Tag - Type: software engineering

dsOMOP: Bridging OMOP CDM and DataSHIELD for Secure Federated Analysis of Standardized Clinical Data.
Sarrat-González, David; Escribà-Montagut, Xavier; Houghtaling, Jared; González, Juan R
Bioinformatics (2025)
PMID: 40327502 DOI: 10.1093/bioinformatics/btaf286 
Citations: -
Tags: Consortia: Tufts Medical Center | Industry: Syntegra | Study: Tufts Synthetic Dataset | Type: data systems | Type: software engineering

Strengths and limitations of non-disclosive data analysis: a comparison of breast cancer survival classifiers using VisualSHIELD.
Tomasoni, Danilo; Lombardo, Rosario; Lauria, Mario
Front Genet, Volume 15 (2024)
PMID: 38348453 DOI: 10.3389/fgene.2024.1270387 
Citations: 1 (Scopus)
Tags: Consortia: ENPADASI | Study: GSE102484 | Study: GSE19615 | Study: GSE2034 | Study: GSE48390 | Study: GSE61304 | Type: clinical research | Type: software engineering | Type: system testing

DistSNE: Distributed computing and online visualization of DNA methylation-based central nervous system tumor classification.
Schmid, Kai; Sehring, Jannik; Németh, Attila; Harter, Patrick N; Weber, Katharina J; Vengadeswaran, Abishaa; Storf, Holger; Seidemann, Christian; Karki, Kapil; Fischer, Patrick; Dohmen, Hildegard; Selignow, Carmen; von Deimling, Andreas; Grau, Stefan; Schröder, Uwe; Plate, Karl H; Stein, Marco; Uhl, Eberhard; Acker, Till; Amsel, Daniel
Brain Pathol, Volume 34, Issue 3 (2024)
PMID: 38012085 DOI: 10.1111/bpa.13228 
Citations: 2 (Scopus)
Tags: Consortia: MIRACUM | Study: Edinger Institute Frankfurt | Study: GSE109381 SuperSeries | Study: The Giessen Institute of Neuropathology | Type: | Type: data systems | Type: data visualization | Type: software engineering

Capability and accuracy of usual statistical analyses in a real-world setting using a federated approach.
Jégou, Romain; Bachot, Camille; Monteil, Charles; Boernert, Eric; Chmiel, Jacek; Boucher, Mathieu; Pau, David
PLoS One, Volume 19, Issue 11 (2024)
PMID: 39541283 DOI: 10.1371/journal.pone.0312697 
Citations: -
Tags: Industry: Roche | Type: clinical research | Type: cohort study | Type: longitudinal study | Type: proof of concept | Type: software engineering

Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform.
Escriba-Montagut, Xavier; Marcon, Yannick; Anguita-Ruiz, Augusto; Avraam, Demetris; Urquiza, Jose; Morgan, Andrei S; Wilson, Rebecca C; Burton, Paul; Gonzalez, Juan R
PLoS Comput Biol, Volume 20, Issue 12 (2024)
PMID: 39652598 DOI: 10.1371/journal.pcbi.1012626 
Citations: 1 (Scopus)
Tags: Consortia: ATHLETE | Consortia: CERCA | Consortia: CINECA | Consortia: Consolidated Group on Health Analytics | Consortia: EUCAN-Connect | Consortia: IBEC | Consortia: PERIS | Type: software engineering

MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD.
Cadman, Tim; Slofstra, Mariska K; van der Geest, Marije A; Avraam, Demetris; Bishop, Tom R P; de Boer, Tommy; Duijts, Liesbeth; Haakma, Sido; Hyde, Eleanor; Jaddoe, Vincent; Karramass, Tarik; Kelpin, Fleur; Marcon, Yannick; Pinot de Moira, Angela; Postma, Dick; Tolboom, Clemens; Veenstra, Ruben L; Wheater, Stuart; Welten, Marieke; Wilson, Rebecca C; Zwart, Erik; Swertz, Morris
Bioinformatics, Volume 41, Issue 1 (2024)
PMID: 39673440 DOI: 10.1093/bioinformatics/btae726 
Citations: 1 (Scopus)
Tags: Consortia: ATHLETE | Consortia: EUCAN-Connect | Consortia: LifeCycle | Type: data systems | Type: software engineering

Accessibility of covariance information creates vulnerability in Federated Learning frameworks.
Huth, Manuel; Arruda, Jonas; Gusinow, Roy; Contento, Lorenzo; Tacconelli, Evelina; Hasenauer, Jan
Bioinformatics, Volume 39, Issue 9 (2023)
PMID: 37647639 DOI: 10.1093/bioinformatics/btad531 
Citations: 6 (Scopus)
Tags: Consortia: ORCHESTRA | Type: data governance | Type: software engineering

