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List of works by Helder I. Nakaya

<scp>MS</scp> ‐Driven Metabolic Alterations Are Recapitulated in <scp>iPSC</scp> ‐Derived Astrocytes

scientific article published on 17 March 2022

A reasonable request for true data sharing

scientific article published in July 2024

ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19

scientific article published on 11 June 2020

ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19

scientific article (preprint)

Abstract 103: Knockout of cellular prion protein in glioblastoma affects the expression of Wnt signaling genes

scientific article published on 15 June 2022

Activation of beta-catenin in dendritic cells regulates immunity versus tolerance in the intestine

scientific article published on August 2010

Acute Zika Virus Infection in an Endemic Area Shows Modest Proinflammatory Systemic Immunoactivation and Cytokine-Symptom Associations.

scientific article published on 3 May 2018

Adjuvanting a Simian Immunodeficiency Virus Vaccine with Toll-Like Receptor Ligands Encapsulated in Nanoparticles Induces Persistent Antibody Responses and Enhanced Protection in TRIM5α Restrictive Macaques

scientific article

Analysis of LexA binding sites and transcriptomics in response to genotoxic stress in Leptospira interrogans

scientific article published on 13 January 2016

Androgen responsive intronic non-coding RNAs

scientific article

Antigenicity prediction and vaccine recommendation of human influenza virus A (H3N2) using convolutional neural networks

scientific article published on 04 August 2020

Antimicrobial peptide LL-37 participates in the transcriptional regulation of melanoma cells

scientific article

Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer

scientific article

Aryl hydrocarbon receptor (AhR) activation contributes to high‐fat diet‐induced vascular dysfunction

scientific article published on 17 February 2022

As antisense RNA gets intronic

scientific article

Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool

scientific article published on 24 October 2019

Automatic detection of the parasite <i>Trypanosoma cruzi</i> in blood smears using a machine learning approach applied to mobile phone images

scientific article published on 27 May 2022

Blood Gene Signatures of Chagas Cardiomyopathy With or Without Ventricular Dysfunction

scientific article published on 21 December 2016

Building capacity for advances in tuberculosis research; proceedings of the third RePORT international meeting

CCR2 deficiency promotes exacerbated chronic erosive neutrophil-dominated chikungunya virus arthritis

scientific article

CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses.

scientific article published on 20 February 2018

Calcium/calmodulin-dependent kinase kinase 2 regulates hematopoietic stem and progenitor cell regeneration

scientific article published on 5 October 2017

Canonical PI3Kγ signaling in myeloid cells restricts Trypanosoma cruzi infection and dampens chagasic myocarditis

scientific article published on 17 April 2018

Chronic but not acute virus infection induces sustained expansion of myeloid suppressor cell numbers that inhibit viral-specific T cell immunity

scientific article published on February 2013

Co-Exposure of Cardiomyocytes to IFN-γ and TNF-α Induces Mitochondrial Dysfunction and Nitro-Oxidative Stress: Implications for the Pathogenesis of Chronic Chagas Disease Cardiomyopathy

scientific article published on 11 November 2021

Concepts on Microarray Design for Genome and Transcriptome Analyses

Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci

scientific article published on 21 May 2008

Corrigendum to: Blood Gene Signatures of Chagas Cardiomyopathy With or Without Ventricular Dysfunction

scientific article published on 01 April 2020

Crucial role for T cell-intrinsic IL-18R-MyD88 signaling in cognate immune response to intracellular parasite infection

scientific article published on 12 September 2017

Cyclic Peptides as Modulators of Protein-Protein Interactions

Daily Rhythms of TNFα Expression and Food Intake Regulate Synchrony of Plasmodium Stages with the Host Circadian Cycle

scholarly article published by Helder Nakaya in 2018

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

scientific article published on 02 August 2016

Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination

scientific article published on 15 August 2016

Dengue virus infection induces expansion of a CD14(+)CD16(+) monocyte population that stimulates plasmablast differentiation

scientific article

Determinants of antibody persistence across doses and continents after single-dose rVSV-ZEBOV vaccination for Ebola virus disease: an observational cohort study

article by Angela Huttner et al published July 2018 in Lancet Infectious Diseases

