ceRNAs in plants: computational approaches and associated challenges for target mimic research. - Alexandre Rossi Paschoal; Irma Lozada-Chávez; Douglas Silva Domingues; Peter F. Stadler (Briefings Bioinform., 2018)

PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants. - Daniel Longhi Fernandes Pedro; Alan Péricles Rodrigues Lorenzetti; Douglas Silva Domingues; Alexandre Rossi Paschoal (Database J. Biol. Databases Curation, 2018)

Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants. - Tatianne da Costa Negri; Wonder Alexandre Luz Alves; Pedro Henrique Bugatti; Priscila Tiemi Maeda Saito; Douglas Silva Domingues; Alexandre Rossi Paschoal (Briefings Bioinform., 2019)

mirtronDB: a mirtron knowledge base. - Bruno Henrique Ribeiro Da Fonseca; Douglas Silva Domingues; Alexandre Rossi Paschoal (Bioinform., 2019)

A Novel Decomposing Model With Evolutionary Algorithms for Feature Selection in Long Non-Coding RNAs. - Robson Parmezan Bonidia; Jaqueline Sayuri Machida; Tatianne da Costa Negri; Wonder Alexandre Luz Alves; André Y. Kashiwabara; Douglas Silva Domingues; André C. P. L. F. de Carvalho; Alexandre Rossi Paschoal; Danilo Sipoli Sanches (IEEE Access, 2020)

Feature extraction approaches for biological sequences: a comparative study of mathematical features. - Robson Bonidia; Lucas Dias H. Sampaio; Douglas Silva Domingues; Alexandre Rossi Paschoal; Fabrício Martins Lopes; André C. P. L. F. de Carvalho; Danilo Sipoli Sanches (Briefings Bioinform., 2021)

TERL: classification of transposable elements by convolutional neural networks. - Murilo Horacio Pereira da Cruz; Douglas Silva Domingues; Priscila Tiemi Maeda Saito; Alexandre Rossi Paschoal; Pedro Henrique Bugatti (Briefings Bioinform., 2021)

Impact of sequencing technologies on long non-coding RNA computational identification. - Alisson Gaspar Chiquitto; Lucas Otávio L. Silva; Liliane S. Oliveira; Douglas Silva Domingues; Alexandre Rossi Paschoal (BIBM, 2022)

MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors. - Robson Bonidia; Douglas Silva Domingues; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho (Briefings Bioinform., 2022)

Make No Mistake! Why Do Tools Make Incorrect Long Non-coding RNA Classification? - Alisson Gaspar Chiquitto; Lucas Otávio L. Silva; Liliane Santana Oliveira; Douglas Silva Domingues; Alexandre Rossi Paschoal (BSB, 2023)

Classification of LTR Retrotransposons via Interaction Prediction. - Silvana C. S. Cardoso; Douglas Silva Domingues; Alexandre Rossi Paschoal; Carlos N. Fischer; Ricardo Cerri (CIBCB, 2024)