Publications

Here you find the list of my publications in descending date order. Check also my profiles on Google Scholar, Scopus, and dblp, or directly my updated Curriculum Vitae.

Journals

Invernici, F., Bernasconi, A., Ceri, S. Exploring the evolution of research topics during the COVID-19 pandemic. Accepted for publication in Expert Systems with Applications [in press] (PDF)
Invernici, F., Bernasconi, A., Ceri, S. Searching COVID-19 clinical research using graphical abstracts. Accepted for publication in the Journal of Medical Internet Research [in press] \url{http://dx.doi.org/10.2196/52655}. (PDF)
Alfonsi, T., Bernasconi, A., Chiara, M., Ceri, S. Data-driven recombination detection in viral genomes. (2024) Nature Communications 15, 3313. (PDF)
Bernasconi., A., Garcia S., A., Ceri, S., & Pastor, O. (2023) PoliViews: A Comprehensive and Modular Approach to the Conceptual Modeling of Genomic Data. Data and Knowledge Engineering, 102201. (PDF)
Pinoli, P., Canakoglu, Ceri, S., Chiara, M., Ferrandi, E., Minotti, L., & Bernasconi, A. (2023) VariantHunter: a tool for fast detection of emerging SARS-CoV-2 variants. Database, 2023, baad044. (PDF)
Garcia S., A., Bernasconi, A., Guizzardi, G., Pastor, O., Storey, V.C. & Panach, I. (2023) An Ontological Analysis and Assessment of Human Genome Conceptual Models. Information Systems, 2023, 102242. (PDF)
Serna Garcia, G., Al Khalaf, R., Invernici, F., Ceri, S., & Bernasconi, A. (2023) CoVEffect: Interactive Deep Learning-based SARS-CoV-2 Mutations and Variants Effect Extraction. GigaScience, 12, giad036. (PDF)
Bernasconi, A., Canakoglu, A., & Comolli, F. (2023) Processing Genome-Wide Association Studies within a repository of heterogeneous genomic datasets. BMC Genomic Data, 24, 13. (PDF)
Giacomelli, A., Righini, E., Micheli, V., Pinoli, P., Bernasconi, A., Rizzo, A., Oreni, L., Ridolfo, A.L., Antinori, S., Ceri, S., & Rizzardini, G. (2023) SARS-CoV-2 viremia and COVID-19 mortality: an observational study. PLOS ONE, 18(4), e0281052. (PDF)
Bernasconi, A., Guizzardi, G., Pastor, O., & Storey, V.C. (2022). Semantic interoperability: ontological unpacking of a viral conceptual model. BMC Bioinformatics, 23(Suppl 11), 491. (PDF)
Alfonsi, T., Bernasconi, A., Canakoglu, A., & Masseroli, M. (2022). Genomic data integration and user-defined sample-set extraction for population variant analysis. BMC Bioinformatics, 23(1), 401. (PDF)
Al Khalaf, R., Bernasconi, A., Pinoli, P. & Ceri, S. (2022). Analysis of co-occurring and mutually exclusive amino acid changes and detection of convergent and divergent evolution events in SARS-CoV-2. Computational and Structural Biotechnology Journal, 20, 4238-4250. (PDF)
Grandi, S., & Bernasconi, A. (2022). Risk perception, spatial data, legal response during COVID-19 pandemic: a conceptual model. GeoProgress Journal, 7(2), 2020, Geoprogress Editions ISSN 2384-9398. (PDF)
Serna G., G., Leone, M., Bernasconi, A., & Carman, M.J. (2022). GeMI: Interactive Interface for Transformer-based Genomic Metadata Integration. Database, 2022. (PDF) – (SuppMat)
Alfonsi, T., Al Khalaf, R., Ceri, S., & Bernasconi, A. (2022). CoV2K model, a comprehensive representation of SARS-CoV-2 knowledge and data interplay. Scientific Data, 9, 260. (PDF)
Bernasconi, A., & Ceri, S. (2022). Interoperability of COVID-19 clinical phenotype data with host and viral genetics data. BioMed, 2(1), 69-81. (PDF)
