Integrative biology applied to human health

• Grant number: 18/14933-2
• Support Opportunities: Research Grants - Young Investigators Grants - Phase 2
• Start date: May 01, 2019
• End date: April 30, 2025
• Field of knowledge: Interdisciplinary Subjects
• Principal Investigator: Helder Takashi Imoto Nakaya
• Grantee: Helder Takashi Imoto Nakaya
• Host Institution: Instituto Israelita de Ensino e Pesquisa Albert Einstein (IIEPAE). Sociedade Beneficente Israelita Brasileira Albert Einstein (SBIBAE). São Paulo , SP, Brazil
• Associated researchers: Esper Georges Kallás ; Fernando Augusto Bozza ; Frederico Moraes Ferreira ; Luciano da Fontoura Costa ; Luis Carlos de Souza Ferreira ; Mario Hiroyuki Hirata ; Paola Marcella Camargo Minoprio ; Patricia Cristina Baleeiro Beltrão Braga ; Ricardo Tostes Gazzinelli ; Sergio Schenkman ; Vanderson de Souza Sampaio
• Associated research grant: 12/19278-6 - Systems biology of long non-coding RNAs, AP.JP
• Associated research grant(s): 19/16444-1 - Systems immunology approach for resolving the mechanisms of vaccine-induced classical swine fever protection, AP.R SPRINT
• Associated scholarship(s): 24/00563-0 - Scientific Journalism for Young Researcher Award Project 2 (2018/14933-2), BP.JC; 24/00562-3 - Scientific Journalism for Young Researcher Award Project 2 (2018/14933-2), BP.JC; 23/09291-0 - Prediction of structural changes in proteins caused by mutations using AlphaFold2 and Molecular Dynamics for Precision Vaccinology, BP.PD; + associated scholarships 20/05284-0 - Interaction of microorganisms and human hosts associated with the clinical outcome of patients with infectious diseases, BP.DD; 20/12017-9 - Machine learning for interpretation and analysis of microscopic images, BP.PD; 19/27139-5 - Application of genomic tools for the study of epidemiological databases, BP.DD; 19/27146-1 - Integration of transcriptome data with clinical and immunological data, BP.DD; 19/16419-7 - Study of transmission of diseases using cell phone from infected people, BP.DD - associated scholarships

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 proposes innovative approaches for: analyzing large epidemiological databases; mapping hotspots of disease transmission; integrating transcriptome data with clinical and immunological data; and using machine learning for interpretation and analysis of microscopic images. State-of-the-art techniques or systems analyses and machine learning will be used and even developed for each approach, taking into account the foundations of integrative biology. We hope that the results of the project can clarify several problems related to human health, from the automatic analysis of microscopic slides to the molecular mechanisms of infectious and inflammatory diseases (AU)

Scientific publications

(31)

(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)

BRANDAO, W. N.; DE OLIVEIRA, M. G.; ANDREONI, R. T.; NAKAYA, H.; FARIAS, A. S.; PERON, J. P. S.. Neuroinflammation at single cell level: What is new?. Journal of Leukocyte Biology, AUG 2020. (13/08216-2, 18/21934-5, 17/50137-3, 17/26170-0, 12/19278-6, 17/22504-1, 17/21363-5, 18/14933-2, 19/06372-3)

LUSCHER-DIAS, THOMAZ; SIQUEIRA DALMOLIN, RODRIGO JULIANI; AMARAL, PAULO DE PAIVA; ALVES, TIAGO LUBIANA; SCHUCH, VIVIANE; FRANCO, GLORIA REGINA; NAKAYA, HELDER I.. The evolution of knowledge on genes associated with human diseases. ISCIENCE, v. 25, n. 1, p. 22-pg., 2022-01-21. (18/14933-2, 18/21934-5)

PINTO, BRUNA G. G.; OLIVEIRA, ANTONIO E. R.; SINGH, YOUVIKA; JIMENEZ, LEANDRO; GONCALVES, ANDRE N. A.; OGAVA, RODRIGO L. T.; CREIGHTON, RACHEL; SCHATZMANN PERON, JEAN PIERRE; NAKAYA, I, HELDER. ACE2 Expression Is Increased in the Lungs of Patients With Comorbidities Associated With Severe COVID-19. Journal of Infectious Diseases, v. 222, n. 4, p. 556-563, AUG 15 2020. (12/19278-6, 18/14933-2, 18/21934-5, 13/08216-2, 17/50137-3)

