Helder Takashi Imoto Nakaya
CV Lattes
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Universidade de São Paulo (USP). Faculdade de Ciências Farmacêuticas (FCF) (Institutional affiliation for the last research proposal) Birthplace: Brazil
Helder Nakaya is an assistant professor at Emory University School of Medicine in the Department of Pathology. He has a PhD in Molecular Biology with extensive training in Bioinformatics. He is an expert in Systems Vaccinology, an interdisciplinary field that combines systems-wide measurements, networks, and predictive modeling in the context of vaccines and infectious disease. Dr. Nakaya has developed systems biology approaches to understand and predict the mechanisms of vaccine induced-immunity for Yellow Fever, seasonal Influenza, Meningococcal, and Tularemia vaccines. Additionally, Dr. Nakaya is a newly appointed professor at the University of Sao Paulo, Brazil, in the Department of Clinical Analyses and Toxicology, Institute of Pharmaceutical Science. His lab will focus on investigating the basis of infectious diseases using computational systems biology. Website: www.csbiology.com (Source: Lattes Curriculum)
- Network statistics: theory, methods, and applications, AP.TEM
Abstract
The importance of statistics in natural sciences is unquestionable. Statistics is essential to analyze data appropriately and to reach reliable conclusions. However, little is known about formal statistical methods on graphs and their theoretical properties even with an increasing number of reports on the analysis of real world networks (e.g. functional brain networks, protein-protein i...
- Integrative biology applied to human health, AP.JP2
Abstract
Data related to human health, from clinical and epidemiological information to medical images and omics data, are being generated and accumulated in an unprecedented amount in history. The analysis and integration of such information is critical to improve our understanding of the pathophysiology of diseases, their transmission, as well as their diagnosis and treatment. This project pro...
- CRID - Center for Research in Inflammatory Diseases, AP.CEPID
Abstract
Inflammatory diseases are a complex and heterogeneous group of diseases that affect more than 10% of the word population. The current options for the treatment of these diseases are still limited and in some cases, inefficient due to limited understanding of the mechanisms underlying these diseases. The development of translational research by a center that can generate scientific knowl...
- Long noncoding RNA interplay with the host microbiome may determine mucosal influenza vaccine immunogenicity, AP.R
Abstract
This project will foster an independently funded collaboration between laboratories of Dr. Thushan de Silva and Dr. Beate Kampmann at Imperial College London and Dr. Helder Nakaya's group (FCF-USP) at USP. By applying a cutting edge systems biology approach to integrate nasopharyngeal microbiome, mucosal and blood transcriptome, immunological and clinical data, we will identify and inve...
- Systems biology of typhoid fever: unravelling regulation of human host-responses to infection with Salmonella Typhi and live oral vaccination, AP.R
Abstract
Infectious diseases caused by enteric pathogens are endemic specifically in developing countries, and are responsible for several thousands of deaths every year. This proposal will focus on enteric fever caused by Salmonella Typhi and Paratyphi as a model for intestinal infections. Typhoid fever significantly affects South America, sub-Saharan Africa and South-East Asia with approximate...
- Transcriptomic meta-analysis of positionally conserved long noncoding RNAs, AP.R
Abstract
It is estimated that thousands of long non-coding RNAs (IncRNAs) are transcribed in the genome of several organisms. Dr. Kouzarides' group at Cambridge University re-analyzed a vast amount of RNA-sequencing data, and identified -600 IncRNAs that were "positionally conserved" (pcRNAs) in human and mo use genomes. Among the genes associated with these pcRNAs, a striking enrichment was obs...
(Only some records are available in English at this moment)
- Study of transmission of diseases using cell phone from infected people, BP.DD
Abstract
Mapping hotspots for transmission of infectious diseases can offer great help in controlling outbreaks and eliminating reservoirs of infection. Usually, hospital staff in endemic areas try to determine such places by asking patients with transmissible infections, those places where they live/work (for diseases which require chronic exposure) or visited a few days prior going to the hosp...
- Comprehensive meta-analysis of gene networks associated to human viral infections, BP.DD
Abstract
Protein-Protein Interaction (PPI) networks have been shown as efficient at identification of genes associated with diseases and can be integrated to transcriptome data for understanding about how genes interactions can result in a pathologic phenotype, this integration will produce the gene networks. Genes shared by the majority of viral infections are already know, between them, genes ...
- Neuroimmune molecular networks in neurodegenerative and in infectious diseases, BP.MS
Abstract
Neurodegenerative disorders and peripheral infections generate a heavy burden onhuman health both in Brazil and worldwide. With the rise of microbial drug-resistance and life expectancy this situation is expected to be further complicated. Furthermore, the incidence of cases of infection and neurodegeneration in the same patients may also increase. It is known that alterations in periph...