Cilibrasi, L., Pinoli, P., Bernasconi, A., Canakoglu, A., Chiara, M., & Ceri, S. (2022). ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time. Bioinformatics, 38(7), 1988–1994. (PDF)
Pinoli, P., Bernasconi, A., Sandionigi, A. & Ceri, S. (2021). VirusLab: a tool for customized SARS-CoV-2 data analysis. BioTech, 10(4), 27. (PDF)
Bernasconi, A., Mari, L., Casagrandi, R. & Ceri, S. (2021). Data-driven analysis of amino acid change dynamics timely reveals SARS-CoV-2 variant emergence. Scientific Reports 11(1), 21068. (PDF)
Bernasconi, A., Cilibrasi, L., Al Khalaf, R., Alfonsi, T., Ceri, S., Pinoli, P., & Canakoglu, A. (2021). EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species. Database, 2021. (PDF)
Menghi, C., Rizzi, A.M., Bernasconi, A. & Spoletini, P. (2021). TOrPEDO: Witnessing Model Correctness with Topological Proofs. Formal Aspects of Computing, 33(6), 1039-1066. (PDF)
Bernasconi, A., Gulino, A., Alfonsi, T., Canakoglu, A., Pinoli, P., Sandionigi, A., & Ceri, S. (2021). VirusViz: Comparative analysis and effective visualization of viral nucleotide and amino acid variants. Nucleic Acids Research, 49(15), e90. (PDF)
Crovari, P., Pidò, S., Pinoli, P., Bernasconi, A., Canakoglu, A., Garzotto, F., & Ceri, S. (2021). GeCoAgent: A Conversational Agent for Empowering Genomic Data Extraction and Analysis. ACM Transactions on Computing for Healthcare, 3(1), 1-29. (PDF)
Bernasconi, A. (2021). Data quality-aware genomic data integration. Computer Methods and Programs in Biomedicine Update, 1, 100009. (PDF)
Bernasconi, A., & Grandi, S. (2021). A Conceptual Model for Geo-Online Exploratory Data Visualization: The Case of the COVID-19 Pandemic. Information, 12(2), 69. (PDF)
Bernasconi, A., Canakoglu, A., Masseroli, M., Pinoli, P., & Ceri, S. (2021). A review on viral data sources and search systems for perspective mitigation of COVID-19. Briefings in bioinformatics, 22(2), 664-675. (PDF)
Canakoglu, A., Pinoli, P., Bernasconi, A., Alfonsi, T., Melidis, D.P., & Ceri, S. (2021). ViruSurf: an integrated database to investigate viral sequences. Nucleic acids research, 49(D1), D817-D824 (PDF)
Bernasconi, A., Canakoglu, A., Masseroli, M., & Ceri, S. (2021). The road towards data integration in human genomics: players, steps and interactions. Briefings in Bioinformatics, 22(1), 30-44. (PDF)
Cappelli, E., Cumbo, F., Bernasconi, A., Canakoglu, A., Ceri, S., Masseroli, M., & Weitschek, E. (2020). OpenGDC: Unifying, Modeling, Integrating Cancer Genomic Data and Clinic(2020)al Metadata. Applied Sciences, 10(18), 6367. (PDF)
Grandi, S., & Bernasconi, A. (2020). Convergenza di Web Design e Informazione Spaziale, Statistica, Genomica ed Epidemiologica: il Caso delle Geo-Dashboard nella Crisi COVID-19. Documenti geografici, (1), 463-476. (PDF)
Bernasconi, A., Canakoglu, A., Masseroli, M., & Ceri, S. (2020). META-BASE: a Novel Architecture for Large-Scale Genomic Metadata Integration. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(1), 543-557. (PDF)
Canakoglu, A., Bernasconi, A., Colombo, A., Masseroli, M., & Ceri, S. (2019). GenoSurf: metadata driven semantic search system for integrated genomic datasets. Database, 2019. (PDF)
Masseroli, M., Canakoglu, A., Pinoli, P., Kaitoua, A., Gulino, A., Horlova, O., Nanni, L., Bernasconi, A., Perna, S., Stamoulakatou, E. and Ceri, S. (2019). Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data. Bioinformatics, 35(5), 729-736. (PDF)

