Shigehiro Kuraku

The paper presents a near-complete genome assembly of the African turquoise killifish and evaluates how TR detection programs and TE workflows affect TE expression profiling.

The paper documents the embryonic and larval development of Pacific saury, highlighting unique developmental patterns and rapid growth compared to related species.

This study investigates the evolutionary origin of sugar sensing in vertebrates, finding that it predates angiosperms and involves multiple independent T1R-based mechanisms.

The paper presents whole genome sequences of two elasmobranchs, analyzing genome size dynamics and genomic architecture, revealing correlations between chromosome size, repetitive elements, and gene duplication patterns.

The paper investigates the location dependence of protein intrinsic disorder in Drosophila melanogaster, finding that disorder is more common at terminals and linked to specific functions like protein-binding.

This paper develops molecular sexing methods for sharks using sex-linked DNA markers to address sex identification challenges in forensic, archival, and developmental samples.

This study shows that reducing gut ceramidase Asah2 activity slows ageing in vertebrates by altering ceramide levels and microbiota composition.

The paper optimizes ATAC-seq for low-input and cryopreserved chicken primordial germ cells, identifying PGC-specific chromatin regions and their functional roles.

The paper shows MEIOSIN has a STRA8-independent activity that drives meiotic entry in vertebrates, with different effects in zebrafish and mice.

This study analyzes globin gene evolution in cartilaginous fish using genomic and transcriptomic data, revealing gene loss, retention, and expression patterns compared to bony vertebrates.

The paper investigates the evolutionary history of visual opsins in vertebrates by analyzing jawless vertebrate genomes and finds evidence of tandem duplications before vertebrate radiation.

The paper presents an improved chromosome-level genome assembly of the whale shark, revealing a chromocline effect in substitution rates across chromosomes.

This study identifies the oldest vertebrate sex chromosomes in sharks and rays, revealing a unique dosage-dependent sex determination mechanism distinct from other vertebrates.

The paper investigates the evolution of the Kazald gene family in vertebrates, identifying its origin and differential roles across species.

The paper shows RNA exosome activity maintains transcriptional condensate stability and fluidity, which is essential for coordinated gene expression and cellular homeostasis.

MedakaBase provides a centralized platform for genomic resources and analysis tools for medaka fish, including gene models and omics data for multiple Oryzias species.

This study constructs a haplotype-phased genome assembly for Haliotis gigantea and identifies non-syntenic homologous chromosomes with structural variations that may contribute to functional diversification.

This paper presents the first chromosome-level genome assembly of the Greenland shark, identifying genetic features associated with its extreme longevity and deep-sea adaptations.

This study presents the first chromosome-scale genome assembly of a chimaera, identifies a sex chromosome in holocephalans, and reveals genomic features related to intron size and sex determination.

The paper identifies cholecystokinin as the FSH-releasing hormone (FSH-RH) in medaka, challenging the solo GnRH model and proposing a dual GnRH model in vertebrates.

This study presents the first whole genome assembly of the Pacific saury using SMRT sequencing, providing resources for fishery science and comparative biology.

The paper estimates genome sizes of elasmobranch species using optimized flow cytometry and qPCR methods, revealing large variation and enabling non-invasive analysis.

The paper identifies truncated radial glia (tRG) as a conserved progenitor subtype in ferret and human corticogenesis, showing their role in brain expansion.

The paper identifies a shared supergene involved in sex chromosome turnover across three Takifugu species, showing repeated translocations of this supergene as the mechanism for sex determination locus changes.

The paper analyzes the whale shark genome to study vertebrate gene family evolution, finding patterns in immunity, gigantism, and cancer-related gene expansion.

This study presents de novo chromosome-scale genome assemblies for cynomolgus macaque and common marmoset using long-read and Hi-C data, achieving high contiguity and accuracy.

The paper describes a method for karyotyping shark species using cell culture, identifying chromosome numbers and sex chromosomes in four carpet shark species.

The paper reconstructs a high-coverage coding gene set for the inshore hagfish Eptatretus burgeri using genome sequencing and RNA-seq data.

This study benchmarks Hi-C methods for chromosome-scale genome scaffolding, identifying key factors that improve scaffolding quality and introduces a new protocol.

This paper introduces a neural network-based classifier for gene regulatory sequences, improves prediction accuracy, and provides visualization tools for understanding regulatory code.