Publications

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1701 Publications visible to you, out of a total of 1701

Abstract

Not specified

Authors: D. A. Prokhorov, S. H. Lee, S. Nagataki, J. Vink, D. Ellison, G. Ferrand, D. Patnaude, F. Roepke, I. Seitenzahl, P. Slane, Cta, K. Abe, S. Abe, A. Acharyya, R. Adam, A. Aguasca-Cabot, I. Agudo, J. Alfaro, N. Alvarez-Crespo, R. Alves Batista, J. P. Amans, E. Amato, F. Ambrosino, E. O. Angüner, L. A. Antonelli, C. Aramo, C. Arcaro, L. Arrabito, K. Asano, J. Aschersleben, H. Ashkar, L. Augusto Stuani, D. Baack, M. Backes, C. Balazs, M. Balbo, A. Baquero Larriva, V. Barbosa Martins, U. Barres de Almeida, J. A. Barrio, D. Bastieri, P. I. Batista, I. Batković, R. W. Batzofin, J. R. Baxter, G. Beck, J. Becker Tjus, L. Beiske, D. Belardinelli, W. Benbow, E. Bernardini, J. Bernete Medrano, K. Bernlöhr, A. Berti, V. Beshley, P. Bhattacharjee, S. Bhattacharyya, B. Bi, N. Biederbeck, A. Biland, E. Bissaldi, O. Blanch, J. Blazek, C. Boisson, J. Bolmont, G. Bonnoli, P. Bordas, Z. Bosnjak, F. Bradascio, C. Braiding, E. Bronzini, R. Brose, A. M. Brown, F. Brun, G. Brunelli, A. Bulgarelli, I. Burelli, L. Burmistrov, M. Burton, T. Bylund, P. G. Calisse, A. Campoy-Ordaz, B. K. Cantlay, M. Capalbi, A. Caproni, R. Capuzzo-Dolcetta, C. Carlile, S. Caroff, A. Carosi, R. Carosi, M. S. Carrasco, E. Cascone, F. Cassol, N. Castrejon, F. Catalani, D. Cerasole, M. Cerruti, S. Chaty, A. W. Chen, M. Chernyakova, A. Chiavassa, J. Chudoba, C. H. Coimbra Araujo, V. Conforti, F. Conte, J. L. Contreras, C. Cossou, A. Costa, H. Costantini, P. Cristofari, O. Cuevas, Z. Curtis-Ginsberg, G. D’Amico, F. D’Ammando, M. Dadina, M. Dalchenko, L. David, I. D. Davids, F. Dazzi, A. De Angelis, M. de Bony de Lavergne, V. De Caprio, G. De Cesare, E. M. de Gouveia Dal Pino, B. De Lotto, M. de Lucia, R. de Menezes, M. de Naurois, E. de Oña Wilhelmi, N. De Simone, V. de Souza, L. Del Peral, M. V. del Valle, E. Delagnes, A. G. Delgado Giler, C. Delgado, M. Dell’aiera, R. Della Ceca, M. Della Valle, D. Della Volpe, D. Depaoli, A. Dettlaff, T. Di Girolamo, A. Di Piano, F. Di Pierro, R. Di Tria, L. Di Venere, C. Dı́az-Bahamondes, C. Dib, S. Diebold, R. Dima, A. Dinesh, A. Djannati-Ataı̈, J. I. Djuvsland, A. Dominguez, R. M. Dominik, A. Donini, D. Dorner, J. Dörner, M. Doro, R. d. C. dos Anjos, J. L. Dournaux, D. Dravins, C. Duangchan, C. Dubos, L. Ducci, V. V. Dwarkadas, J. Ebr, C. Eckner, K. Egberts, S. Einecke, D. Elsässer, G. Emery, M. Escobar Godoy, J. Escudero, P. Esposito, D. Falceta-Gonçalves, V. Fallah Ramazani, A. Faure, E. Fedorova, S. Fegan, K. Feijen, Q. Feng, F. Ferrarotto, E. Fiandrini, A. Fiasson, V. Fioretti, L. Foffano, L. Font Guiteras, G. Fontaine, S. Fröse, S. Fukami, Y. Fukui, S. Funk, D. Gaggero, G. Galanti, G. Galaz, Y. A. Gallant, S. Gallozzi, V. Gammaldi