Consortium Papers Journals

COVID-19 Host Genetics Initiative (2021). Mapping the human genetic architecture of COVID-19. Nature 600, 472–477 (2021). https://doi.org/10.1038/s41586-021-03767-x [Bernasconi, A. contributed as part of the “Project management group (Data dictionary)”]
Van Blokland, I.V., Lanting, P., Ori, A.P., Vonk, J.M., Warmerdam, R.C., Herkert, J.C., Boulogne, F., Claringbould, A., Lopera-Maya, E.A., Bartels, M. and Hottenga, J.J., Ganna, A., Karjalainen, J., Lifelines COVID-19 cohort study, The COVID-19 HostGeneticsInitiative, et al. (2021) Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility. PloS one, 16(8), e0255402. https://doi.org/10.1371/journal.pone.0255402 [Bernasconi, A. was part of the “COVID-19 Host Genetics Initiative Coordination (Data dictionary)”]

Conferences

Ceri, S., Bernasconi, A., & Gagliardi, A. Reactive Knowledge Management. Accepted for publication in ICDE 2024, Future Technologies Special Session. [in press] (PDF)
Ceri, S., Bernasconi, A., Gagliardi, A., Martinenghi, D., Bellomarini, L., & Magnanimi, D. PG-Triggers: Triggers for Property Graphs. Accepted for publication in SIGMOD 2024, industrial track. [in press] (PDF)
Al Khalaf, R., Bernasconi, A., & Garcia S., A. OntoEffect: an OntoUML-based ontology to explain SARS-CoV-2 variants’ effects. 15th International Conference on Knowledge Engineering and Ontology Development (KEOD 2023). In Proceedings of the 15th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management – Volume 2: , 62-72, 2023 , Rome, Italy (PDF)
Costa, M., Garcia S., A., León, A., Bernasconi, A., & Pastor, O. (2023, October) A Reference Meta-Model to Understand DNA Variant Interpretation Guidelines. In International Conference on Conceptual Modeling (pp. 375-393). Springer, Cham. (PDF)
Bernasconi, A. The Opportunity of Data-Driven Services for Viral Genomic Surveillance. In IEEE International Conference on Service-Oriented System Engineering (SOSE), Athens, Greece, 2023, pp. 172-181. (PDF)
Bernasconi, A., Garcia, A.S., Guizzardi, G., Bonino da Silva Santos, L.O., & Storey, V.C. Ontological representation of FAIR principles: A blueprint for FAIRer data sources. In: Indulska, M., Reinhartz-Berger, I., Cetina, C., Pastor, O. (eds) Advanced Information Systems Engineering. CAiSE 2023. Lecture Notes in Computer Science, vol 13901. Springer, Cham. (PDF)
Alfonsi, T., Bellomarini, L., Bernasconi, A., & Ceri, S. Expressing Biological Problems with Logical Reasoning Languages. Proceedings of the 6th International Joint Conference on Rules and Reasoning (RuleML+RR 2022) — 16th International Rule Challenge. (Vol. 3229). CEUR-WS} (PDF)
Bernasconi, A., Garcia, A.S., Ceri, S., & Pastor, O. A comprehensive approach for the conceptual modeling of genomic data. In: Ralyté, J., Chakravarthy, S., Mohania, M., Jeusfeld, M.A., Karlapalem, K. (eds) Conceptual Modeling. ER 2022. Lecture Notes in Computer Science, vol 13607. Springer, Cham. (PDF)
Bernasconi, A. & Pinoli, P. Conceptual models and databases for searching the genome. In: Stoyanovich, J., and Teubner, J., and Guagliardo, P., and Nikolic, M., and Pieris, A., and Mühlig, J., and Özcan, F., and Schelter, S., and Jagadish, H.V., and Zhang, M. (eds) Proceedings of the 25th International Conference on Extending Database Technology, EDBT 2022, Edinburgh, UK, March 29 – April 1, 2022. OpenProceedings.org 2022.(PDF)
