Publications

2024

Vieira Junior, M.G. Carneiro, F.R.G. Cortes, A.M.A. Carels, N.Silva, F.A.B. (2024).Unveiling dynamics behind Glioblastoma Multiforme single-cell data heterogeneity International Journal of Molecular Sciences (accepted for publication)

Sgariglia, A. J., Carneiro, F. R. G., Vidal de Carvalho, L. A.,  Pedreira, C. E., Carels, N.,  Silva, F. A. B. D. (2024). Optimizing Therapeutic Targets for Breast Cancer Using Boolean Network Models. Computational Biology and Chemistry 108022. 

Romão, B., et al. (2024).  Detection of potential safety signals related to the use of remdesivir and tocilizumab in the COVID era during pregnancy, resorting to open data from the FDA Adverse Event Reporting System (FAERS). Frontiers in Pharmacology 15:1349543.

2023

Chagas, M., et al. (2023).  Boolean Model of the Gene Regulatory Network of Pseudomonas aeruginosa CCBH4851. Frontiers in Microbiology, 14, 1274740.

Carels, N., et al. (2023).  A Strategy Utilizing Protein-Protein Interaction Hubs for the Treatment of Cancer Diseases. International Journal of Molecular Sciences, 24(22), 16098.

Vieira Junior, M.G.,  Carneiro, F.R.G. Cortes, A.M.A. Carels, N., Silva, F.A.B. (2023). Unveiling dynamics behind Glioblastoma Multiforme single-cell data heterogeneity.  BioRxiv.

Castro, M. C. S., Silva, V. S., Costa, M. O., Silva, H. S., Walter, M. E. M., Melo, A. C., … & Silva, F. A. B. (2023). CellHeap: A scRNA-Seq Workflow for Large Scale Bioinformatics Data Analysis. BioRxiv

Sgariglia, A. J., Carneiro, F. R. G., Vidal de Carvalho, L. A.,  Pedreira, C. E., Carels, N.,  Silva, F. A. B. D. (2023). Optimizing Therapeutic Targets for Breast Cancer Using Boolean Network Models. BioRxiv

2022

Henriques-Pons, A., Beghini, D. G., Silva, V. D. S., Iwao Horita, S., & Silva, F. A. B. D. (2022). Pulmonary mesenchymal stem cells in mild cases of COVID-19 are dedicated to proliferation; in severe cases, they control inflammation, make cell dispersion, and tissue regeneration. Frontiers in Immunology, 12, 780900.

Barbosa-Silva, A., Magalhães, M., Da Silva, G. F., Da Silva, F. A. B., Carneiro, F. R. G., & Carels, N. (2022). A Data Science Approach for the Identification of Molecular Signatures of Aggressive Cancers. Cancers, 14(9), 2325.

Duré, F. M., Silveira, M. C., Rocha-de-Souza, C. M., Leão, R. S., de Oliveira Santos, I. C., Albano, R. M., … & da Silva, F. A. B. (2022). CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes. Frontiers in Microbiology, 13.

Silva, F. A. B. D., Tuszynski, J. A., Nakaya, H., & Paller, C. J. (2022). Big Data and machine learning in cancer theranostics. Frontiers in Big Data, 67.

Barbosa, L. H. L. A., Silva, A. R. O., Carvalho-Assef, A. P. D. A., Lima, E. C., & da Silva, F. A. B. (2022). Potential safety signals for antibacterial agents from the Brazilian national pharmacovigilance database (Vigimed/VigiFlow). Frontiers in Pharmacology, 3935.

da Silva Chagas, M., Medeiros Filho, F., Dos Santos, M. T., de Menezes, M. A., Carvalho-Assef, A. P. D. A., & da Silva, F. A. B. (2022). An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851. Memórias do Instituto Oswaldo Cruz, 117.

2021

Pires, J. G., Da Silva, G. F., Weyssow, T., Conforte, A. J., Pagnoncelli, D., Da Silva, F. A. B., & Carels, N. (2021). Galaxy and MEAN Stack to create a user-friendly workflow for the rational optimization of cancer chemotherapy. Frontiers in Genetics, 12, 624259.