Life course of retrospective harmonization initiatives: key elements to consider.
Fortier, Isabel; Wey, Tina W; Bergeron, Julie; Pinot de Moira, Angela; Nybo-Andersen, Anne-Marie; Bishop, Tom; Murtagh, Madeleine J; Miočević, Milica; Swertz, Morris A; van Enckevort, Esther; Marcon, Yannick; Mayrhofer, Michaela Th; Ornelas, Jos Pedro; Sebert, Sylvain; Santos, Ana Cristina; Rocha, Artur; Wilson, Rebecca C; Griffith, Lauren E; Burton, Paul
J Dev Orig Health Dis, Volume 14, Issue 2 (2023)
PMID: 35957574 DOI: 10.1017/S2040174422000460 
Citations: 11 (Scopus)
Tags: Consortia: EUCAN-Connect | Consortia: RECAP Preterm | Type: data harmonization | Type: software engineering

Software Application Profile: ShinyDataSHIELD—an R Shiny application to perform federated non-disclosive data analysis in multicohort studies
Escribà-Montagut, Xavier; Marcon, Yannick; Avraam, Demetris; Banerjee, Soumya; Bishop, Tom R P; Burton, Paul; González, Juan R
International Journal of Epidemiology, Volume 52, Issue 1 (2023)
DOI: 10.1093/ije/dyac201 
Citations: 1 (Scopus)
Tags: Consortia: ATHLETE | Consortia: EUCAN-Connect | Type: review | Type: software engineering

dsSurvival 2.0: privacy enhancing survival curves for survival models in the federated DataSHIELD analysis system.
Banerjee, Soumya; Bishop, Tom R P
BMC Res Notes, Volume 16, Issue 1 (2023)
PMID: 37280717 DOI: 10.1186/s13104-023-06372-5 
Citations: 1 (Scopus)
Tags: Consortia: EUCAN-Connect | Type: software engineering | Type: survival analysis

dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning.
Cao, Han; Zhang, Youcheng; Baumbach, Jan; Burton, Paul R; Dwyer, Dominic; Koutsouleris, Nikolaos; Matschinske, Julian; Marcon, Yannick; Rajan, Sivanesan; Rieg, Thilo; Ryser-Welch, Patricia; Späth, Julian; Herrmann, Carl; Schwarz, Emanuel
Bioinformatics, Volume 38, Issue 21 (2022)
PMID: 36073911 DOI: 10.1093/bioinformatics/btac616 
Citations: 8 (Scopus)
Tags: Study: GSE21138  | Study: GSE35977 | Study: GSE53987 | Study: phs000979.v3.p2 | Type: data systems | Type: proof of concept | Type: software engineering

Individual Data Protected Integrative Regression Analysis of High-Dimensional Heterogeneous Data.
Cai, Tianxi; Liu, Molei; Xia, Yin
J Am Stat Assoc, Volume 117, Issue 540 (2022)
PMID: 37975021 DOI: 10.1080/01621459.2021.1904958 
Citations: 20 (Scopus)
Tags: Study: Partner's Healthcare System | Type: software engineering | Type: statistical methods

dsSynthetic: synthetic data generation for the DataSHIELD federated analysis system.
Banerjee, Soumya; Bishop, Tom R P
BMC Res Notes, Volume 15, Issue 1 (2022)
PMID: 35761417 DOI: 10.1186/s13104-022-06111-2 
Citations: 5 (Scopus)
Tags: Consortia: EUCAN-Connect | Type: data synthesis | Type: software engineering

dsSurvival: Privacy preserving survival models for federated individual patient meta-analysis in DataSHIELD.
Banerjee, Soumya; Sofack, Ghislain N; Papakonstantinou, Thodoris; Avraam, Demetris; Burton, Paul; Zöller, Daniela; Bishop, Tom R P
BMC Res Notes, Volume 15, Issue 1 (2022)
PMID: 35659747 DOI: 10.1186/s13104-022-06085-1 
Citations: 13 (Scopus)
Tags: Consortia: EUCAN-Connect | Type: software engineering | Type: survival analysis

