LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. - Felipe Torres; Raúl Arias-Carrasco; José C. Caris-Maldonado; Aldina Barral; Vinicius Maracaja-Coutinho; Artur T. L. De Queiroz (Database J. Biol. Databases Curation, 2017)

StructRNAfinder: an automated pipeline and web server for RNA families prediction. - Raúl Arias-Carrasco; Yessenia Vásquez-Morán; Helder I. Nakaya; Vinicius Maracaja-Coutinho (BMC Bioinform., 2018)

CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. - Pedro S. T. Russo; Gustavo R. Ferreira; Lucas E. Cardozo; Matheus C. Bürger; Raúl Arias-Carrasco; Sandra R. Maruyama; Thiago D. C. Hirata; Diógenes S. Lima; Fernando M. Passos; Kiyoshi F. Fukutani; Melissa Lever; João S. Silva; et al. (BMC Bioinform., 2018)

OUTBREAK: A user-friendly georeferencing online tool for disease surveillance. - Raúl Arias-Carrasco; Jeevan Giddaluru; Lucas E. Cardozo; Felipe Martins; Vinicius Maracaja-Coutinho; Helder I. Nakaya (CoRR, 2020)

RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction. - Thaís Ramos; Nilbson R. O. Galindo; Raúl Arias-Carrasco; Cecília Silva; Vinicius Maracaja-Coutinho; Thaís Gaudencio do Rêgo (F1000Research, 2021)

Ten quick tips for harnessing the power of ChatGPT in computational biology. - Tiago Lubiana; Rafael Lopes; Pedro Medeiros; Juan Carlo Silva; Andre Nicolau Aquime Goncalves; Vinicius Maracaja-Coutinho; Helder I. Nakaya (PLoS Comput. Biol., 2023)

Computational approaches for circRNAs prediction and in silico characterization. - Camilo Rebolledo; Juan Pablo Silva; Nicolás Saavedra; Vinicius Maracaja-Coutinho (Briefings Bioinform., 2023)

The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation. - Raúl Arias-Carrasco; Victor Aliaga-Tobar; Sebastián Abades; Vinicius Maracaja-Coutinho (Biosyst., 2025)