Extending the method of mathematically controlled comparison to include numerical comparisons. - Rui Alves; Michael A. Savageau (Bioinform., 2000)

Comparing systemic properties of ensembles of biological networks by graphical and statistical methods. - Rui Alves; Michael A. Savageau (Bioinform., 2000)

Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. - Rui Alves; Michael A. Savageau (Bioinform., 2000)

Coded PPM based modulations for infrared wlan's. - Rui Alves; Atílio Gameiro (ACST, 2006)

Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock. - Ester Vilaprinyó; Rui Alves; Albert Sorribas (BMC Bioinform., 2006)

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. - Rui Alves; Albert Sorribas (BMC Syst. Biol., 2007)

Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes. - Ester Vilaprinyó; Rui Alves; Albert Sorribas (PLoS Comput. Biol., 2010)

Biblio-MetReS: A bibliometric network reconstruction application and server. - Anabel Usie; Hiren Karathia; Ivan Teixido; Joan Valls; Xavier Faus; Rui Alves; Francesc Solsona (BMC Bioinform., 2011)

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models. - Carlos Pozo; Alberto Marín-Sanguino; Rui Alves; Gonzalo Guillén-Gosálbez; Laureano Jiménez; Albert Sorribas (BMC Syst. Biol., 2011)

Augmenting Customer Journey Maps with quantitative empirical data: a case on EEG and eye tracking - Rui Alves; Veraneka Lim; Evangelos Niforatos; Mon-Chu Chen; Evangelos Karapanos; Nuno Jardim Nunes (CoRR, 2012)

Enwildering the lab: merging field evaluation with in-lab experience sampling. - Evangelos Niforatos; Evangelos Karapanos; Rui Alves; Maria Clara Correia Martins; Monchu Chen; Nuno Jardim Nunes (CHI Extended Abstracts, 2013)

Improving software effort estimation with human-centric models: a comparison of UCP and iUCP accuracy. - Rui Alves; Pedro Valente; Nuno Jardim Nunes (EICS, 2013)

Resource Constrained Project Scheduling with General Precedence Relations Optimized with SAT. - Rui Alves; Filipe Pereira Alvelos; Sérgio Dinis T. Sousa (EPIA, 2013)

Towards a Taxonomy of Service Design Methods and Tools. - Rui Alves; Nuno Jardim Nunes (IESS, 2013)

P-Biblio-MetReS, a parallel data mining tool for the reconstruction of molecular networks. - Ivan Teixido; Anabel Usie; Josep L. Lérida; Francesc Solsona; Jorge Comas; Nestor Torres; Hiren Karathia; Rui Alves (EuroMPI, 2013)

Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization. - Gonzalo Guillén-Gosálbez; Antoni Miró; Rui Alves; Albert Sorribas; Laureano Jiménez (BMC Syst. Biol., 2013)

Towards a measurement framework for tools' ceiling and threshold. - Rui Alves; Claudio Teixeira; Monica Nascimento; Amanda Marinho; Nuno Jardim Nunes (EICS, 2014)

MetReS: A Metabolic Reconstruction Database for Cloud Computing. - Jordi Vilaplana; Francesc Solsona; Ivan Teixido; Jordi Mateo; Anabel Usie; Nestor Torres; Jorge Comas; Rui Alves (INCoS, 2014)

The state of user experience evaluation practice. - Rui Alves; Pedro Valente; Nuno Jardim Nunes (NordiCHI, 2014)

CheNER: chemical named entity recognizer. - Anabel Usie; Rui Alves; Francesc Solsona; Miguel Vazquez; Alfonso Valencia (Bioinform., 2014)

S-PC: An e-treatment application for management of smoke-quitting patients. - Jordi Vilaplana; Francesc Solsona; Francesc Abella; Josep Cuadrado; Rui Alves; Jordi Mateo (Comput. Methods Programs Biomed., 2014)

Gobal optimization of hybrid kinetic/FBA models via outer-approximation. - Carlos Pozo; Antoni Miró; Gonzalo Guillén-Gosálbez; Albert Sorribas; Rui Alves; Laureano Jiménez (Comput. Chem. Eng., 2015)

The CHEMDNER corpus of chemicals and drugs and its annotation principles. - Martin Krallinger; Obdulia Rabal; Florian Leitner; Miguel Vazquez; David Salgado; Zhiyong Lu; Robert Leaman; Yanan Lu; Donghong Ji; Daniel M. Lowe; Roger A. Sayle; Riza Theresa Batista-Navarro; et al. (J. Cheminformatics, 2015)

