K-mer Mapping and de Bruijn graphs: The case for velvet fragment assembly. - Elvismary Molina de Armas; Edward Hermann Haeusler; Sérgio Lifschitz; Maristela Terto de Holanda; Waldeyr Mendes Cordeiro da Silva; Paulo Cavalcanti Gomes Ferreira (BIBM, 2016)

An evaluation of data replication for bioinformatics workflows on NoSQL systems. - Iasmini Lima; Matheus Oliveira; Diego Kieckbusch; Maristela Holanda; Maria Emília M. T. Walter; Aletéia Patrícia Favacho de Araújo; Márcio Victorino; Waldeyr Mendes Cordeiro da Silva; Sérgio Lifschitz (BIBM, 2016)

2Path: A terpenoid metabolic network modeled as graph database. - Waldeyr Mendes Cordeiro da Silva; Danilo Vilar; Daniel S. Souza; Maria Emília Telles Walter; Marcelo M. Brigido; Maristela Holanda (BIBM, 2016)

AProvBio: An architecture for data provenance in bioinformatics workflows using graph database. - Rodrigo F. Almeida; Waldeyr Mendes Cordeiro da Silva; Klayton Castro; Maria Emília Telles Walter; Aletéia Patrícia Favacho de Araújo; Maristela Holanda; Sérgio Lifschitz (BIBM, 2017)

Data provenance management for bioinformatics workflows using NoSQL database systems in a cloud computing environment. - Fernanda Hondo; Polyane Wercelens; Waldeyr Mendes Cordeiro da Silva; Klayton Castro; Ingrid Santana; Maria Emília Telles Walter; Aletéia Patrícia Favacho de Araújo; Maristela Holanda; Sérgio Lifschitz (BIBM, 2017)

A terpenoid metabolic network modelled as graph database. - Waldeyr Mendes Cordeiro da Silva; Danilo Vilar; Daniel S. Souza; Maria Emília Telles Walter; Maristela Terto de Holanda; Marcelo de Macedo Brígido (Int. J. Data Min. Bioinform., 2017)

Graph Databases in Molecular Biology. - Waldeyr Mendes Cordeiro da Silva; Polyane Wercelens; Maria Emília M. T. Walter; Maristela Holanda; Marcelo M. Brigido (BSB, 2018)

An Argumentation Theory-Based Multiagent Model to Annotate Proteins. - Daniel S. Souza; Waldeyr Mendes Cordeiro da Silva; Célia Ghedini Ralha; Maria Emília M. T. Walter (BSB, 2018)

GRAPHED: A Graph Description Diagram for Graph Databases. - Gustavo Cordeiro Galvão Van Erven; Waldeyr Mendes Cordeiro da Silva; Rommel N. Carvalho; Maristela Holanda (WorldCIST (1), 2018)

Human-Computer Interaction Communicability Evaluation Method Applied to Bioinformatics. - Gabriella Esteves; Waldeyr Mendes Cordeiro da Silva; Maria Emília Telles Walter; Marcelo M. Brigido; Fernanda Lima (WorldCIST (2), 2018)

Big Data Trends in Bioinformatics. - Dennis Sávio M. da Silva; Waldeyr M. C. Silva; Guo RuiZhe; Ana Paula Bernardi; Ari Melo Mariano; Maristela Holanda (BIBM, 2019)

Data Provenance Management of Bioinformatics Workflows in Federated Clouds. - Polyane Wercelens; Waldeyr Mendes Cordeiro da Silva; Klayton Castro; Aletéia P. F. Araújo; Sérgio Lifschitz; Maristela Holanda (BIBM, 2019)

Enhancing Open Government Data With Data Provenance. - Cleyton P. dos Reis; Waldeyr M. C. Silva; Luiz C. B. Martins; Rodrigo Pinheiro; Márcio Victorino; Maristela Holanda (MEDES, 2019)

Venom Gland Peptides of Arthropods from the Brazilian Cerrado Biome Unveiled by Transcriptome Analysis. - Giovanni M. Guidini; Waldeyr M. C. Silva; Thalita S. Camargos; Caroline F. B. Mourão; Priscilla Galante; Tainá Raiol; Marcelo de Macedo Brígido; Maria Emília M. T. Walter; Elisabeth N. F. Schwartz (BSB, 2019)

A NoSQL Solution for Bioinformatics Data Provenance Storage. - Ingrid Santana; Waldeyr Mendes Cordeiro da Silva; Maristela Holanda (WorldCIST (1), 2019)

Managing data provenance for bioinformatics workflows using AProvBio. - Rodrigo F. Almeida; Waldeyr Mendes Cordeiro da Silva; Klayton Castro; Aletéia Patrícia Favacho de Araújo; Maria Emília Telles Walter; Sérgio Lifschitz; Maristela Holanda (Int. J. Comput. Biol. Drug Des., 2019)

Designing Graph Databases With GRAPHED. - Gustavo Cordeiro Galvão Van Erven; Rommel Novaes Carvalho; Waldeyr Mendes Cordeiro da Silva; Sérgio Lifschitz; Harley Vera Olivera; Maristela Holanda (J. Database Manag., 2019)

Anti-CD3 Stimulated T Cell Transcriptome Reveals Novel ncRNAs and Correlates with a Suppressive Profile. - Manuela M. do Almo; Isabel G. Sousa; Waldeyr Mendes Cordeiro da Silva; Thomas Gatter; Peter F. Stadler; Steve Hoffmann; Andrea Queiroz Maranhão; Marcelo M. Brigido (BSB, 2020)

Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. - Waldeyr Mendes Cordeiro da Silva; Daniela P. de Andrade; Jakob L. Andersen; Maria Emília Telles Walter; Marcelo M. Brigido; Peter F. Stadler; Christoph Flamm (BSB, 2020)

Resource Prediction Service for Efficient Execution of Bioinformatics Workflows in Federated Cloud with Machine Learning. - Matheus Sobrinho; Michel J. F. Rosa; Waldeyr M. C. Silva; Aletéia Patrícia Favacho de Araújo (BIBM, 2021)

Machine Learning Studies of Non-coding RNAs based on Artificially Constructed Training Data. - Mirele C. S. F. Costa; João Victor de Araújo Oliveira; Waldeyr M. C. Silva; Rituparno Sen; Jörg Fallmann; Peter F. Stadler; Maria Emília M. T. Walter (BIOINFORMATICS, 2021)

In Silico Analysis of the Genomic Potential for the Production of Specialized Metabolites of Ten Strains of the Bacillales Order Isolated from the Soil of the Federal District, Brazil. - Felipe de Araújo Mesquita; Waldeyr Mendes Cordeiro da Silva; Marlene Teixeira De-Souza (BSB, 2022)

transcAnalysis: A Snakemake Pipeline for Differential Expression and Post-transcriptional Modification Analysis. - Pedro H. A. Barros; Waldeyr M. C. Silva; Marcelo M. Brigido (BSB, 2023)

Hierarchical Article Classification: A Multi-Level Framework for Organizing Scholarly Literature. - Luís Paulo F. Garcia; Jesús P. Mena-Chalco; Rafaela L. Grando; Waldeyr Mendes Cordeiro da Silva; Felipe Pontes Guimarães; Vanessa de A. Jorge (IEEE Access, 2025)