inferring timetrees from temporally sampled molecular sequences, which is more accurate and computationally efficient than existing Bayesian methods.

Knowledge of Chagas disease in Latin American migrant population living in Japan and factors associated with knowledge level

This study evaluates knowledge of Chagas disease among Latin American migrants in Japan before and after an educational activity, finding that prior testing and longer residence in Japan are associated with better knowledge.

Predicting clone genotypes from tumor bulk sequencing of multiple samples

The paper evaluates nine computational methods for inferring clone genotypes from bulk tumor sequencing data, finding that most perform poorly on datasets with mixed clonal lineages.

Computational enhancement of single-cell sequences for inferring tumor evolution

This paper introduces BEAM, a Bayesian method for improving single-cell tumor sequencing data by leveraging evolutionary information, showing it outperforms existing methods in imputing missing bases and correcting false positives/negatives.