ProtozoaDB: dynamic visualization and exploration of protozoan genomes. - Alberto M. R. Dávila; Pablo N. Mendes; Glauber Wagner; Diogo A. Tschoeke; Rafael R. C. Cuadrat; Felipe Liberman; Luciana Matos; Thiago S. Satake; Kary A. C. S. Ocaña; Omar Triana; Sérgio Manuel Serra da Cruz; Henrique C. L. Jucá; et al. (Nucleic Acids Res., 2008)

A Performance Evaluation of X-Ray Crystallography Scientific Workflow Using SciCumulus. - Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Jonas Dias; Fernanda Araújo Baião; Marta Mattoso (IEEE CLOUD, 2011)

Optimizing Phylogenetic Analysis Using SciHmm Cloud-based Scientific Workflow. - Kary A. C. S. Ocaña; Daniel de Oliveira 001; Jonas Dias; Eduardo S. Ogasawara; Marta Mattoso (eScience, 2011)

SciPhy: A Cloud-Based Workflow for Phylogenetic Analysis of Drug Targets in Protozoan Genomes. - Kary A. C. S. Ocaña; Daniel de Oliveira 001; Eduardo S. Ogasawara; Alberto M. R. Dávila; Alexandre A. B. Lima; Marta Mattoso (BSB, 2011)

Discovering drug targets for neglected diseases using a pharmacophylogenomic cloud workflow. - Kary A. C. S. Ocaña; Daniel de Oliveira 001; Jonas Dias; Eduardo S. Ogasawara; Marta Mattoso (eScience, 2012)

Enabling Re-executions of Parallel Scientific Workflows Using Runtime Provenance Data. - Flavio Costa; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Marta Mattoso (IPAW, 2012)

Using Domain-Specific Data to Enhance Scientific Workflow Steering Queries. - João Carlos de A. R. Gonçalves; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Marta Mattoso (IPAW, 2012)

Using Provenance Analyzers to Improve the Performance of Scientific Workflows in Cloud Environments. - João Carlos de A. R. Gonçalves; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Jonas Dias; Marta Mattoso (SBBD (Short Papers), 2012)

Handling Failures in Parallel Scientific Workflows Using Clouds. - Flavio Costa; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Jonas Dias; Marta Mattoso (SC Companion, 2012)

Abstract: Using Provenance to Visualize Data from Large-Scale Experiments. - Felipe Horta; Jonas Dias; Kary A. C. S. Ocaña; Daniel de Oliveira 001; Eduardo S. Ogasawara; Marta Mattoso (SC Companion, 2012)

Exploring Molecular Evolution Reconstruction Using a Parallel Cloud Based Scientific Workflow. - Kary A. C. S. Ocaña; Daniel de Oliveira 001; Felipe Horta; Jonas Dias; Eduardo S. Ogasawara; Marta Mattoso (BSB, 2012)

An adaptive parallel execution strategy for cloud-based scientific workflows. - Daniel de Oliveira 001; Eduardo S. Ogasawara; Kary A. C. S. Ocaña; Fernanda Araújo Baião; Marta Mattoso (Concurr. Comput. Pract. Exp., 2012)

A Provenance-based Adaptive Scheduling Heuristic for Parallel Scientific Workflows in Clouds. - Daniel de Oliveira 001; Kary A. C. S. Ocaña; Fernanda Araújo Baião; Marta Mattoso (J. Grid Comput., 2012)

Capturing and querying workflow runtime provenance with PROV: a practical approach. - Flavio Costa; Vítor Silva 003; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Jonas Dias; Marta Mattoso (EDBT/ICDT Workshops, 2013)

Provenance traces from Chiron parallel workflow engine. - Felipe Horta; Vítor Silva 003; Flavio Costa; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Jonas Dias; Marta Mattoso (EDBT/ICDT Workshops, 2013)

Dimensioning the virtual cluster for parallel scientific workflows in clouds. - Daniel de Oliveira 001; Vitor Viana; Eduardo S. Ogasawara; Kary A. C. S. Ocaña; Marta Mattoso (ScienceCloud@HPDC, 2013)