Garcia S., A., Guizzardi, G., Pastor, O., Storey, V.C. & Bernasconi, A. Ontological Characterization of a Conceptual Model of the Human Genome. In: De Weerdt, J., Polyvyanyy, A. (eds) Intelligent Information Systems. CAiSE 2022. Lecture Notes in Business Information Processing, vol 452. Springer, Cham.(PDF)
Grandi, S., & Bernasconi, A. Geo-online explanatory data visualization tools as crisis management and communication instruments. Proc. Int. Cartogr. Assoc., 4, 41, 2021.(PDF)
Guizzardi, G., Bernasconi, A., Pastor, O., & Storey, V. Ontological Unpacking as Explanation: The Case of the Viral Conceptual Model. In: Ghose A., Horkoff J., Silva Souza V.E., Parsons J., Evermann J. (eds) Conceptual Modeling. ER 2021. Lecture Notes in Computer Science, vol 13011. Springer, Cham. (PDF)
Al Khalaf, R., Alfonsi, T., Ceri, S., Bernasconi, A. (2021, May). CoV2K: A Knowledge Base of SARS-CoV-2 Variant Impacts. In: Cherfi S., Perini A., Nurcan S. (eds) Research Challenges in Information Science. RCIS 2021. Lecture Notes in Business Information Processing, vol 415. Springer, Cham. (PDF)
Bernasconi, A., Canakoglu, A., Pinoli, P., & Ceri, S. (2020, November). Empowering Virus Sequence Research through Conceptual Modeling. In: Dobbie G., Frank U., Kappel G., Liddle S.W., Mayr H.C. (eds) Conceptual Modeling. ER 2020. Lecture Notes in Computer Science, vol 12400. Springer, Cham. (PDF) (Conference presentation video)
Cannizzaro, G., Leone, M., Bernasconi, A., Canakoglu, A., & Carman, M.J. (2021). Automated Integration of Genomic Metadata with Sequence-to-Sequence Models. In: Dong Y., Ifrim G., Mladenić D., Saunders C., Van Hoecke S. (eds) Machine Learning and Knowledge Discovery in Databases. Applied Data Science and Demo Track. ECML PKDD 2020. Lecture Notes in Computer Science, vol 12461. Springer, Cham. (PDF)
Menghi, C., Rizzi, A. M., & Bernasconi, A. (2020, April). Integrating Topological Proofs with Model Checking to Instrument Iterative Design. In FASE (pp. 53-74). (PDF)
Bernasconi, A., Canakoglu, A., & Ceri, S. (2019, November). From a conceptual model to a knowledge graph for genomic datasets. In International Conference on Conceptual Modeling (pp. 352-360). Springer, Cham. (PDF)
Bernasconi, A., Canakoglu, A., Colombo, A., & Ceri, S. (2018, December). Ontology-driven metadata enrichment for genomic datasets. In 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018 (Vol. 2275, pp. 1-10). CEUR-WS. (PDF)
Bernasconi, A., Ceri, S., Campi, A., & Masseroli, M. (2017, November). Conceptual modeling for genomics: building an integrated repository of open data. In International Conference on Conceptual Modeling (pp. 325-339). Springer, Cham. (PDF)
Bernasconi, A., Menghi, C., Spoletini, P., Zuck, L. D., & Ghezzi, C. (2017, September). From model checking to a temporal proof for partial models. In International Conference on Software Engineering and Formal Methods (pp. 54-69). Springer, Cham. (PDF)
Ceri, S., Bernasconi, A., Canakoglu, A., Gulino, A., Kaitoua, A., Masseroli, M., Nanni, L., & Pinoli, P. (2017, October). Overview of GeCo: A project for exploring and integrating signals from the genome. In International Conference on Data Analytics and Management in Data Intensive Domains (pp. 46-57). Springer, Cham. (PDF)