Differentiation of Memory CD8 T Cells Unravel Gene Expression Pattern Common to Effector and Memory Precursors

scientific article published on 01 January 2022

Discordant congenital Zika syndrome twins show differential in vitro viral susceptibility of neural progenitor cells

scientific article published on 2 February 2018

Distinct TLR adjuvants differentially stimulate systemic and local innate immune responses in nonhuman primates

scientific article published on 12 January 2012

Down-regulation of 14q32-encoded miRNAs and tumor suppressor role for miR-654-3p in papillary thyroid cancer

scientific article published on 24 December 2016

Drug repositioning for psychiatric and neurological disorders through a network medicine approach

scientific article published on 12 May 2020

Editorial: User-Friendly Tools Applied to Genetics or Systems Biology

scientific article published on 09 September 2020

Efferocytosis of SARS-CoV-2-infected dying cells impairs macrophage anti-inflammatory functions and clearance of apoptotic cells

scientific article published on 6 June 2022

Elevated Glucose Levels Favor SARS-CoV-2 Infection and Monocyte Response through a HIF-1α/Glycolysis-Dependent Axis

scientific article published on 17 July 2020

Elevated Glucose Levels Favor SARS-CoV-2 Infection and Monocyte Response through a HIF-1α/Glycolysis-Dependent Axis

scientific article published on 01 September 2020

Elevated Glucose Levels Favor Sars-Cov-2 Infection and Monocyte Response Through a Hif-1α/Glycolysis Dependent Axis

scientific article

Evolution and epidemic spread of SARS-CoV-2 in Brazil

scientific article published on 23 July 2020

Evolution and epidemic spread of SARS-CoV-2 in Brazil

preprint article published on 12 June 2020

Exacerbation of Chikungunya Virus Rheumatic Immunopathology by a High Fiber Diet and Butyrate

scientific article published on 26 November 2019

Flavivirus-Mediating B Cell Differentiation Into Antibody-Secreting Cells in Humans Is Associated With the Activation of the Tryptophan Metabolism

scientific article published on 11 February 2020

Gene profiling of Chikungunya virus arthritis in a mouse model reveals significant overlap with rheumatoid arthritis

scientific article

Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

article

Gene signatures of autopsy lungs from obese patients with COVID-19

publication published on 26 May 2021

Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response

scientific article

Genetic control of immune response and susceptibility to infectious diseases

scientific article published on 13 February 2014

Genetic sequence characterization and naturally acquired immune response to Plasmodium vivax Rhoptry Neck Protein 2 (PvRON2)

scientific article published on 31 October 2018

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription

scientific article published on January 2007

Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells

scientific article published on 22 January 2014

Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

scientific article

Genomics, epigenomics and pharmacogenomics of Familial Hypercholesterolemia (FHBGEP): A study protocol

scientific article published on 28 October 2020

HIV infection increases the risk of acquiring Plasmodium vivax malaria: a 4-year cohort study in the Brazilian Amazon HIV and risk of vivax malaria

scientific article published on 31 May 2022

Hydroquinone exposure alters the morphology of lymphoid organs in vaccinated C57Bl/6 mice

scientific article published on 16 November 2019

Immature neutrophil signature associated with the sexual dimorphism of systemic juvenile idiopathic arthritis

scientific article published on 13 August 2020

Immune Signatures and Microbial Load at the Nasopharyngeal Interface in Children With Acute Respiratory Infection

scientific article published on 09 November 2018

Immunity to viruses: learning from successful human vaccines

scientific article published on September 2013

In-depth Analysis of Laboratory Parameters Reveals the Interplay Between Sex, Age and Systemic Inflammation in Individuals with COVID-19

scholarly article by Felipe ten-Caten published in 2021

Induction of Cell Cycle and NK Cell Responses by Live-Attenuated Oral Vaccines against Typhoid Fever

scientific article published on 12 October 2017

Inflammation induced by influenza virus impairs human innate immune control of pneumococcus

article

Inflammation induced by influenza virus impairs innate control of human pneumococcal carriage

scientific article published on 21 June 2018

Initial viral load determines the magnitude of the human CD8 T cell response to yellow fever vaccination

scientific article

Insight Into the Long Noncoding RNA and mRNA Coexpression Profile in the Human Blood Transcriptome Upon <i>Leishmania infantum</i> Infection

scientific article published on 15 March 2022

Integration of miRNA and gene expression profiles suggest a role for miRNAs in the pathobiological processes of acute Trypanosoma cruzi infection

scientific article published on 21 December 2017

Integrative Biology Approaches Applied to Human Diseases

Is the gut microbiome key to modulating vaccine efficacy?

