K. Tamura

Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework

The paper develops Triterpene RDF, a manually curated database of plant enzymes and transcription factors involved in triterpene biosynthesis, to improve functional annotation of genomes and transcriptomes.

The Arabidopsis katamari2 Mutant Exhibits a Hypersensitive Seedling Arrest Response at the Phase Transition from Heterotrophic to Autotrophic Growth

This study shows that Arabidopsis seedlings, including the katamari2 mutant, exhibit a growth arrest response during the phase transition from heterotrophic to autotrophic growth, which is an adaptive stress response rather than a carbon source deficiency.

Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses in Arabidopsis thaliana

This study performs a meta-analysis of RNA-Seq data from Arabidopsis thaliana under ABA-related abiotic stresses to identify novel stress-responsive genes.

Comprehensive Analysis of Peptide-Coding Genes Identifies an LRR-only Microprotein That Regulates Reproductive Organs in Marchantia polymorpha

This study identifies an LRR-only microprotein, MpSGF10B, that regulates reproductive organ development in Marchantia polymorpha by affecting antheridiophore formation.

A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan

This paper presents a high-quality genome assembly of red perilla, identifying potential targets for genome editing to enhance metabolite production.

Meta-analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia

This study performs a meta-analysis of RNA-Seq data from Arabidopsis and rice under hypoxia, identifying 40 upregulated and 19 downregulated genes common to both species.

Intranasal vaccination induced cross-protective secretory IgA antibodies against SARS-CoV-2 variants with reducing the potential risk of lung eosinophilic immunopathology

This study shows that an intranasal vaccine with CpG ODN2006 induces secretory IgA antibodies against SARS-CoV-2 variants and reduces lung eosinophilic immunopathology compared to subcutaneous vaccination.

Morphological evolution and diversity of pectoral fin skeletons in teleosts

The paper compares pectoral fin skeletons across 27 teleost species to identify morphological variations and evolutionary patterns.

Stomatal regulators are co-opted for seta development in the astomatous liverwort Marchantia polymorpha

The paper shows that a Ia-IIIb bHLH TF module regulates seta development in liverwort Marchantia polymorpha, similar to its role in stomatal formation in stomatous plants.

Evolutionary trajectories of three independent neo-sex chromosomes in Drosophila

The paper compares the evolutionary patterns of neo-sex chromosomes in three Drosophila species, finding accelerated pseudogenization and shared functional constraints across neo-X and neo-Y chromosomes.

PLZF is a new substrate of CRBN with thalidomide and 5-hydroxythalidomide

The paper identifies PLZF as a CRBN substrate degraded by thalidomide and 5-hydroxythalidomide, linking it to teratogenesis.

High-Throughput Functional Evaluation of BRCA2 Variants of Unknown Significance

The paper develops a high-throughput method to evaluate BRCA2 variants of unknown significance, classifying 186 variants into neutral, intermediate, or deleterious categories with high sensitivity and specificity.

KAKU4-mediated deformation of the vegetative nucleus controls its precedent migration over sperm cells in pollen tubes

This study shows that KAKU4 controls vegetative nucleus shape, influencing its migration order over sperm cells in pollen tubes and affecting pollen competitiveness.

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

The paper introduces a new method to calculate reliable confidence intervals for divergence times estimated using the RelTime method, showing good coverage probabilities in simulations.

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.

Modelling the emergence of an egalitarian society in the n-player game framework

This study models the evolution of egalitarian behavior using an n-player game framework, finding that social control and coalition benefits promote egalitarian societies.

Chemo-mechanical Coupling in the Transport Cycle of a Type II ABC Transporter

This study uses molecular dynamics simulations to uncover new conformations and the role of LSGG[Q/E] motifs in ATPase activity regulation in an ABC transporter.

A new method for detecting autocorrelation of evolutionary rates in large phylogenies

This paper introduces a machine learning method to detect evolutionary rate autocorrelation in large phylogenies, finding it common across multiple taxa.

RelTime relaxes the strict molecular clock throughout the phylogeny

This paper clarifies that RelTime does not enforce a strict molecular clock, and discusses the impact of rate equality options and prior assumptions on divergence time estimation.

Adaptive landscape of protein variation in human exomes

The paper develops an Evolutionary Probability Approach (EPA) to identify candidate adaptive polymorphisms in human exomes, finding thousands of missense variants likely under beneficial selection.

Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

This paper provides a formal mathematical foundation for the RelTime method, which estimates divergence times by relaxing the strict molecular clock assumption and incorporating relative rate comparisons.