Date Published: 1st Sep 2024

Publication Type: InProceedings

Abstract

Not specified

Authors: J. M. Pollin, S. A. Sim, R. Pakmor, F. P. Callan, C. E. Collins, L. J. Shingles, F. K. Röpke, S. Srivastav

Date Published: 1st Sep 2024

Publication Type: Journal

Abstract (Expand)

Introduction: NFDI4Health is a consortium funded by the German Research Foundation to make structured health data findable and accessible internationally according to the FAIR principles. Its goal iss. Its goal is bringing data users and Data Holding Organizations (DHOs) together. It mainly considers DHOs conducting epidemiological and public health studies or clinical trials. Methods: Local data hubs (LDH) are provided for such DHOs to connect decentralized local research data management within their organizations with the option of publishing shareable metadata via centralized NFDI4Health services such as the German central Health Study Hub. The LDH platform is based on FAIRDOM SEEK and provides a complete and flexible, locally controlled data and information management platform for health research data. A tailored NFDI4Health metadata schema for studies and their corresponding resources has been developed which is fully supported by the LDH software, e.g. for metadata transfer to other NFDI4Health services. Results: The SEEK platform has been technically enhanced to support extended metadata structures tailored to the needs of the user communities in addition to the existing metadata structuring of SEEK. Conclusion: With the LDH and the MDS, the NFDI4Health provides all DHOs with a standardized and free and open source research data management platform for the FAIR exchange of structured health data.

Authors: Xiaoming Hu, Haitham Abaza, Rene Hänsel, Masoud Abedi, Martin Golebiewski, Wolfgang Müller, Frank Meineke

Date Published: 30th Aug 2024

Publication Type: InProceedings

Abstract (Expand)

The National Research Data Infrastructure for Personal Health Data (NFDI4Health) uses Local Data Hubs (LDHs) to manage locally research studies, documents and sensitive personal data to support controlledort controlled data sharing. While research data management (RDM) systems facilitate the storage and preparation of data and metadata as well as organizational access, they often lack support for interoperability standards of the application domain. To support the exchange with external registries of research studies, we chose 17 attributes to characterize the most relevant aspects of clinical trials (in the following named “metadata profile”). We implemented the metadata profile in the RDM system FAIRDOM SEEK using core attributes and SEEK’s extended metadata feature and created a mapping conforming to the Health Level 7 Fast Healthcare Interoperability Resources (FHIR) standard version R4. Finally, we implemented a prototype application interface for exports in FHIR-JSON format. We plan to extend the interface to serve central registries and support specific FHIR Implementation Guides from various use cases.

Authors: Matthias Löbe, Xiaoming Hu, Sophie A.I. Klopfenstein

Date Published: 22nd Aug 2024

Publication Type: Journal

Abstract

Not specified

Authors: Ganna Gryn’ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth Merz

Date Published: 12th Aug 2024

Publication Type: Journal

Abstract

Not specified

Authors: Ganna Gryn’ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth Merz

Date Published: 12th Aug 2024

Publication Type: Journal

Abstract (Expand)

In the field of population genetics, the driving forces of evolution within species can be studied with trees. Along a genome, each tree describes the local ancestries of a small genomic region. Together, those trees form a tree sequence that describes the ancestry of a population at every site of the sequence. Inferring tree sequences for whole genomes with many haplotype samples is a computationally expensive task, however. The state-of-the-art tool to infer tree sequences is tsinfer, which infers ancestries for human chromosomes from 5000 samples within a few hours. The tool has the capability to parallelize the computation, but we identify a structure in the input data that limits its parallelizability. We propose a novel parallelization scheme aiming to improve scaling at high thread counts, independently of this structure. Furthermore, we propose several optimizations for the inference algorithm, improving cache efficiency and reducing the number of operations per iteration. We provide a proof-of-concept implementation, and compare the computation speed of our implementation and tsinfer. When inferring ancestries for the 1000 Genomes Project, our implementation is consistently faster by a factor of 1.9 to 2.4. Additionally, depending on the choice of parameters, our parallelization scheme scales better between 32 and 96 cores, improving its speed advantage, especially at higher core counts. In phases where our novel parallelization scheme does not apply, our optimizations still improve the runtime by a factor of 2.2. As available genomic data sets are growing rapidly in size, our contribution decreases the computation time and enables better parallelization, allowing the processing of larger data sets in reasonable time frames

Authors: Johannes Hengstler, Lukas Hübner, Alexandros Stamatakis

Date Published: 1st Aug 2024

Publication Type: Master's Thesis

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