scientific article

Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination

scientific article published on 09 August 2019

Lower temperatures reduce type I interferon activity and promote alphaviral arthritis

scientific article published on 27 December 2017

Machine Learning for Predicting Vaccine Immunogenicity

article

Metabolic Phenotypes of Response to Vaccination in Humans

scientific article published on 9 May 2017

Methods for predicting vaccine immunogenicity and reactogenicity

scientific article published on 23 December 2019

MicroRNA Transcriptome Profiling in Heart of Trypanosoma cruzi-Infected Mice: Parasitological and Cardiological Outcomes

scientific article published on 18 June 2015

Molecular alterations in human milk in simulated maternal nasal mucosal infection with live attenuated influenza vaccination

scientific article published on 23 June 2022

Molecular alterations in the extracellular matrix in the brains of newborns with congenital Zika syndrome

scientific article published on 09 June 2020

Molecular degree of perturbation of plasma inflammatory markers associated with tuberculosis reveals distinct disease profiles between Indian and Chinese populations.

scientific article

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

scientific article published on 15 December 2013

Monitoring social distancing and SARS-CoV-2 transmission in Brazil using cell phone mobility data

scientific article published on 05 May 2020

Morphological, cellular, and molecular basis of brain infection in COVID-19 patients

scientific article published in 2022

Multiple immune factors are involved in controlling acute and chronic chikungunya virus infection

scientific article

Myeloperoxidase in human peripheral blood lymphocytes: Production and subcellular localization

scientific article published on 26 November 2015

N-Methyl-d-Aspartate (NMDA) Receptor Blockade Prevents Neuronal Death Induced by Zika Virus Infection

scientific article

Neonatal T Follicular Helper Cells Are Lodged in a Pre-T Follicular Helper Stage Favoring Innate Over Adaptive Germinal Center Responses

scientific article published on 13 August 2019

Network vaccinology

scientific article published on 05 November 2020

Neuroinflammation at single cell level: What is new?

scientific article published on 10 August 2020

Noninvasive prenatal paternity determination using microhaplotypes: a pilot study

scientific article published on 23 October 2020

Novel therapeutic avenues for the study of chronic liver disease and regeneration: The foundation of the Iberoamerican Consortium for the study of liver Cirrhosis

scientific article published in June 2022

Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation

scientific article

Phenotype, function, and gene expression profiles of programmed death-1(hi) CD8 T cells in healthy human adults

scientific article published on 07 March 2011

Platelet disturbances correlate with endothelial cell activation in uncomplicated Plasmodium vivax malaria

scientific article published on 20 July 2020

Platelet-monocyte interaction amplifies thromboinflammation through tissue factor signaling in COVID-19

scientific article published on 14 April 2022

Predicting RNA Families in Nucleotide Sequences Using StructRNAfinder

scientific article published on 01 January 2019

Prior upregulation of interferon pathways in the nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children

Programming the magnitude and persistence of antibody responses with innate immunity

scientific article

Publisher Correction: Discordant congenital Zika syndrome twins show differential in vitro viral susceptibility of neural progenitor cells

scientific article published on 13 March 2018

RASL11A, member of a novel small monomeric GTPase gene family, is down-regulated in prostate tumors

scientific article

RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma

scientific article

Repression of bacterial lipoprotein production by Francisella novicida facilitates evasion of innate immune recognition

scientific article

SARS-CoV-2 infects brain astrocytes of COVID-19 patients and impairs neuronal viability

scientific article

SARS-CoV-2 uses CD4 to infect T helper lymphocytes

scientific article published on 31 July 2023

Science Family skills: An Alexa Assistant Tailored for Laboratory Routine

scientific article

SerpinB2 Deficiency Results in a Stratum Corneum Defect and Increased Sensitivity to Topically Applied Inflammatory Agents

scientific article

SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages

scientific article published on 27 August 2019

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States

scientific article published in March 2022

Specific inhibition of NLRP3 in chikungunya disease reveals a role for inflammasomes in alphavirus-induced inflammation.