SciLightning: A Cloud Provenance-Based Event Notification for Parallel Workflows. - Julliano Trindade Pintas; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Marta Mattoso (ICSOC Workshops, 2013)

User-steering of HPC workflows: state-of-the-art and future directions. - Marta Mattoso; Kary A. C. S. Ocaña; Felipe Horta; Jonas Dias; Eduardo S. Ogasawara; Vítor Silva 003; Daniel de Oliveira 001; Flavio Costa; Igor Araújo (SWEET@SIGMOD, 2013)

Runtime Dynamic Structural Changes of Scientific Workflows in Clouds. - Igor Dos Santos; Jonas Dias; Daniel de Oliveira 001; Eduardo S. Ogasawara; Kary A. C. S. Ocaña; Marta Mattoso (UCC, 2013)

Designing a parallel cloud based comparative genomics workflow to improve phylogenetic analyses. - Kary A. C. S. Ocaña; Daniel de Oliveira 001; Jonas Dias; Eduardo S. Ogasawara; Marta Mattoso (Future Gener. Comput. Syst., 2013)

Performance evaluation of parallel strategies in public clouds: A study with phylogenomic workflows. - Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Jonas Dias; João Carlos de A. R. Gonçalves; Fernanda Araújo Baião; Marta Mattoso (Future Gener. Comput. Syst., 2013)

Performance Analysis of Data Filtering in Scientific Workflows. - João Carlos de A. R. Gonçalves; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Jonas Dias; Marta Mattoso (J. Inf. Data Manag., 2013)

Evaluating Grasp-based cloud dimensioning for comparative genomics: A practical approach. - Rafaelli de C. Coutinho; Lúcia M. A. Drummond; Yuri Frota; Daniel de Oliveira 001; Kary A. C. S. Ocaña (CLUSTER, 2014)

Exploiting the Parallel Execution of Homology Workflow Alternatives in HPC Compute Clouds. - Kary A. C. S. Ocaña; Daniel de Oliveira 001; Vítor Silva 003; Silvia Benza; Marta Mattoso (ICSOC Workshops, 2014)

Towards Supporting Provenance Gathering and Querying in Different Database Approaches. - Flavio Costa; Vítor Silva 003; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Marta Mattoso (IPAW, 2014)

Exploring Large Scale Receptor-Ligand Pairs in Molecular Docking Workflows in HPC Clouds. - Kary A. C. S. Ocaña; Silvia Benza; Daniel de Oliveira 001; Jonas Dias; Marta Mattoso (IPDPS Workshops, 2014)

Debugging Scientific Workflows with Provenance: Achievements and Lessons Learned. - Daniel de Oliveira 001; Flavio Costa; Vítor Silva 003; Kary A. C. S. Ocaña; Marta Mattoso (SBBD, 2014)

Captura e Consulta a Dados de Proveniência Retrospectiva Implícita Intra-Atividade. - Wellington Moreira de Oliveira; Vitor C. Neves; Kary A. C. S. Ocaña; Leonardo Murta 001; Daniel de Oliveira 001; Vanessa Braganholo (SBBD, 2014)

Data Analytics in Bioinformatics: Data Science in Practice for Genomics Analysis Workflows. - Kary A. C. S. Ocaña; Vítor Silva 003; Daniel de Oliveira 001; Marta Mattoso (e-Science, 2015)

Uma Abordagem para Publicação de Dados de Proveniência de Workflows Científicos na Web Semântica. - Rachel Castro; Renan Souza 001; Vítor Silva 003; Kary A. C. S. Ocaña; Daniel de Oliveira 001; Marta Mattoso (SBBD (Short Papers), 2015)

Dynamic steering of HPC scientific workflows: A survey. - Marta Mattoso; Jonas Dias; Kary A. C. S. Ocaña; Eduardo S. Ogasawara; Flavio Costa; Felipe Horta; Vítor Silva 003; Daniel de Oliveira 001 (Future Gener. Comput. Syst., 2015)

Analyzing Provenance Across Heterogeneous Provenance Graphs. - Wellington Moreira de Oliveira; Paolo Missier; Kary A. C. S. Ocaña; Daniel de Oliveira 001; Vanessa Braganholo (IPAW, 2016)

