Rafael S. Costa

26 papers B 1Journal 20Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A Physics-Informed Neural Network (PINN) framework for generic bioreactor modelling. Comput. Chem. Eng. Monesh kumar Thirugnanasambandam, José Pinto, Ekaterina Moskovkina, Rafael S. Costa, Rui Oliveira
2025	J	`jnl`	Bottlenecks in advancing and applying multiomic data integration - common data resources as rate-limiting drivers - the high-impact use case of atherosclerotic cardiovascular disease. Briefings Bioinform. Stephanie Bezzina Wettinger, Kanita Karaduzovic-Hadziabdic, Ritienne Attard, Rosienne Farrugia, Brooke N. Wolford, Marco Chierici, Giuseppe Jurman, Panagiotis Alexiou, José L. Peñalvo, Rafael S. Costa, José Basilio, Frantisek Sabovcik, Rui Vitorino, Johannes A. Schmid, Rajesh Shigdel, Baiba Vilne, Artemis G. Hatzigeorgiou, Miron Sopic, Yvan Devaux, Paolo Magni, Maria Tellez-Plaza, David P. Kreil, Aleksandra Gruca
2025	J	`jnl`	Integrating statistical significance and discriminative power in pattern discovery. Knowl. Based Syst. Leonardo Alexandre, Rafael S. Costa, Rui Henriques
2024	J	`jnl`	Integrating Statistical Significance and Discriminative Power in Pattern Discovery. CoRR Leonardo Alexandre, Rafael S. Costa, Rui Henriques
2024	J	`jnl`	TriSig: Evaluating the statistical significance of triclusters. Pattern Recognit. Leonardo Alexandre, Rafael S. Costa, Rui Henriques
2023	J	`jnl`	SBML2HYB: a Python interface for SBML compatible hybrid modeling. Bioinform. José Pinto, Rafael S. Costa, Leonardo Alexandre, João Ramos, Rui Oliveira
2023	J	`jnl`	TriSig: Assessing the statistical significance of triclusters. CoRR Leonardo Alexandre, Rafael S. Costa, Rui Henriques
2022	J	`jnl`	A general deep hybrid model for bioreactor systems: Combining first principles with deep neural networks. Comput. Chem. Eng. José Pinto, Mykaella Mestre, J. Ramos, Rafael S. Costa, Gerald Striedner, Rui Oliveira
2022	B	`conf`	Context-situated visualization of biclusters to aid decisions: going beyond subspaces with parallel coordinates. AVI Daniel Gonçalves, Rafael S. Costa, Rui Henriques
2022	J	`jnl`	Enrichment analysis on regulatory subspaces: A novel direction for the superior description of cellular responses to SARS-CoV-2. Comput. Biol. Medicine Pedro Rodrigues, Rafael S. Costa, Rui Henriques
2022	J	`jnl`	IPOscore: An interactive web-based platform for postoperative surgical complications analysis and prediction in the oncology domain. Comput. Methods Programs Biomed. Hugo Mochão, Daniel Gonçalves, Leonardo Alexandre, Carolina Castro, Duarte Valério, Pedro Barahona, Daniel Moreira-Gonçalves, Paulo Matos da Costa, Rui Henriques, Lucio Lara-Santos, Rafael S. Costa
2022	J	`jnl`	Scaling pattern mining through non-overlapping variable partitioning. CoRR Leonardo Alexandre, Rafael S. Costa, Rui Henriques
2021	J	`jnl`	DI2: prior-free and multi-item discretization of biological data and its applications. BMC Bioinform. Leonardo Alexandre, Rafael S. Costa, Rui Henriques
2021	J	`jnl`	DI2: prior-free and multi-item discretization ofbiomedical data and its applications. CoRR Leonardo Alexandre, Rafael S. Costa, Rui Henriques
2021	J	`jnl`	Mining Pre-Surgical Patterns Able to Discriminate Post-Surgical Outcomes in the Oncological Domain. IEEE J. Biomed. Health Informatics Leonardo Alexandre, Rafael S. Costa, Lucio Lara-Santos, Rui Henriques
2021	J	`jnl`	On the predictability of postoperative complications for cancer patients: a Portuguese cohort study. BMC Medical Informatics Decis. Mak. Daniel Gonçalves, Rui Henriques, Lucio Lara-Santos, Rafael S. Costa
2020	J	`jnl`	KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. Database J. Biol. Databases Curation Hugo Mochão, Pedro Barahona, Rafael S. Costa
2016	J	`jnl`	Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber
2014	—	`conf`	Exploring the Cellular Objective in Flux Balance Constraint-Based Models. CMSB Rafael S. Costa, Son Nguyen, András Hartmann, Susana Vinga
2014	J	`jnl`	Identifying IIR filter coefficients using particle swarm optimization with application to reconstruction of missing cardiovascular signals. Eng. Appl. Artif. Intell. András Hartmann, João Miranda Lemos, Rafael S. Costa, Susana Vinga
2014	J	`jnl`	KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. BMC Syst. Biol. Rafael S. Costa, André Veríssimo, Susana Vinga
2012	—	`conf`	Multi-level Dynamic Modeling in Biological Systems - Application of Hybrid Petri Nets to Network Simulation. BIOINFORMATICS Rafael S. Costa, Daniel Machado, Ana Rute Neves, Susana Vinga
2010	J	`jnl`	Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosyst. Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira
2010	—	`conf`	Model Transformation of Metabolic Networks using a Petri Net Based Framework. ACSD/Petri Nets Workshops Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2009	—	`conf`	A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. IWANN (2) Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2009	—	`conf`	Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli . IWANN (2) Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira