Jumpei Ito

ViroChart maps host responses from virome RNA-seq data to identify phenotypic profiles of viruses, revealing host response patterns in animal infections.

This study analyzes poxvirus gene repertoires and finds that they evolve through expansion-biased birth-and-death dynamics and genome architectural constraints.

This paper develops a CRISPR-Cas3-based diagnostic platform for emerging RNA viruses, enabling rapid assay design and deployment with high sensitivity and portability.

This study identifies key ACE2 residues that influence sarbecovirus infectivity in African Rhinolophus bats and reports novel ACE2 sequences from R. simulator and R. blasii.

This study experimentally infects horseshoe bats with SARS-CoV-2, showing low-level persistent viral replication without disease, and identifies host mechanisms that enable viral coexistence.

The paper develops a host-response-based framework to detect viral infections by analyzing ISG expression in RNA-seq data from diverse species, revealing hidden infections missed by conventional methods.

This study introduces a pLM entropy metric to assess protein site conservation and variability, showing that fine-tuning pLMs on evolutionarily related proteins improves their ability to capture context-specific site variation.

This study identifies the non-spike R204P mutation in the SARS-CoV-2 Omicron XEC variant as a driver of increased inflammation and pathogenicity through NF-κB activation.

This study evaluates the humoral immune response induced by LP.8.1-based vaccines against multiple SARS-CoV-2 variants, showing effective cross-neutralization and immune boosting.

This study identifies ACE2 diversity in horseshoe bats and shows bidirectional evolutionary shaping between ACE2 and sarbecovirus spike proteins.

This study investigates the ACE2 tropism of sarbecoviruses across 17 mammals using pseudovirus assays, structural analysis, and phylogenetics to identify genetic factors influencing host range.

This study uses a protein language model to map influenza virus antigenicity from genotype data, revealing evolutionary patterns and improving vaccine strain selection.

This paper introduces CoVFit, a protein language model that predicts SARS-CoV-2 variant fitness using spike protein sequences, identifying fitness-enhancing mutations and predicting emerging variants.

This study investigates the evolutionary changes from BA.2.86 to JN.1, showing that non-spike protein mutations compensate for reduced spike protein replication, enhancing viral fitness.

This study analyzes the virological characteristics of the SARS-CoV-2 XEC variant, showing it has higher infectivity and immune evasion compared to KP.3.1.1, contributing to its higher reproductive number and potential dominance.

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

This paper investigates the virological properties of the SARS-CoV-2 KP.3.1.1 variant, finding it has higher transmissibility and immune evasion compared to KP.3.

This study evaluates the virological properties of SARS-CoV-2 variants KP.3, LB.1, and KP.2.3, finding higher reproduction numbers and immune evasion compared to JN.1.

This study investigates the virological properties of the SARS-CoV-2 KP.2 variant, finding it has higher viral fitness and immune resistance compared to JN.1, contributing to its rapid spread.

This study investigates the virological properties of the SARS-CoV-2 JN.1 variant, focusing on its mutations and potential immune evasion capabilities.

The paper develops a CRISPR-based method to infer viral sequences and predict hosts from metagenomic data, identifying numerous viral genomes and analyzing the evolution of a retroelement locus.

This study identifies LTR5_Hs, a hominoid-specific ERV, as rewiring the gene regulatory network shared between primordial germ cells and naive pluripotent cells through enhancer activity.

This study establishes an in vitro protocol to generate human prospermatogonia-like cells from induced pluripotent stem cells and characterizes their lineage trajectory using single-cell RNA-sequencing.

The paper analyzes HHV-6 integration in human genomes, identifies co-evolution with chr22q, and reports evidence of in vivo excision and reactivation.

This study shows that gorilla APOBEC3G restricts SIVcpz transmission and that a single amino acid change in Vif allows viral evasion, influencing lentiviral evolution in great apes.