Gerência de Incerteza em Bancos de Dados de Proveniência de Workflows de Bioinformática. - Gustavo Tallarida; Kary A. C. S. Ocaña; Aline Paes; Vanessa Braganholo; Daniel de Oliveira 001 (SBBD, 2016)

Um Sistema de Informação para Gerência de Projetos Científicos baseados em Simulações Computacionais [An IS for Managing Scientific Projects]. - Leonardo S. Ramos; Kary A. C. S. Ocaña; Daniel Oliveira 001 (SBSI, 2016)

A Dynamic Cloud Dimensioning Approach for Parallel Scientific Workflows: a Case Study in the Comparative Genomics Domain. - Rafaelli de C. Coutinho; Yuri Frota; Kary A. C. S. Ocaña; Daniel de Oliveira 001; Lúcia M. A. Drummond (J. Grid Comput., 2016)

SciAgile: Aplicação de Metodologias Ágeis em Experimentos Científicos Baseados em Simulação. - Augusto Romeiro; Kary A. C. S. Ocaña; Marcos Kalinowski; Daniel de Oliveira 001 (CIbSE, 2017)

Towards preserving results confidentiality in cloud-based scientific workflows. - Isabel Rosseti; Kary A. C. S. Ocaña; Daniel de Oliveira 001 (WORKS@SC, 2017)

Deriving scientific workflows from algebraic experiment lines: A practical approach. - Anderson Marinho; Daniel de Oliveira 001; Eduardo S. Ogasawara; Vítor Silva 003; Kary A. C. S. Ocaña; Leonardo Murta 001; Vanessa Braganholo; Marta Mattoso (Future Gener. Comput. Syst., 2017)

Querying Provenance along with External Domain Data Using Prolog. - Wellington Moreira de Oliveira; Kary A. C. S. Ocaña; Daniel de Oliveira 001; Vanessa Braganholo (J. Inf. Data Manag., 2017)

Managing Provenance of Implicit Data Flows in Scientific Experiments. - Vitor C. Neves; Daniel de Oliveira 001; Kary A. C. S. Ocaña; Vanessa Braganholo; Leonardo Murta 001 (ACM Trans. Internet Techn., 2017)

Mirror Mirror on the Wall, How Do I Dimension My Cloud After All? - Rafaelli de C. Coutinho; Yuri Frota; Kary A. C. S. Ocaña; Daniel de Oliveira 001; Lúcia M. A. Drummond (Cloud Computing, 2nd Ed., 2017)

Scientific Data Analysis Using Data-Intensive Scalable Computing: The SciDISC Project. - Patrick Valduriez; Marta Mattoso; Reza Akbarinia; Heraldo Borges; José J. Camata; Alvaro L. G. A. Coutinho; Daniel Gaspar; Noel Moreno Lemus; Ji Liu 003; Hermano Lustosa; Florent Masseglia; Fabrício Nogueira da Silva; et al. (LADaS@VLDB, 2018)

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments. - Maria Luiza Mondelli; Thiago Magalhães; Guilherme Loss; Michael Wilde; Ian T. Foster; Marta Mattoso; Daniel S. Katz; Helio J. C. Barbosa; Ana Tereza Ribeiro de Vasconcelos; Kary A. C. S. Ocaña; Luiz M. R. Gadelha Jr. (CoRR, 2018)

Performance Evaluation of Parallel Inference of Large Phylogenetic Trees in Santos Dumont Supercomputer: A Practical Approach. - Kary A. C. S. Ocaña; Carla Osthoff; Micaella Coelho; Marcelo Galheigo; Isabela Canuto; Douglas E. M. de Oliveira; Daniel de Oliveira 001 (CARLA, 2019)

Towards a Science Gateway for Bioinformatics: Experiences in the Brazilian System of High Performance Computing. - Kary Ann del Carmen Ocaña Gautherot; Marcelo Galheigo; Carla Osthoff; Luiz M. R. Gadelha Jr.; Antônio Tadeu A. Gomes; Daniel de Oliveira 001; Fábio Porto 001; Ana Tereza Ribeiro de Vasconcelos (CCGRID, 2019)

ArrOW: Experiencing a Parallel Cloud-Based De Novo Assembler Workflow. - Kary A. C. S. Ocaña; Thaylon Guedes; Daniel de Oliveira 001 (IPDPS Workshops, 2019)