AQUIME GONCALVES, ANDRE NICOLAU; MASO, VANESSA ESCOLANO; SANTOS DE CASTRO, ICARO MAIA; VASCONCELOS, AMANDA PEREIRA; TOMIO OGAVA, RODRIGO LUIZ; NAKAYA, HELDER, I. High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, v. N/A, n. 181, p. 22-pg., 2022-03-01. (18/14933-2, 13/08216-2, 19/13880-5, 19/16418-0, 19/27146-1, 12/19278-6, 20/05284-0, 17/50137-3, 18/21934-5)

GONZALEZ-DIAS, PATRICIA; LEE, EVA K.; SORGI, SARA; DE LIMA, DIOGENES S.; URBANSKI, ALYSSON H.; SILVEIRA, EDUARDO LV; NAKAYA, HELDER I.. Methods for predicting vaccine immunogenicity and reactogenicity. HUMAN VACCINES & IMMUNOTHERAPEUTICS, v. 16, n. 2, DEC 2019. (13/08216-2, 18/21934-5, 18/14933-2)

JIMENEZ, LEANDRO; CODO, ANA CAMPOS; SAMPAIO, VANDERSON DE SOUZA; OLIVEIRA, ANTONIO E. R.; KOBO FERREIRA, LUCAS KAORU; DAVANZO, GUSTAVO GASTAO; MONTEIRO, LAUAR DE BRITO; VIRGILIO-DA-SILVA, JOAO VICTOR; SILVA BORBA, MAYLA GABRIELA; DE SOUZA, GABRIELA FABIANO; et al. Acid pH Increases SARS-CoV-2 Infection and the Risk of Death by COVID-19. FRONTIERS IN MEDICINE, v. 8, AUG 20 2021. (18/14933-2, 20/04836-0)

BRANDAO, W. N.; DE OLIVEIRA, M. G.; ANDREONI, R. T.; NAKAYA, H.; FARIAS, A. S.; PERON, J. P. S.. Neuroinflammation at single cell level: What is new?. Journal of Leukocyte Biology, v. 108, n. 4, p. 9-pg., 2020-08-10. (17/22504-1, 13/08216-2, 18/14933-2, 19/06372-3, 17/21363-5, 17/26170-0, 12/19278-6, 17/50137-3, 18/21934-5)

ARAUJO, JOSE DENEY; SANTOS-E-SILVA, JUAN CARLO; COSTA-MARTINS, ANDRE GUILHERME; SAMPAIO, VANDERSON; CASTRO, DANIEL BARROS DE; SOUZA, ROBSON F. DE; GIDDALURU, JEEVAN; RAMOS, PABLO IVAN P.; PITA, ROBESPIERRE; BARRETO, MAURICIO L.; et al. Tucuxi-BLAST: Enabling fast and accurate record linkage of large-scale health-related administrative databases through a DNA-encoded approach. PeerJ, v. 10, p. 17-pg., 2022-07-11. (18/14933-2, 19/27139-5)

CANDIDO, DARLAN S.; CLARO, INGRA M.; DE JESUS, JAQUELINE G.; SOUZA, WILLIAM M.; MOREIRA, FILIPE R. R.; DELLICOUR, SIMON; MELLAN, THOMAS A.; DU PLESSIS, LOUIS; PEREIRA, RAFAEL H. M.; SALES, FLAVIA C. S.; et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, v. 369, n. 6508, SI, p. 1255+, SEP 4 2020. (20/04558-0, 16/00194-8, 19/21301-5, 18/14389-0, 18/14933-2, 17/13981-0, 20/04836-0, 18/25468-9, 16/18445-7, 18/09383-3, 18/17176-8, 19/12000-1, 19/07544-2, 19/24251-9)

ALVES, EDUARDO; NAKAYA, HELDER; GUIMARES, EUZEBIO; GARCIA, CELIA R. S.. Combining IP3 affinity chromatography and bioinformatics reveals a novel protein-IP3 binding site on Plasmodium falciparum MDR1 transporter*. CURRENT RESEARCH IN MICROBIAL SCIENCES, v. 4, p. 7-pg., 2022-12-19. (17/08684-7, 18/14933-2, 18/07177-7)