Silveira, M. C., Rocha-de-Souza, C. M., de Oliveira Santos, I. C., Pontes, L. D. S., Oliveira, T. R. T. E., Tavares-Teixeira, C. B., … & Carvalho-Assef, A. P. D. A. (2021). Genetic Basis of Antimicrobial Resistant Gram-Negative Bacteria Isolated From Bloodstream in Brazil. Frontiers in Medicine, 8, 635206.

Campos, M. L., Silva, E., Cerceau, R., Cruz, S. M. S. D., Silva, F. A., Gouveia, F., … & Dávila, A. (2021). Towards Machine-Readable (Meta) Data and the FAIR Value for Artificial Intelligence Exploration of COVID-19 and Cancer Research Data. Frontiers in Big Data, 60.

Medeiros Filho, F., Nascimento, A. P. B. D., Costa, M. D. O. C. E., Merigueti, T. C., Menezes, M. A. D., Nicolas, M. F., … & Silva, F. A. B. D. (2021). A systematic strategy to find potential therapeutic targets for Pseudomonas aeruginosa using integrated computational models. Frontiers in Molecular Biosciences, 8, 728129.

Sgariglia, D., Conforte, A. J., Pedreira, C. E., Vidal de Carvalho, L. A., Carneiro, F. R. G., Carels, N., & Silva, F. A. B. D. (2021). Data-Driven Modeling of Breast Cancer Tumors Using Boolean Networks. Frontiers in Big Data, 4, 656395.

Silva, V. S., Costa, M. O., Castro, M. C. S., Silva, H. S., Walter, M. E. M., Melo, A. C., … & Silva, F. A. (2021). CellHeap: A Workflow for Optimizing COVID-19 Single-Cell RNA-Seq Data Processing in the Santos Dumont Supercomputer. In Brazilian Symposium on Bioinformatics (pp. 41-52). Springer, Cham.

2020

Conforte, A. J., Alves, L., Coelho, F. C., Carels, N., & Silva, F. A. B. D. (2020). Modeling basins of attraction for breast cancer using Hopfield networks. Frontiers in Genetics, 11, 314.

Vieira, J. M. D. L., de Matos, G. C., da Silva, F. A. B., Bracken, L. E., Peak, M., & Lima, E. D. C. (2020). Serious adverse drug reactions and safety signals in children: a nationwide database study. Frontiers in Pharmacology, 11, 964.

do Nascimento, A. P. B., Medeiros Filho, F., Pauer, H., Antunes, L. C. M., Sousa, H., Senger, H., … & da Silva, F. A. B. (2020). Characterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis. Scientific reports, 10(1), 1-15.

Henriques-Pons, A., Beatrici, C. P., Sánchez-Arcila, J. C., & Da Silva, F. A. B. (2020). Multiparametric Color Tendency Analysis (MCTA): A Method to Analyze Several Flow Cytometry Labelings Simultaneously. Frontiers in Bioengineering and Biotechnology, 8, 526814.

da Silva, F. A. B., Carels, N., dos Santos, M. T., & Lopes, F. J. P. (Eds.). (2020). Networks in Systems Biology: Applications for Disease Modeling (Vol. 32). Springer Nature.

Ferreira, L. H. O., Castro, M. C. S. D., Conforte, A. J., Carels, N., & Silva, F. A. B. D. (2020). Cellular Regulatory Network Modeling Applied to Breast Cancer. In Networks in Systems Biology (pp. 339-365). Springer, Cham.

Carels, N., Conforte, A. J., Lima, C. R., & Silva, F. A. B. D. (2020). Challenges for the optimization of drug therapy in the treatment of cancer. In Networks in Systems Biology (pp. 163-198). Springer, Cham.

2019

Duval, F. V., & Silva, F. A. B. D. (2019). Mining in Twitter for adverse events from malaria drugs: the case of doxycycline. Cadernos de Saúde Pública, 35.

