Selected Publications

For a full list of publications please access our google scholar profile

  1. DeepSEA: an alignment-free explainable approach to annotate antimicrobial resistance proteins

    Borelli, T. C.; Paschoal, A. R.; da Silva, R. R.

    BMC Bioinformatics, 26(1):224, 2025.

  2. A multi-omics reciprocal analysis for characterization of bacterial metabolism

    Arini, G. S., Borelli, T. C., Ferreira, E. G., de Felício, R., Rezende-Teixeira, P., Pedrino, M., Rabiço, F., Siqueira, G. M. V., Mencucini, L. G., Tsuji, H., Andrade, L. S. N., Garrido, L. M., Padilla, G., Gil-de-la-Fuente, A., Wang, M., Lopes, N. P., Trivella, D. B. B., Costa-Lotufo, L. V., Guazzaroni, M.-E., da Silva, R. R.

    Frontiers in Molecular Biosciences, 2025.

  3. A complementary approach for detecting biological signals through a semi-automated feature selection tool

    Arini, G. S.; Mencucini, L. G. S.; de Felício, R.; Feitosa, L. G. P.; Rezende-Teixeira, P.; de Oliveira Tsuji, H. M. Y.; Pilon, A. C.; Pinho, D. R.; Costa Lotufo, L. V.; Lopes, N. P.; Trivella, D. B. B.; da Silva, R. R.

    Frontiers in Chemistry, 12:1477492, 2024.

  4. Improving annotation propagation on molecular networks through random walks: Introducing ChemWalker

    Borelli, T. C.; Arini, G. S.; Feitosa, L. G. P.; Dorrestein, P. C.; Lopes, N. P.; Silva., R. R. D..

    Bioinformatics, 39(3):btad078, 2023.

  5. Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data

    Nora, L. C.; Cassiano, M. H. A.; Santana, Í. P.; Guazzaroni, M.-E.; Silva-Rocha, R.; da Silva, R. R.

    Frontiers in Microbiology, 13:1069443, 2023.

  6. ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

    Tamasco, G.; Kumar, M.; Zengler, K.; Silva-Rocha, R.; da Silva, R. R.

    BMC Bioinformatics, 23(1):512, 2022.