Helder Imoto Nakaya

The paper uses graph neural networks to interpret microbial association patterns in IBD, showing that coordinated associations, not just abundance shifts, are predictive.

This study compares HPV16 and HPV18 cervical cancers using gene expression data to identify genotype-specific host pathway alterations and viral gene expression programs.

This study identifies NLRP3 inflammasome signaling as critical for organizing hepatic granulomas and promoting protective immunity against Leishmania infantum.

The paper identifies a neuroimmune signature in HTLV-1 infection that correlates with disease progression and severity using bulk and single-cell transcriptomic data.

The paper identifies lncRNA expression signatures associated with Ebola vaccine-induced immunity using RNA-sequencing data from three human cohorts.

This study investigates the impact of the HNRNPH2-R114W mutation on RNA splicing in human brain organoids, identifying junction-level dysregulation and potential therapeutic targets.

This study identifies innate antiviral readiness as a key driver of TSCM cell expansion, showing its predictive value for viral clearance and vaccine design.

This study identifies PAX6 as a critical predictor of MDD using transcriptomic data from 3,114 individuals and validates its expression in PBMCs and the amygdala.

This paper uses molecular dynamics simulations to show that base flipping in Tc3a transposase reshapes DNA structure during recognition, challenging existing models of transposon activity.

This study identifies genetic risk factors for tuberculosis in Brazil using GWAS and single-cell transcriptomics, finding SNPs associated with gene expression in multiple cell types.

Immunaut identifies distinct immunophenotypic responder groups shaped by baseline immune landscapes using a comprehensive LAIV dataset, advancing precision vaccinology and guiding personalized immunization strategies.

The paper creates a synovial fluid TCR, cytokine, and cell repertoire atlas to compare disease mechanisms across arthritic conditions using systems immunology approaches.

The paper identifies synaptic-related gene dysregulation in PBMCs of MDD patients, highlighting shared molecular signatures with brain regions and potential biomarkers for depression.

This study shows ICOS limits the function of exhausted PD-1+ CD8 T cells by promoting their differentiation into less functional effector-like cells, and inhibiting ICOS improves anti-tumor responses.

This study identifies that SARS-CoV-2 increases unproductive splicing isoforms of immune-related genes, potentially subverting antiviral responses.

The paper introduces WikiGOA, a gene set enrichment analysis method using Wikipedia and Gene Ontology, showing it provides understandable results for gene expression data analysis.

This study characterizes metabolic alterations in iPSC-derived astrocytes from MS patients, identifying mitochondrial dysfunction and distinct metabolic profiles linked to disease mechanisms.

This study tracks the evolution of gene-disease associations over 30 years using text-mining to reveal shared mechanisms and drug targets across diseases.

The paper introduces the fcoex package, which infers coexpression modules from scRNA-seq data to identify overlapping cell classes and improve cell type atlases.

The paper finds that ACE2 expression is increased in the lungs of patients with comorbidities linked to severe COVID-19, suggesting a potential mechanism for increased disease severity.

This study integrates transcriptomic, proteomic, and genomic data from CZS neonates to identify collagen gene reductions and associated polymorphisms, linking them to neuronal migration defects and CZS susceptibility.

The paper introduces an Alexa Assistant tailored for laboratory routines to improve efficiency and reduce stress.