Barcelos, F. C., Matos, G. C. D., Silva, M. J. S. D., Silva, F. A. B. D., & Lima, E. D. C. (2019). Suspected adverse drug reactions related to breast cancer chemotherapy: disproportionality analysis of the brazilian spontaneous reporting system. Frontiers in Pharmacology, 10, 498.

Medeiros, F., do Nascimento, A. P. B., Dos Santos, M. T., Carvalho-Assef, A. P. D. A., & da Silva, F. A. B. (2019). Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa. Memórias do Instituto Oswaldo Cruz, 114.

Merigueti, T. C., Carneiro, M. W., Carvalho-Assef, A. P. D. A., Silva-Jr, F. P., & Silva, F. A. B. D. (2019). FindTargetsWEB: a user-friendly tool for Identification of potential therapeutic targets in metabolic networks of bacteria. Frontiers in genetics, 10, 633.

Conforte, A. J., Tuszynski, J. A., Silva, F. A. B. D., & Carels, N. (2019). Signaling complexity measured by Shannon entropy and its application in personalized medicine. Frontiers in Genetics, 10, 930.

do Nascimento, A. P. B., Medeiros Filho, F., Pauer, H., Antunes, L. C. M., Sousa, H., Senger, H., … & da Silva, F. A. B. Comparative genome analysis of a multidrug-resistant Pseudomonas aeruginosa sequence type 277 clone that harbours two copies of the blaSPM-1 gene and multiple single nucleotide polymorphisms in other resistance-associated genes. BioRxiv

2018

Da Silva, F. A. B., Carels, N., & Junior, F. P. S. (Eds.). (2018). Theoretical and Applied Aspects of Systems Biology (Vol. 27). Springer.

Silva, F. A. B. D., Merigueti, T. C., Giannini, T., Brum, R., Faria, L. M. D., Nascimento, A. P. B. D., … & Carvalho-Assef, A. P. D. A. (2018). Computational Modeling of Multidrug-Resistant Bacteria. In Theoretical and Applied Aspects of Systems Biology (pp. 195-220). Springer, Cham.

Santos, M. T. D., Nascimento, A. P. B. D., & Silva, F. A. B. D. (2018). Modeling Gene Transcriptional Regulation: A Primer. In Theoretical and Applied Aspects of Systems Biology (pp. 27-39). Springer, Cham.

Sgariglia, D., Conforte, A. J., Carvalho, L. A. V. D., Carels, N., & Silva, F. A. B. D. (2018). Cellular Reprogramming. In Theoretical and Applied Aspects of Systems Biology (pp. 41-55). Springer, Cham.

Conforte, A. J., Magalhães, M., Tilli, T. M., Silva, F. A. B. D., & Carels, N. (2018). The challenge of translating system biology into targeted therapy of cancer. In Theoretical and Applied Aspects of Systems Biology (pp. 175-194). Springer, Cham.

Before 2018 - Selected Papers

de Castro, M. R., Tostes, C. D. S., Dávila, A. M., Senger, H., & da Silva, F. A. (2017). SparkBLAST: scalable BLAST processing using in-memory operations. BMC Bioinformatics, 18(1), 1-13.

Rodrigues, L. M. L., da Silva, F. A. B., Correia, R. J. C., Rijo, R. P. C. L., & Alves, D. (2017). Proposal of a gold standard database model of adverse drug reactions reports. Procedia Computer Science, 121, 883-888.

Senger, H., Gil‐Costa, V., Arantes, L., Marcondes, C. A., Marin, M., Sato, L. M., & Da Silva, F. A. (2016). BSP cost and scalability analysis for MapReduce operations. Concurrency and Computation: Practice and Experience, 28(8), 2503-2527.

Ribeiro-Vaz, I., Silva, F. A. B., Silva, A. M. M., Alves, D., & Cruz-Correia, R. (2016). Pharmacovigilance Informatics. In Encyclopedia of E-Health and Telemedicine (pp. 299-315). IGI Global.

Ferreira, L. H. O., de Castro, M. C. S., & da Silva, F. A. (2016). Modeling gene regulatory networks: a network simplification algorithm. In AIP Conference Proceedings (Vol. 1790, No. 1, p. 100003). AIP Publishing LLC.