ViaComplex: software for landscape analysis of gene expression networks in genomic context. - Mauro A. A. Castro; José L. Rybarczyk Filho; Rodrigo J. S. Dalmolin; Marialva Sinigaglia; José C. F. Moreira; José C. M. Mombach; Rita M. C. de Almeida (Bioinform., 2009)

Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks. - Felipe A. Kuentzer; Alexandre S. Pereira; Alexandre M. Amory; Gabriel Perrone; Samoel R. M. Silva; Joao M. Dinis; Rita M. C. Almeida (BIBE, 2014)

Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction. - Diego A. A. Morais; Rita M. C. Almeida; Rodrigo J. S. Dalmolin (Bioinform., 2019)