NAKAYA, HELDER I.; THAKAR, JUILEE; MARACAJA-COUTINHO, VINICIUS. Editorial: User-Friendly Tools Applied to Genetics or Systems Biology. FRONTIERS IN GENETICS, v. 11, p. 2-pg., 2020-09-09. (18/14933-2)

PERON, J. P. S.; NAKAYA, H., I; SCHLINDWEIN, M. A. M.; GONCALVES, M. V. M.. COVID-19 Pandemic and Dysbiosis: Can the Ivermectin Hysteria Lead to an Increase of Autoimmune Neuroinflammatory Diseases?. CRITICAL REVIEWS IN IMMUNOLOGY, v. 40, n. 6, p. 6-pg., 2020-01-01. (17/22504-1, 19/06372-3, 13/08216-2, 17/21363-5, 18/14933-2, 18/21934-5, 12/19278-6)

AGUIAR, RENATO S.; POHL, FABIO; MORAIS, GUILHERME L.; NOGUEIRA, FABIO C. S.; DE CARVALHO, JOSEANE B.; GUIDA, LETICIA; ARGE, LUIS W. P.; MELO, ADRIANA; MOREIRA, MARIA E. L.; CUNHA, DANIELA P.; et al. Molecular alterations in the extracellular matrix in the brains of newborns with congenital Zika syndrome. SCIENCE SIGNALING, v. 13, n. 635, p. 13-pg., 2020-06-09. (13/08216-2, 17/50137-3, 18/14933-2, 18/21934-5, 12/19278-6)

ARIAS-CARRASCO, RAUL; GIDDALURU, JEEVAN; CARDOZO, LUCAS E.; MARTINS, FELIPE; MARACAJA-COUTINHO, VINICIUS; NAKAYA, HELDER I.. OUTBREAK: a user-friendly georeferencing online tool for disease surveillance. Biological Research, v. 54, n. 1, JUL 8 2021. (18/14933-2, 13/08216-2, 19/16419-7, 18/21934-5, 17/50137-3)

MONTEIRO, CINTIA J.; DUARTE, MAX J.; MACHADO, MAYARA CRISTINA V.; MASCARENHAS, ROMARIO S.; PALMA, PATRICIA V. BONINI; GARCIA, HENRY D. MOGOLLON; NAKAYA, HELDER I.; CUNHA, THIAGO M.; DONADI, EDUARDO A.; PASSOS, GERALDO A.. The single-cell transcriptome of mTECs and CD4⁺ thymocytes under adhesion revealed heterogeneity of mTECs and a network controlled by Aire and lncRNAs. FRONTIERS IN IMMUNOLOGY, v. 15, p. 18-pg., 2024-08-26. (18/14933-2, 20/09664-2, 21/02081-4, 17/10780-4)

COSTA-GOUVEA, TIFFANY B. L.; FRANCOSO, KATIA S.; MARQUES, RODOLFO F.; GIMENEZ, ALBA MARINA; FARIA, ANA C. M.; CARISTE, LEONARDO M.; DOMINGUEZ, MARIANA R.; VASCONCELOS, JOSE RONNIE C.; NAKAYA, HELDER I.; SILVEIRA, EDUARDO L. V.; et al. Poly I:C elicits broader and stronger humoral and cellular responses to a Plasmodium vivax circumsporozoite protein malaria vaccine than Alhydrogel in mice. FRONTIERS IN IMMUNOLOGY, v. 15, p. 15-pg., 2024-04-08. (19/06494-1, 14/18102-7, 18/14933-2, 17/11931-6, 19/25373-0, 12/13032-5)

VASCONCELOS, AMANDA PEREIRA; SANTOS E SILVA, JUAN CARLO; SIMIZO, ADRIANA; AVILA, JONATHAN PENA; GOLDSTEIN, GABRIEL NASSAR REICH; DE OLIVEIRA, PEDRO HENRIQUE PRADO; GARCIA, HENRY MOGOLLON; DE CARVALHO FRAGA, CARLOS ALBERTO; NAKAYA, HELDER, I. Sex-Based Differences in Thyroid Plasma B Cell Infiltration: Implications for Autoimmune Disease Susceptibility. Endocrinology, v. 165, n. 12, p. 6-pg., 2024-11-20. (18/14933-2, 19/27146-1, 19/27139-5, 23/13452-9)