- Analysis of long non-coding RNAs in transcriptome of mammals infected with zika virus, BP.MS
Abstract
Zika virus (ZIKV) is an arbovirus that has gained high relevance in recent years. Outbreaks of infection began to become prevalent globally from the year 2007, with an epidemic in Micronesia. Since then, five of the seven continents have been affected. Infected individuals commonly present symptoms similar to those of other arboviruses, such as dengue. However, Zika infection can affect...
- Studying Juvenile Idiopathic Arthritis through a network Medicine approach, BP.DD
Abstract
Juvenile Idiopathic Arthritis (JIA) is recognized worldwide as the most common rheumatologic disease in paediatric patients. Despite the absence of official data regarding the prevalence of this condition in Brazil, at least 464 new children were diagnosed during 2010 in the city of São Paulo, constituting the most common paediatric rheumatologic condition in this city. Brazilian patien...
- ConsensusGraph: identifying consensus gene networks, BP.DD
Abstract
Systems Biology approaches provide a holistic view of biological processes, integrating the many different molecular components inside cells through highly complex networks. By analyzing these networks, it is possible to create mathematical and computational models that help us understand the molecular mechanisms triggered by different types of stimuli or perturbations. However, even ve...
(Only some records are available in English at this moment)
- Immunometabolism of inflammatory diseases: comparing the gene signatures of chikungunya-induced arthritis and obesity, BE.EP.DD
Abstract
Metabolic Syndrome (MS) comprises a broad range of diseases in which immunometabolism and inflammation have a great influence. The increasing prevalence of obesity and MS has lead researchers investigate their influence in chronic inflammatory diseases. Despite this, little is known about the molecular pathways and gene networks that are in common between MS and inflammatory diseases. T...
| 3 / 3 | Ongoing research grants |
| 4 / 4 | Completed research grants |
| 3 / 3 | Ongoing scholarships in Brazil |
| 8 / 8 | Completed scholarships in Brazil |
| 1 / 1 | Completed scholarships abroad |
| 19 / 19 | All research grants and scholarships |
| Associated processes | |
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
| Publications | 12 |
| Citations | 53 |
| Cit./Article | 4.4 |
| Data from Web of Science | |
CARDOZO, LUCAS E.; RUSSO, PEDRO S. T.; GOMES-CORREIA, BRUNO; ARAUJO-PEREIRA, MARIANA; SEPULVEDA-HERMOSILLA, GONZALO; MARACAJA-COUTINHO, VINICIUS; NAKAYA, I, HELDER. webCEMiTool: Co-expression Modular Analysis Made Easy. FRONTIERS IN GENETICS, v. 10, MAR 6 2019. Web of Science Citations: 0. (13/08216-2, 12/19278-6, 18/10748-6, 17/05762-7)
FUKUTANI, KIYOSHI F.; NASCIMENTO-CARVALHO, CRISTIANA M.; BOUZAS, MAIARA L.; OLIVEIRA, JULIANA R.; BARRAL, ALDINA; DIERCKX, TIM; KHOURI, RICARDO; NAKAYA, HELDER I.; ANDRADE, BRUNO B.; VAN WEYENBERGH, JOHAN; et al. In situ Immune Signatures and Microbial Load at the Nasopharyngeal Interface in Children With Acute Respiratory Infection. FRONTIERS IN MICROBIOLOGY, v. 9, NOV 9 2018. Web of Science Citations: 0. (12/19278-6, 17/50137-3)
