Optimizing Parallel CFD Simulations of 2D Compressible Flows. - Ana Claudia Sima; Emil Slusanschi (SYNASC, 2012)

Cyclone: Unified Stream and Batch Processing. - Matús Harvan; Thomas Locher; Ana Claudia Sima (ICPP Workshops, 2016)

A Hybrid Approach for Alarm Verification using Stream Processing, Machine Learning and Text Analytics. - Ana Claudia Sima; Kurt Stockinger; Katrin Affolter; Martin Braschler; Peter Monte; Lukas Kaiser (EDBT, 2018)

Enabling semantic queries across federated bioinformatics databases. - Ana Claudia Sima; Tarcisio Mendes de Farias; Erich Zbinden; Maria Anisimova; Manuel Gil; Heinz Stockinger; Kurt Stockinger; Marc Robinson-Rechavi; Christophe Dessimoz (Database J. Biol. Databases Curation, 2019)

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. - Ana Claudia Sima; Christophe Dessimoz; Kurt Stockinger; Monique Zahn-Zabal; Tarcisio Mendes de Farias (F1000Research, 2019)

Big Data architecture for intelligent maintenance: a focus on query processing and machine learning algorithms. - Claude Lehmann; Lilach Goren Huber; Thomas Horisberger; Georg Scheiba; Ana Claudia Sima; Kurt Stockinger (J. Big Data, 2020)

Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (SSDBM, 2021)

INODE: Building an End-to-End Data Exploration System in Practice [Extended Vision]. - Sihem Amer-Yahia; Georgia Koutrika; Frederic B. Bastian; Theofilos Belmpas; Martin Braschler; Ursin Brunner; Diego Calvanese; Maximilian Fabricius; Orest Gkini; Catherine Kosten; Davide Lanti; Antonis Litke; et al. (CoRR, 2021)

Federating and querying heterogeneous and distributed Web APIs and triple stores. - Tarcisio Mendes de Farias; Christophe Dessimoz; Aarón Ayllón-Benítez; Chen Yang; Jiao Long; Ana Claudia Sima (CoRR, 2022)

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (Distributed Parallel Databases, 2022)

On the Potential of Artificial Intelligence Chatbots for Data Exploration of Federated Bioinformatics Knowledge Graphs. - Ana Claudia Sima; Tarcisio Mendes de Farias (SeWeBMeDA@ESWC, 2023)

Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets. - Tarcisio Mendes de Farias; Tatsuya Kushida; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frédéric B. Bastian; Hiroshi Masuya (SWAT4HCLS, 2023)

Towards predicting essential proteins via federated SPARQL queries. - Petros Liakopoulous; Borbala Banfalvi; Xinyi Wang; Sina Majidian; Tarcisio Mendes de Farias; Christophe Dessimoz; Ana Claudia Sima (SWAT4HCLS, 2023)

LLM-based SPARQL Query Generation from Natural Language over Federated Knowledge Graphs. - Vincent Emonet; Jerven T. Bolleman; Severine Duvaud; Tarcisio Mendes de Farias; Ana Claudia Sima (HGAIS@ISWC, 2024)

BioDataFuse: Enhancing data interoperability through modular queries and knowledge graph construction. - Tooba Abbassi-Daloii; Yojana Gadiya; Ammar Ammar; Egon L. Willighagen; Ana Claudia Sima; Hasan Balci (SWAT4HCLS, 2024)

CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods. - Jerven T. Bolleman; Elias Crum; Iulian Dragan; Jakub Galgonek; Mark Ibberson; Tarcisio Mendes de Farias; Marek Moos; Marco Pagni; Ruben Taelman; Jirí Vondrásek; Ana Claudia Sima (SWAT4HCLS, 2024)

SPARQL generation: an analysis on fine-tuning OpenLLaMA for Question Answering over a Life Science Knowledge Graph. - Julio Cesar Rangel Reyes; Tarcisio Mendes de Farias; Ana Claudia Sima; Norio Kobayashi (SWAT4HCLS, 2024)

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications. - Jerven T. Bolleman; Vincent Emonet; Adrian M. Altenhoff; Amos Bairoch; Marie-Claude Blatter; Alan J. Bridge; Severine Duvaud; Elisabeth Gasteiger; Dmitry Kuznetsov; Sébastien Moretti; Pierre-André Michel; Anne Morgat; et al. (CoRR, 2024)

A user-friendly SPARQL query editor powered by lightweight metadata. - Vincent Emonet; Ana Claudia Sima; Tarcisio Mendes de Farias (CoRR, 2025)

Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs. - Tatsuya Kushida; Tarcisio Mendes de Farias; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frederic B. Bastian; Hiroshi Masuya (BMC Medical Informatics Decis. Mak., 2025)