scientific article

Splice variants of TLE family genes and up-regulation of a TLE3 isoform in prostate tumors

scientific article published on 26 October 2007

StructRNAfinder: an automated pipeline and web server for RNA families prediction

scientific article published on 17 February 2018

Susceptibility of the Elderly to SARS-CoV-2 Infection: ACE-2 Overexpression, Shedding, and Antibody-dependent Enhancement (ADE)

scientific article published on 15 May 2020

Synergy of Omeprazole and Praziquantel In Vitro Treatment against Schistosoma mansoni Adult Worms

scientific article

Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures

scientific article published on December 2015

Systems Biology of Infectious Diseases and Vaccines

Systems Immunology of Diabetes-Tuberculosis Comorbidity Reveals Signatures of Disease Complications

scientific article

Systems Vaccinology Applied to DNA Vaccines: Perspective and Challenges

scientific article published on 20 September 2016

Systems analysis of protective immune responses to RTS,S malaria vaccination in humans

scientific article published on 13 February 2017

Systems analysis of subjects acutely infected with the Chikungunya virus

scientific article published in June 2019

Systems biological approaches to measure and understand vaccine immunity in humans

scientific article published on 21 June 2013

Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans

scientific article (publication date: 2009)

Systems biology of immunity to MF59-adjuvanted versus nonadjuvanted trivalent seasonal influenza vaccines in early childhood

scientific article published on 11 January 2016

Systems biology of vaccination for seasonal influenza in humans

scientific article

Systems biology of vaccination in the elderly

scientific article published on January 2013

Systems immunology of flavivirus infection

scientific article

Systems vaccinology

scientific article

Systems vaccinology: Enabling rational vaccine design with systems biological approaches

scientific article

Systems vaccinology: its promise and challenge for HIV vaccine development

scientific article published on January 2012

Systems vaccinology: learning to compute the behavior of vaccine induced immunity

scientific article published on 19 October 2011

São Paulo School of Advanced Sciences on Vaccines: an overview

scientific article published on 06 April 2020

TGF-β signalling defect is linked to low CD39 expression on regulatory T cells and methotrexate resistance in rheumatoid arthritis.

scientific article published on 6 February 2018

TLR5-mediated sensing of gut microbiota is necessary for antibody responses to seasonal influenza vaccination

scientific article

Ten quick tips for harnessing the power of ChatGPT in computational biology

scientific article published on 10 August 2023

The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling.

scientific article

The amino acid sensor GCN2 controls gut inflammation by inhibiting inflammasome activation

scientific article published on 16 March 2016

The evolution of knowledge on genes associated with human diseases

scientific article

The impact of early social distancing at COVID-19 Outbreak in the largest Metropolitan Area of Brazil.

scientific article published on 08 April 2020

The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation.

scientific article

The iron stimulon of Xylella fastidiosa includes genes for type IV pilus and colicin V-like bacteriocins

scientific article published on 25 January 2008

The role of prophage in plant-pathogenic bacteria

scientific article published on 24 May 2013

Towards a pragmatic definition of cell type

scientific article

Toxicogenomic and bioinformatics platforms to identify key molecular mechanisms of a curcumin-analogue DM-1 toxicity in melanoma cells

scientific article published on 4 September 2017

Transcriptomic signatures induced by the Ebola virus vaccine rVSVΔG-ZEBOV-GP in adult cohorts in Europe, Africa, and North America: a molecular biomarker study

scientific article published in February 2022

Tucuxi-BLAST: Enabling fast and accurate record linkage of large-scale health-related administrative databases through a DNA-encoded approach

scientific article published in 2022

Using coexpression to explore cell-type diversity with the fcoex package

scientific article published on 9 December 2021

Vaccine activation of the nutrient sensor GCN2 in dendritic cells enhances antigen presentation

scientific article

Vaccinology in the era of high-throughput biology

scientific article published in June 2015

Variants in the Kisspeptin-GnRH Pathway Modulate the Hormonal Profile and Reproductive Outcomes

scientific article published on 29 April 2020

Why should obese youth be prioritized in COVID-19 vaccination programs? A nationwide retrospective study

scientific article published in March 2022

miRNAs may play a major role in the control of gene expression in key pathobiological processes in Chagas disease cardiomyopathy

scientific article published on 22 December 2020

webCEMiTool: Co-expression Modular Analysis Made Easy

scholarly article by Lucas E Cardozo et al published 2019 in Frontiers in Genetics

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