LUBIANA, TIAGO; LOPES, RAFAEL; MEDEIROS, PEDRO; SILVA, JUAN CARLO; GONCALVES, ANDRE NICOLAU AQUIME; MARACAJA-COUTINHO, VINICIUS; NAKAYA, HELDER I.. Ten quick tips for harnessing the power of ChatGPT in computational biology. PLOS COMPUTATIONAL BIOLOGY, v. 19, n. 8, p. 9-pg., 2023-08-01. (19/27139-5, 19/26284-1, 18/14933-2)

AGUIAR, RENATO S.; POHL, FABIO; MORAIS, GUILHERME L.; NOGUEIRA, FABIO C. S.; DE CARVALHO, JOSEANE B.; GUIDA, LETICIA; ARGE, LUIS W. P.; MELO, ADRIANA; MOREIRA, MARIA E. L.; CUNHA, DANIELA P.; et al. Molecular alterations in the extracellular matrix in the brains of newborns with congenital Zika syndrome. Science Signaling, v. 13, n. 635, JUN 9 2020. (13/08216-2, 12/19278-6, 18/21934-5, 17/50137-3, 18/14933-2)

PERON, J. P. S.; NAKAYA, I, H.; SCHLINDWEIN, M. A. M.; GONCALVES, M. V. M.. COVID-19 Pandemic and Dysbiosis: Can the Ivermectin Hysteria Lead to an Increase of Autoimmune Neuroinflammatory Diseases?. CRITICAL REVIEWS IN IMMUNOLOGY, v. 40, n. 6, SI, p. 537-542, 2020. (17/22504-1, 18/14933-2, 12/19278-6, 13/08216-2, 18/21934-5, 19/06372-3, 17/21363-5)

LUSCHER-DIAS, THOMAZ; CONCEICAO, IZABELA MAMEDE; SCHUCH, VIVIANE; MARACAJA-COUTINHO, VINICIUS; AMARAL, PAULO P.; NAKAYA, HELDER I.; HON, CC. Long non-coding RNAs associated with infection and vaccine-induced immunity. NON-CODING GENOME, v. 65, n. 4, p. 13-pg., 2021-01-01. (18/14933-2, 13/08216-2, 20/04836-0, 17/27131-9, 18/21934-5)

CAFUNDO MORAIS, MAURO CESAR; SILVA, DIOGO; MILAGRE, MATHEUS MARQUES; DE OLIVEIRA, MAYKON TAVARES; PEREIRA, THAIS; SILVA, JOAO SANTANA; COSTA, LUCIANO DA F.; MINOPRIO, PAOLA; CESAR JUNIOR, ROBERTO MARCONDES; GAZZINELLI, RICARDO; et al. Automatic detection of the parasite Trypanosoma cruzi in blood smears using a machine learning approach applied to mobile phone images. PeerJ, v. 10, p. 19-pg., 2022-05-27. (20/12017-9, 18/14933-2)

GONCALVES, ANDRE N. A.; LEVER, MELISSA; RUSSO, PEDRO S. T.; GOMES-CORREIA, BRUNO; URBANSKI, ALYSSON H.; POLLARA, GABRIELE; NOURSADEGHI, MAHDAD; MARACAJA-COUTINHO, VINICIUS; NAKAYA, I, HELDER. Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool. FRONTIERS IN GENETICS, v. 10, OCT 24 2019. (13/08216-2, 12/19278-6, 18/14933-2)

SANTOS E SILVA, JUAN CARLO; VASCONCELOS, AMANDA PEREIRA; YONEHARA NOMA, ISABELLA HARUMI; NORONHA, NATALIA YUMI; AQUINO, RODRIGO; GIDDALURU, JEEVAN; DURAO, LUIZ; COSTA-MARTINS, ANDRE GUILHERME; SCHUCH, VIVIANE; MORAES-VIEIRA, PEDRO M.; et al. Gene signatures of autopsy lungs from obese patients with COVID-19. CLINICAL NUTRITION ESPEN, v. 44, p. 475-478, AUG 2021. (19/27139-5, 18/14933-2, 20/04579-7, 19/27146-1)