CheNER: a tool for the identification of chemical entities and their classes in biomedical literature. - Anabel Usie; Joaquim Cruz; Jorge Comas; Francesc Solsona; Rui Alves (J. Cheminformatics, 2015)

Ceiling and Threshold of PaaS Tools: The Role of Learnability in Tool Adoption. - Rui Alves; Nuno Jardim Nunes (HCSE/HESSD, 2016)

Wind power curtailment optimization for day-ahead operational planning. - Rui Alves; F. S. Reis; Hong Shen (ISGT Europe, 2016)

HBPF: a Home Blood Pressure Framework with SLA guarantees to follow up hypertensive patients. - Josep Cuadrado; Jordi Vilaplana; Jordi Mateo; Francesc Solsona; Sara Solsona; Josep Rius 002; Rui Alves; Miguel Camafort (PeerJ Prepr., 2016)

Gisplay- Extensible Web API for Thematic Maps with WebGL. - Diogo Cardoso; Rui Alves; João Moura Pires; Fernando Pedro Birra; Ricardo Silva (ICCSA (6), 2017)

TControl: A mobile app to follow up tobacco-quitting patients. - Marc Pifarré; Adrián Carrera; Jordi Vilaplana; Josep Cuadrado; Sara Solsona; Francesc Abella; Francesc Solsona; Rui Alves (Comput. Methods Programs Biomed., 2017)

Rare Disease Discovery: An Optimized Disease Ranking System. - Marc Piñol; Rui Alves; Ivan Teixido; Jordi Mateo; Francesc Solsona; Ester Vilaprinyó (IEEE Trans. Ind. Informatics, 2017)

Practices and Architectures for TSO-DSO Data Exchange: European Landscape. - Eric Lambert; Hugo Morais; Francisco Reis; Rui Alves; Gareth Taylor; Andrej Souvent; Nermin Suljanovic (ISGT Europe, 2018)

MetReS, an Efficient Database for Genomic Applications. - Jordi Vilaplana; Rui Alves; Francesc Solsona; Jordi Mateo; Ivan Teixido; Marc Pifarré (J. Comput. Biol., 2018)

EasyModel 1.1: User-friendly Stochastic and Deterministic Simulations for Systems Biology Models. - Jordi Bartolomé; Rui Alves; Francesc Solsona (BIOINFORMATICS, 2020)

Extending Heterogeneous Applications to Remote Co-processors with rOpenCL. - Rui Alves; José Rufino (SBAC-PAD, 2020)

EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology. - Jordi Bartolomé; Rui Alves; Francesc Solsona; Ivan Teixido (Bioinform., 2020)

eHealthCare - A Medication Monitoring Approach for the Elderly People. - António Pinto; Ana Correia; Rui Alves; Paulo Matos; João Ascensão; Diogo Camelo (MobiHealth, 2021)

Design and Implementation of a Wind Farm Controller Using Aerodynamics Estimated From LIDAR Scans of Wind Turbine Blades. - Adam Stock; Lindsey Amos; Rui Alves; William E. Leithead (IEEE Control. Syst. Lett., 2021)

Mech Desk: An ontology based system to help drivers diagnosis vehicle problems. - Diogo Camelo; João Ascensão; Rui Alves; Paulo Matos (ICFET, 2022)

eSleepApnea - A Tool to Aid the Detection of Sleep Apnea. - Rui Alves; Paulo Matos; João Ascensão; Diogo Camelo (MobiHealth, 2022)

Query Log Analysis for SQL Injection Detection. - Alexandra Rocha; Rui Alves; Tiago Pedrosa (ICISSP, 2023)

Remote Execution of OpenCL and SYCL Applications via rOpenCL. - Rui Alves; José Rufino (IPDPS Workshops, 2023)

A Solution to Prevent and Minimize the Consequences of Accidents with Farm Tractors in the Context of Mountainous Regions with Low Population Density. - Rui Alves; Paulo Matos (Sensors, 2023)

Leveraging Shared Accelerators in Kubernetes Clusters with rOpenCL. - Rui Alves; José Rufino (SERA, 2024)

ForestForward: visualizing and accessing integrated world forest data from the last 50 years. - E. L. Tejada-Gutiérrez; Jordi Mateo-Fornés; Francesc Solsona; Rui Alves (Database J. Biol. Databases Curation, 2025)