Development of a computational platform extensible and modular for analysis of metabolomics and metagenomics experiments: Innovating with the discovery of new enzymatic activities and derived natural products of interest

• Grant number: 19/05026-4
• Support Opportunities: Scholarships in Brazil - BIOTA - Young Researchers
• Start date: March 01, 2019
• End date: August 22, 2023
• Field of knowledge: Interdisciplinary Subjects
• Principal Investigator: Ricardo Roberto da Silva
• Grantee: Ricardo Roberto da Silva
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 17/18922-2 - Development of a computing platform extensible and modular for metabolomics and metagenomics analysis: innovation with the discovery of new enzymatic activities and natural products of pharmaceutical interest derived, AP.BTA.JP

Scientific publications

(13)

(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)

FAEDO, RAQUEL ROMAN; DA SILVA, GABRIEL; DA SILVA, RODRIGO MOREIRA; USHIDA, TATIANE RESENDE; DA SILVA, RICARDO ROBERTO; LACCHINI, RICCARDO; MATOS, LEANDRO LUONGO; KOWALSKI, LUIZ PAULO; LOPES, NOBERTO PEPORINE; LEOPOLDINO, ANDREIA MACHADO. Sphingolipids signature in plasma and tissue as diagnostic and prognostic tools in oral squamous cell carcinoma. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, v. 1867, n. 1, JAN 2022. (17/18922-2, 18/17480-9, 16/19103-2, 19/05026-4, 18/03278-3)

KONG, YA-SHUAI; REN, HONG-YU; LIU, RUI; DA SILVA, RICARDO R.; AKSENOV, ALEXANDER A.; V. MELNIK, ALEXEY; ZHAO, MING; LE, MIAO-MIAO; REN, ZHI-WEI; XU, FENG-QING; et al. Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation. Journal of Agricultural and Food Chemistry, v. 70, n. 18, p. 14-pg., 2022-05-11. (19/05026-4, 17/18922-2)

TAMASCO, GUSTAVO; KUMAR, MANISH; ZENGLER, KARSTEN; SILVA-ROCHA, RAFAEL; DA SILVA, RICARDO ROBERTO. ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization. BMC Bioinformatics, v. 23, n. 1, p. 13-pg., 2022-11-30. (17/18922-2, 19/05026-4, 19/15675-0)

DOS SANTOS, ANCELY F.; INAGUE, ALEX; ARINI, GABRIEL S.; TERRA, LETICIA F.; WAILEMANN, ROSANGELA A. M.; PIMENTEL, ANDRE C.; YOSHINAGA, MARCOS Y.; SILVA, RICARDO R.; SEVERINO, DIVINOMAR; DE ALMEIDA, DARIA RAQUEL Q.; et al. Distinct photo-oxidation-induced cell death pathways lead to selective killing of human breast cancer cells. CELL DEATH & DISEASE, v. 11, n. 12, DEC 14 2020. (19/09517-2, 17/13804-1, 19/05026-4, 16/04676-7, 17/23914-9, 17/18922-2, 17/03618-6, 15/02654-3, 13/07937-8)

LEAO, TIAGO; WANG, MINGXUN; MOSS, NATHAN; DA SILVA, RICARDO; SANDERS, JON; NURK, SERGEY; GUREVICH, ALEXEY; HUMPHREY, GREGORY; REHER, RAPHAEL; ZHU, QIYUN; et al. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. MARINE DRUGS, v. 19, n. 1, JAN 2021. (19/05026-4)

DE ALMEIDA, DARIA R. Q.; DOS SANTOS, ANCELY F.; WAILEMANN, ROSANGELA A. M.; TERRA, LETICIA F.; GOMES, VINICIUS M.; ARINI, GABRIEL S.; BERTOLDI, ESTER R. M.; REIS, EDUARDO M.; BAPTISTA, MAURICIO S.; LABRIOLA, LETICIA. Necroptosis activation is associated with greater methylene blue-photodynamic therapy-induced cytotoxicity in human pancreatic ductal adenocarcinoma cells. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, v. N/A, p. 16-pg., 2022-12-10. (17/18922-2, 17/13804-1, 19/05026-4, 15/02654-3, 16/04676-7, 17/03618-6, 19/09517-2, 13/07937-8)

DA COSTA, BRUNO RUIZ BRANDAO; DA SILVA, RICARDO ROBERTO; BIGAO, VITOR LUIZ CALEFFO PIVA; PERIA, FERNANDA MARIS; DE MARTINIS, BRUNO SPINOSA. Hybrid volatilomics in cancer diagnosis by HS-GC-FID fingerprinting. JOURNAL OF BREATH RESEARCH, v. 17, n. 2, p. 15-pg., 2023-04-01. (19/05026-4, 20/02207-5, 17/18922-2)

BIN KANG, KYO; WOO, SUNMIN; ERNST, MADELEINE; VAN DER HOOFT, JUSTIN J. J.; NOTHIAS, LOUIS-FELIX; DA SILVA, RICARDO R.; DORRESTEIN, PIETER C.; SUNG, SANG HYUN; LEE, MINA. Assessing specialized metabolite diversity of Alnus species by a digitized LC-MS/MS data analysis workflow. Phytochemistry, v. 173, MAY 2020. (17/18922-2, 19/05026-4)

KAZANDJIAN, T. D.; PETRAS, D.; ROBINSON, S. D.; VAN THIEL, J.; GREENE, H. W.; ARBUCKLE, K.; BARLOW, A.; CARTER, D. A.; WOUTERS, R. M.; WHITELEY, G.; et al. Convergent evolution of pain-inducing defensive venom components in spitting cobras. Science, v. 371, n. 6527, p. 386+, JAN 22 2021. (19/05026-4, 17/18922-2)

MCAVOY, ANDREW C.; JAIYESIMI, OLAKUNLE; THREATT, PAXTON H.; SELADI, TYLER; GOLDBERG, JOANNA B.; DA SILVA, RICARDO R.; GARG, NEHA. Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim. ACS INFECTIOUS DISEASES, v. 6, n. 5, p. 1154-1168, MAY 8 2020. (17/18922-2, 19/05026-4)

CARABALLO-RODRIGUEZ, ANDRES MAURICIO; PUCKETT, SARA P.; KYLE, KATHLEEN E.; PETRAS, DANIEL; DA SILVA, RICARDO; NOTHIAS, LOUIS-FELIX; ERNST, MADELEINE; VAN DER HOOFT, JUSTIN J. J.; TRIPATHI, ANUPRIYA; WANG, MINGXUN; et al. Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden. MSYSTEMS, v. 6, n. 4, AUG 2021. (17/18922-2, 19/05026-4)

LEO, TIAGO F.; WANG, MINGXUN; DA SILVA, RICARDO; GUREVICH, ALEXEY; BAUERMEISTER, ANELIZE; GOMES, PAULO WENDER P.; BREJNROD, ASKER; GLUKHOV, EVGENIA; ARON, ALLEGRA T.; LOUWEN, JORIS J. R.; et al. NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. PNAS NEXUS, v. 1, n. 5, p. 15-pg., 2022-11-01. (17/18922-2, 19/05026-4)

BORELLI, TIAGO CABRAL; ARINI, GABRIEL SANTOS; FEITOSA, LUIS G. P.; DORRESTEIN, PIETER C.; LOPES, NORBERTO PEPORINE; DA SILVA, RICARDO R.. Improving annotation propagation on molecular networks through random walks: introducing ChemWalker. Bioinformatics, v. 39, n. 3, p. 2-pg., 2023-03-01. (21/08235-3, 20/02207-5, 17/18922-2, 19/05026-4, 21/10401-9)