PANNARAJ, PIA S.; DA COSTA-MARTINS, ANDRE GUILHERME; CERINI, CHIARA; LI, FAN; WONG, SOOK-SAN; SINGH, YOUVIKA; URBANSKI, ALYSSON H.; GONZALEZ-DIAS, PATRICIA; YANG, JULIANA; WEBBY, RICHARD J.; et al. Molecular alterations in human milk in simulated maternal nasal mucosal infection with live attenuated influenza vaccination. MUCOSAL IMMUNOLOGY, v. N/A, p. 8-pg., 2022-06-23. (18/14933-2)

CREIGHTON, RACHEL; SCHUCH, VIVIANE; URBANSKI, ALYSSON H.; GIDDALURU, JEEVAN; COSTA-MARTINS, ANDRE G.; NAKAYA, I, HELDER. Network vaccinology. SEMINARS IN IMMUNOLOGY, v. 50, AUG 2020. (18/14933-2, 17/27131-9, 13/08216-2, 18/21934-5)

JEAN PIERRE SCHATZMANN PERON; HELDER NAKAYA. Susceptibility of the Elderly to SARS-CoV-2 Infection: ACE-2 Overexpression, Shedding, and Antibody-dependent Enhancement (ADE). Clinics, v. 75, 2020-05-15. (18/14933-2, 12/19278-6, 17/22504-1, 17/50137-3, 17/26170-0, 13/08216-2, 18/21934-5)

CARVALHO, PATRICIA CONCEICAO GONZALEZ DIAS; HIRATA, THIAGO DOMINGUEZ CRESPO; ALVES, LEANDRO YUKIO MANO; MOSCARDINI, ISABELLE FRANCO; DO NASCIMENTO, ANA PAULA BARBOSA; COSTA-MARTINS, ANDRE G.; SORGI, SARA; HARANDI, ALI M.; FERREIRA, DANIELA M.; VIANELLO, ELEONORA; et al. Baseline gene signatures of reactogenicity to Ebola vaccination: a machine learning approach across multiple cohorts. FRONTIERS IN IMMUNOLOGY, v. 14, p. 10-pg., 2023-11-08. (18/14933-2)

BRUNETTI, NATALIA S.; DAVANZO, GUSTAVO G.; DE MORAES, DIOGO; FERRARI, ALLAN J. R.; SOUZA, GABRIELA F.; MURARO, STEFANIE PRIMON; KNITTEL, THIAGO L.; BOLDRINI, VINICIUS O.; MONTEIRO, LAUAR B.; VIRGILIO-DA-SILVA, JOO VICTOR; et al. SARS-CoV-2 uses CD4 to infect T helper lymphocytes. eLIFE, v. 12, p. 26-pg., 2023-07-31. (20/04558-0, 15/15626-8, 19/06459-1, 19/04726-2, 19/16116-4, 19/05155-9, 19/13552-8, 16/18031-8, 19/00098-7, 20/04583-4, 16/00194-8, 21/08354-2, 19/17007-4, 19/22398-2, 17/01184-9, 19/14465-1, 20/04579-7, 13/08293-7, 18/14933-2, 17/23920-9, 19/06372-3, 16/24163-4, 16/23328-0, 20/04919-2, 20/04746-0)

URBAN, BRITTA C.; GONCALVES, ANDRE N. A.; LOUKOV, DESSI; PASSOS, FERNANDO M.; REINE, JESUS; GONZALEZ-DIAS, PATRICIA; SOLORZANO, CARLA; MITSI, ELENA; NIKOLAOU, ELISSAVET; O'CONNOR, DANIEL; et al. Inflammation of the nasal mucosa is associated with susceptibility to experimental pneumococcal challenge in older adults. MUCOSAL IMMUNOLOGY, v. 17, n. 5, p. 17-pg., 2024-10-09. (18/14933-2)

LUBIANA, TIAGO; NAKAYA, HELDER I.. A reasonable request for true data sharing. LANCET REGIONAL HEALTH-AMERICAS, v. 35, p. 2-pg., 2024-05-28. (19/26284-1, 18/14933-2)