JOCHEMS, SIMON P.; MARCON, FERNANDO; CARNIEL, BEATRIZ F.; HOLLOWAY, MARK; MITSI, ELENA; SMITH, EMMA; GRITZFELD, JENNA F.; SOLORZANO, CARLA; REINE, JESUS; POJAR, SHERIN; et al. Inflammation induced by influenza virus impairs human innate immune control of pneumococcus. NATURE IMMUNOLOGY, v. 19, n. 12, p. 1299+, DEC 2018. Web of Science Citations: 8. (13/08216-2, 12/19278-6)
DE LIMA, DIOGENES S.; CARDOZO, LUCAS E.; MARACAJA-COUTINHO, VINICIUS; SUHRBIER, ANDREAS; MANE, KARIM; JEFFRIES, DAVID; SILVEIRA, EDUARDO L. V.; AMARAL, PAULO P.; RAPPUOLI, RINO; DE SILVA, THUSHAN I.; et al. Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 116, n. 34, p. 17121-17126, AUG 20 2019. Web of Science Citations: 0. (13/08216-2, 12/19278-6, 17/50137-3)
SCHRODER, WAYNE A.; HIRATA, THIAGO D.; LE, THUY T.; GARDNER, JOY; BOYLE, GLEN M.; ELLIS, JONATHAN; NAKAYAMA, ERI; PATHIRANA, DILAN; NAKAYA, HELDER I.; SUHRBIER, ANDREAS. SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages. SCIENTIFIC REPORTS, v. 9, AUG 27 2019. Web of Science Citations: 0. (17/17345-1, 14/24162-2)
RUSSO, PEDRO S. T.; FERREIRA, GUSTAVO R.; CARDOZO, LUCAS E.; BUERGER, MATHEUS C.; ARIAS-CARRASCO, RAUL; MARUYAMA, SANDRA R.; HIRATA, THIAGO D. C.; LIMA, DIOGENES S.; PASSOS, FERNANDO M.; FUKUTANI, KIYOSHI F.; et al. CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. BMC Bioinformatics, v. 19, FEB 20 2018. Web of Science Citations: 12. (13/08216-2, 15/20897-0, 12/19278-6, 15/25825-8, 14/24162-2, 17/05762-7, 14/19323-7)
ARIAS-CARRASCO, RAUL; VASQUEZ-MORAN, YESSENIA; NAKAYA, HELDER I.; MARACAJA-COUTINHO, VINICIUS. StructRNAfinder: an automated pipeline and web server for RNA families prediction. BMC Bioinformatics, v. 19, FEB 17 2018. Web of Science Citations: 3. (12/19278-6)
BLOHMKE, CHRISTOPH J.; HILL, JENNIFER; DARTON, THOMAS C.; CARVALHO-BURGER, MATHEUS; EUSTACE, ANDREW; JONES, CLAIRE; SCHREIBER, FERNANDA; GOODIER, MARTIN R.; DOUGAN, GORDON; NAKAYA, HELDER I.; et al. Induction of Cell Cycle and NK Cell Responses by Live-Attenuated Oral Vaccines against Typhoid Fever. FRONTIERS IN IMMUNOLOGY, v. 8, OCT 12 2017. Web of Science Citations: 4. (14/50828-8, 12/19278-6)
FERREIRA, GUSTAVO RODRIGUES; NAKAYA, HELDER IMOTO; COSTA, LUCIANO DA FONTOURA. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs. Physical Review E, v. 97, n. 4, APR 27 2018. Web of Science Citations: 0. (14/19323-7, 12/19278-6, 15/22308-2)
AMARAL, PAULO P.; LEONARDI, TOMMASO; HAN, NAMSHIK; VIRE, EMMANUELLE; GASCOIGNE, DENNIS K.; ARIAS-CARRASCO, RAUL; BUSCHER, MAGDALENA; PANDOLFINI, LUCA; ZHANG, ANDA; PLUCHINO, STEFANO; et al. Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci. Genome Biology, v. 19, MAR 15 2018. Web of Science Citations: 26. (14/50308-4)
MASTELIC-GAVILLET, BEATRIS; VONO, MARIA; GONZALEZ-DIAS, PATRICIA; FERREIRA, FREDERICO MORAES; CARDOZO, LUCAS; LAMBERT, PAUL-HENRI; NAKAYA, I, HELDER; SIEGRIST, CLAIRE-ANNE. Neonatal T Follicular Helper Cells Are Lodged in a Pre-T Follicular Helper Stage Favoring Innate Over Adaptive Germinal Center Responses. FRONTIERS IN IMMUNOLOGY, v. 10, AUG 13 2019. Web of Science Citations: 0. (12/19278-6, 17/50137-3)
SOARES-SCHANOSKI, ALESSANDRA; BAPTISTA CRUZ, NATALIA; DE CASTRO-JORGE, LUIZA ANTUNES; HOMEM DE CARVALHO, RENAN VILLANOVA; DOS SANTOS, CLIOMAR ALVES; DA ROS, NANCY; OLIVEIRA, URSULA; COSTA, DANUZA DUARTE; SIMOES DOS SANTOS, CECILIA LUIZA; CUNHA, MARIELTON DOS PASSOS; et al. Systems analysis of subjects acutely infected with the Chikungunya virus. PLOS PATHOGENS, v. 15, n. 6, JUN 2019. Web of Science Citations: 0. (13/08216-2, 17/50137-3, 15/25055-8, 12/19278-6, 13/07467-1, 16/08204-2)