Um Estudo Comparativo de Mecanismos de Privacidade Diferencial sobre um Dataset de Ocorrências do ZIKV no Brasil. - Daniel de Oliveira 001; Eduardo Rodrigues Duarte Neto; Serafim Costa; Paulo Roberto Pessoa Amora; Asley Caldas; Marco Horta; Ana Maria de Fillippis; Kary A. C. S. Ocaña; Vânia Maria P. Vidal; Javam C. Machado (SBBD, 2019)

Análise Integrada de Grafos de Proveniência Heterogêneos por meio de uma Abordagem PolyStore. - Yan Mendes; Victor Ströele; Daniel de Oliveira 001; Kary A. C. S. Ocaña (SBBD, 2019)

A provenance-based heuristic for preserving results confidentiality in cloud-based scientific workflows. - Marcos A. Guerine; Murilo B. Stockinger; Isabel Rosseti; Luidi Gelabert Simonetti; Kary A. C. S. Ocaña; Alexandre Plastino 001; Daniel de Oliveira 001 (Future Gener. Comput. Syst., 2019)

Xi-DL: um Sistema de Gerência de Data Lake para Monitoramento de Dados da Saúde. - Lucas Tito; Cristina Motinha; Filipe Santiago; Kary A. C. S. Ocaña; Marcos V. N. Bedo; Daniel de Oliveira 001 (SBBD, 2020)

Provenance-based fault tolerance technique recommendation for cloud-based scientific workflows: a practical approach. - Thaylon Guedes; Leonardo Araújo de Jesus; Kary A. C. S. Ocaña; Lúcia M. A. Drummond; Daniel de Oliveira 001 (Clust. Comput., 2020)

Capturing and Analyzing Provenance from Spark-based Scientific Workflows with SAMbA-RaP. - Thaylon Guedes; Lucas Bertelli Martins; Maria Luiza Furtuozo Falci; Vítor Silva 003; Kary A. C. S. Ocaña; Marta Mattoso; Marcos V. N. Bedo; Daniel de Oliveira 001 (Future Gener. Comput. Syst., 2020)

BioinfoPortal: A scientific gateway for integrating bioinformatics applications on the Brazilian national high-performance computing network. - Kary A. C. S. Ocaña; Marcelo Galheigo; Carla Osthoff; Luiz M. R. Gadelha Jr.; Fábio Porto 001; Antônio Tadeu A. Gomes; Daniel de Oliveira 001; Ana Tereza Ribeiro de Vasconcelos (Future Gener. Comput. Syst., 2020)

ParslRNA-Seq: An Efficient and Scalable RNAseq Analysis Workflow for Studies of Differentiated Gene Expression. - Kary A. C. S. Ocaña; Lucas Cruz; Micaella Coelho; Rafael Terra; Marcelo Galheigo; Andre Ramos Carneiro; Diego Carvalho 001; Luiz M. R. Gadelha Jr.; Francieli Zanon Boito; Philippe O. A. Navaux; Carla Osthoff (CARLA, 2022)

Parallel Performance and I/O Profiling of HPC RNA-Seq Applications. - Lucas Cruz; Micaella Coelho; Marcelo Galheigo; André Ramos Carneiro; Diego Carvalho 001; Luiz M. R. Gadelha Jr.; Francieli Zanon Boito; Philippe O. A. Navaux; Carla Osthoff; Kary A. C. S. Ocaña (Computación y Sistemas, 2022)

An Exploratory Study of Deep Learning for Predicting Computational Tasks Behavior in HPC Systems. - Alexandre H. L. Porto; Micaella Coelho; Kary A. C. S. Ocaña; Carla Osthoff; Francieli Boito; Douglas de O. Cardoso (SBAC-PADW, 2023)

Assuming the best: Towards a reliable protocol for resource usage prediction for high-performance computing based on machine learning. - Alexandre H. L. Porto; Micaella Coelho; Hiago Mayk G. de A. Rocha; Carla Osthoff; Kary A. C. S. Ocaña; Douglas de O. Cardoso (Future Gener. Comput. Syst., 2026)