Tequila - a query language for the Semantic Web. - Jakub Galgonek (DATESO, 2009)

On the Effectiveness of Distances Measuring Protein Structure Similarity. - Jakub Galgonek; David Hoksza (SISAP, 2009)

SProt - from local to global protein structure similarity. - Jakub Galgonek; David Hoksza (BIBM Workshops, 2010)

SMILE - A Framework for Semantic Applications. - Jakub Galgonek; Tomás Knap; Martin Krulis; Martin Necaský (OTM Workshops, 2010)

On metric approximations of the SProt measure. - Jakub Galgonek; David Hoksza (SISAP, 2011)

Protein sequences identification using NM-tree. - Jirí Novák; Tomás Skopal; David Hoksza; Jakub Lokoc; Jakub Galgonek (SISAP, 2011)

On the Parallelization of the SProt Measure and the TM-Score Algorithm. - Jakub Galgonek; Martin Krulis; David Hoksza (Euro-Par Workshops, 2012)

P3S: Protein Structure Similarity Search. - Jakub Galgonek; Tomás Skopal; David Hoksza (Euro-Par Workshops, 2012)

SimTandem: Similarity Search in Tandem Mass Spectra. - Jirí Novák; Jakub Galgonek; David Hoksza; Tomás Skopal (SISAP, 2012)

On InChI and evaluating the quality of cross-reference links. - Jakub Galgonek; Jirí Vondrásek (J. Cheminformatics, 2014)

Advanced SPARQL querying in small molecule databases. - Jakub Galgonek; Tomás Hurt; Vendula Michlíková; Petr Onderka; Jan Schwarz; Jirí Vondrásek (J. Cheminformatics, 2016)

Amino Acid Interaction (INTAA) web server. - Jakub Galgonek; Jirí Vymetal; David Jakubec; Jirí Vondrásek (Nucleic Acids Res., 2017)

Sachem: a chemical cartridge for high-performance substructure search. - Miroslav Kratochvíl; Jirí Vondrásek; Jakub Galgonek (J. Cheminformatics, 2018)

Interoperable chemical structure search service. - Miroslav Kratochvíl; Jirí Vondrásek; Jakub Galgonek (J. Cheminformatics, 2019)

Correction to: Interoperable chemical structure search service. - Miroslav Kratochvíl; Jirí Vondrásek; Jakub Galgonek (J. Cheminformatics, 2020)

IDSM ChemWebRDF: SPARQLing small-molecule datasets. - Jakub Galgonek; Jirí Vondrásek (J. Cheminformatics, 2021)

Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. - Jirí Vymetal; David Jakubec; Jakub Galgonek; Jirí Vondrásek (Nucleic Acids Res., 2021)

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL. - Jakub Galgonek; Jirí Vondrásek (J. Cheminformatics, 2023)

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)