Workshops Papers, Posters, and Abstracts

Bernasconi, A., Cappiello, C., Ceri, S., & Pinoli, P. (February, 2024). Achieving data FAIRification in a distributed analytics research platform for rare diseases. In 15th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2024. (PDF)
Bernasconi, A. (2022, September). A Sound and Repeatable Approach to Building Integrated Repositories of Genomic Data. In Proceedings of the 1st Italian Conference on Big Data and Data Science (ITADATA 2022). Milan, Italy, September 20-21, 2022. Vol. 3340, pp. 212-213. CEUR-WS. (PDF)
Giacomelli, A., Righini, E., Micheli, V., Pinoli, P., Bernasconi, A., Rizzo, A., Oreni, L., Ridolfo, A.L., Antinori, S., Ceri, S., Rizzardini, G. SARS-CoV-2 viremia e mortalità in pazienti ospedalizzati per COVID-19: studio osservazionale prospettico. XXI National Congress SIMIT (Società Italiana Malattie Infettive e Tropicali)
García S., A., Bernasconi, A., Guizzardi, G., Pastor, O., Storey, V.C., Costa, M. (2022). An Initial Empirical Assessment of an Ontological Model of the Human Genome. In: Guizzardi, R., Neumayr, B. (eds) Advances in Conceptual Modeling. ER 2022. Lecture Notes in Computer Science, vol 13650. Springer, Cham. (PDF)
Bernasconi, A., Al Khalaf, R., Alfonsi, T., Canakoglu, A., Cilibrasi, L., Gulino, A., Pinoli, P., & Ceri, S. (January, 2022). A unique approach to SARS-CoV-2 data and knowledge ingestion, integration and querying. In 13th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2022. (PDF)
Bernasconi, A. (2021, April). Extreme Requirements Elicitation: Lessons Learnt from the COVID-19 Case Study. In Joint Proceedings of REFSQ 2021 Workshops, OpenRE, Poster and Tools Track, and Doctoral Symposium co-located with the 27th International Conference on Requirements Engineering: Foundation for Software Quality (REFSQ 2021) (Vol. 2857). CEUR-WS. (PDF)
Bernasconi, A., Canakoglu, A., & Ceri, S. (2019, November). Exploiting conceptual modeling for searching genomic metadata: A quantitative and qualitative empirical study. In International Conference on Conceptual Modeling (pp. 83-94). Springer, Cham. (PDF)
Settino, M., Bernasconi, A., Ceddia, G., Agapito, G., Masseroli, M., & Cannataro, M. (2019, September). Using GMQL-Web for Querying, Downloading and Integrating Public with Private Genomic Datasets. In Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (pp. 688-693). (PDF)
Cannizzaro, G., Bernasconi, A., Canakoglu, A., Leone, M., & Carman, M.J. (2019, June). Sequence Labelling Techniques for Automatically Integrating Unstructured Genomic Metadata. In BITS 2019. (PDF)
Masseroli, M., Pinoli, P., Canakoglu, C., Bernasconi, A., Gulino, A., Nanni, L., Orlova, O., Pallotta, S., Ceri, S. (June, 2019). Genomic big data management, modeling and computing. In Analysis of Big Omics Data Workshop at BITS 2019. (PDF)
Bernasconi, A. (2019). Using metadata for locating genomic datasets on a global scale. In 2018 Conference on Information and Knowledge Management Workshops, CIKM 2018 (Vol. 2482, pp. 1-8). CEUR-WS. (PDF)
Cappelli, E., Cumbo, F., Bernasconi, A., Masseroli, M., & Weitschek, E. (2018). OpenGDC: standardizing, extending, and integrating genomics data of cancer. In ESCS 2018: 8th European Student Council Symposium, International Society for Computational Biology (ISCB) (pp. 1-1). (PDF)

Book chapters

Bernasconi, A., & García, A. G. “Conceptual Modeling for Bioinformatics”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 2, 2024.
Al Khalaf, R., Bernasconi, A., & Masseroli, M. “Biological and Medical Ontologies: Disease Ontology (DO)”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 2, 2024.
Al Khalaf, R., Bernasconi, A., & Masseroli, M. “Biological and Medical Ontologies: Human Phenotype Ontology (PO)”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 2, 2024.
Al Khalaf, R., & Bernasconi, A. “Transformer-based biomedical text extraction”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 2, 2024.
Bernasconi, A. “Data-driven methods for viral variants’ identification”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 2, 2024.
Bernasconi, A. Model, Integrate, Search… Repeat: a Sound Approach to Building Integrated Repositories of Genomic Data. In: Piroddi L. (eds) Special Topics in Information Technology. SpringerBriefs in Applied Sciences and Technology (pp. 89-99). Springer, Cham. (PDF)
Bernasconi, A., & Cascianelli, S. Scenarios for the Integration of Microarray Gene Expression Profiles in COVID-19–Related Studies. In: Agapito G. (eds) Microarray Data Analysis (pp. 195-215). Methods in Molecular Biology, vol 2401, 2022. Humana, New York, NY.
Bernasconi, A., & Masseroli, M. “Biological and Medical Ontologies: Disease Ontology (DO)”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 1, 2019, pp. 838-847.
Bernasconi, A., & Masseroli, M. “Biological and Medical Ontologies: Human Phenotype Ontology (HPO)”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 1, 2019, pp. 848-857.
Bernasconi, A., & Masseroli, M. “Biological and Medical Ontologies: Systems Biology Ontology (SBO)”. In Reference Module in Life Sciences, Encyclopedia of Bioinformatics and Computational Biology. Volume 1, 2019, pp. 858-866.

Blog posts

Chiara, M., Pinoli, P., Minotti, L., Bernasconi, A., Canakoglu, A., Ferrandi, E., & Ceri, S. Using VariantHunter for detecting emerging SARS-CoV-2 variants. Posted on Virological.org on May 11th, 2022
Bernasconi, A., Pinoli, P., Al Khalaf, R., Alfonsi, T., Canakoglu, A., Cilibrasi, L., & Ceri, S. Report on Omicron Spike mutations on epitopes and immunological/epidemiological/kinetics effects from literature. Posted on Virological.org on Nov. 30th, 2021