An Ontology to Integrate Transcriptomics and Interatomics Data Involved in Gene Pathways of Genome Stability. - Giovani Rubert Librelotto; José Carlos Merino Mombach; Marialva Sinigaglia; Éder Simão; Heleno Borges Cabral; Mauro A. A. Castro (BSB, 2009)

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)

Estudo da diversidade tumoral e desenvolvimento de ferramentas de bioinformática para análise citogenética e molecular de neoplasias sólidas - Mauro A. A. Castro (2009)

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations. - Xin Wang 008; Mauro A. A. Castro; Klaas W. Mulder; Florian Markowetz (PLoS Comput. Biol., 2012)

GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks. - Esther Camilo; Luiz A. Bovolenta; Marcio Luis Acencio; José L. Rybarczyk Filho; Mauro A. A. Castro; José C. F. Moreira; Ney Lemke (Bioinform., 2013)

RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons. - Vinicius S. Chagas; Clarice S. Groeneveld; Kelin G. Oliveira; Sheyla Trefflich; Rodrigo C. de Almeida; Bruce A. J. Ponder; Kerstin B. Meyer; Steven J. M. Jones; A. Gordon Robertson; Mauro A. A. Castro (Bioinform., 2019)

RTNsurvival: an R/Bioconductor package for regulatory network survival analysis. - Clarice S. Groeneveld; Vinicius S. Chagas; Steven J. M. Jones; A. Gordon Robertson; Bruce A. J. Ponder; Kerstin B. Meyer; Mauro A. A. Castro (Bioinform., 2019)

TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves. - Milena A. Cardoso; Luis E. A. Rizzardi; Leonardo W. Kume; Clarice S. Groeneveld; Sheyla Trefflich; Diego A. A. Morais; Rodrigo J. S. Dalmolin; Bruce A. J. Ponder; Kerstin B. Meyer; Mauro A. A. Castro (Bioinform., 2022)

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. - Fabio Boniolo; Markus Hoffmann; Norman Roggendorf; Bahar Tercan; Jan Baumbach; Mauro A. A. Castro; A. Gordon Robertson; Dieter Saur; Markus List (Bioinform., 2023)