A deterministic approach for protecting privacy in sensitive personal data.
Avraam, Demetris; Jones, Elinor; Burton, Paul
BMC Med Inform Decis Mak, Volume 22, Issue 1 (2022)
PMID: 35090447 DOI: 10.1186/s12911-022-01754-4 
Citations: 4 (Scopus)
Tags: Consortia: ATHLETE | Consortia: BioSHaRE-EU | Consortia: Connected Health Cities North East North Cumbria | Consortia: EUCAN-Connect | Study: NCDS | Type: data governance | Type: software engineering

Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD.
Marcon, Yannick; Bishop, Tom; Avraam, Demetris; Escriba-Montagut, Xavier; Ryser-Welch, Patricia; Wheater, Stuart; Burton, Paul; González, Juan R
PLoS Comput Biol, Volume 17, Issue 3 (2021)
PMID: 33784300 DOI: 10.1371/journal.pcbi.1008880 
Citations: 31 (Scopus)
Tags: Consortia: ATHLETE | Consortia: Connected Health Cities North East North Cumbria | Consortia: EUCAN-Connect | Consortia: VEIS: 001-P-001647 | Type: data systems | Type: software engineering

Deep generative models in DataSHIELD.
Lenz, Stefan; Hess, Moritz; Binder, Harald
BMC Med Res Methodol, Volume 21, Issue 1 (2021)
PMID: 33812380 DOI: 10.1186/s12874-021-01237-6 
Citations: 16 (Scopus)
Tags: Consortia: GEMOLS | Consortia: MIRACUM | Type: data systems | Type: proof of concept | Type: software engineering

Privacy preserving data visualizations.
Avraam, Demetris; Wilson, Rebecca; Butters, Oliver; Burton, Thomas; Nicolaides, Christos; Jones, Elinor; Boyd, Andy; Burton, Paul
EPJ Data Sci, Volume 10, Issue 1 (2021)
PMID: 33442528 DOI: 10.1140/epjds/s13688-020-00257-4 
Citations: 19 (Scopus)
Tags: Consortia: ATHLETE | Consortia: Connected Health Cities North East North Cumbria | Consortia: EUCAN-Connect | Type: data visualization | Type: software engineering

Recovery of original individual person data (IPD) inferences from empirical IPD summaries only: Applications to distributed computing under disclosure constraints.
Bonofiglio, Federico; Schumacher, Martin; Binder, Harald
Stat Med, Volume 39, Issue 8 (2020)
PMID: 31944335 DOI: 10.1002/sim.8470 
Citations: 15 (Scopus)
Tags: Consortia: MIRACUM | Study: IST | Type: data governance | Type: software engineering | Type: statistical methods

A Queue-Poll Extension and DataSHIELD: Standardised, Monitored, Indirect and Secure Access to Sensitive Data.
Gruendner, Julian; Prokosch, Hans-Ulrich; Schindler, Sebastian; Lenz, Stefan; Binder, Harald
Stud Health Technol Inform, Volume 258 (2019)
PMID: 30942726 DOI: 10.3233/978-1-61499-959-1-115 
Citations: 5 (Scopus)
Tags: Consortia: MIRACUM | Study: Erlangen University Hospital | Study: Freiburg University Hospital | Study: Magdeburg University Hospital | Type: data governance | Type: software engineering

KETOS: Clinical decision support and machine learning as a service - A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services.
Gruendner, Julian; Schwachhofer, Thorsten; Sippl, Phillip; Wolf, Nicolas; Erpenbeck, Marcel; Gulden, Christian; Kapsner, Lorenz A; Zierk, Jakob; Mate, Sebastian; Stürzl, Michael; Croner, Roland; Prokosch, Hans-Ulrich; Toddenroth, Dennis
PLoS One, Volume 14, Issue 10 (2019)
PMID: 31581246 DOI: 10.1371/journal.pone.0223010 
Citations: 42 (Scopus)
Tags: Consortia: MIRACUM | Study: Erlangen University Hospital | Type: data systems | Type: software engineering

Distributed Multivariate Regression Modeling For Selecting Biomarkers Under Data Protection Constraints
Zöller, Daniela; Binder, Harald
(2018)
DOI: 10.48550/ARXIV.1803.00422 
Citations: -
Tags: Consortia: GESA | Type: data systems | Type: software engineering

A software package for the application of probabilistic anonymisation to sensitive individual-level data: a proof of principle with an example from the ALSPAC birth cohort study
Avraam, Demetris; Boyd, Andy; Goldstein, Harvey; Burton, Paul
Longitudinal and Life Course Studies, Volume 9, Issue 4 (2018)
DOI: 10.14301/llcs.v9i4.478 
Citations: 7 (Scopus)
Tags: Consortia: CLOSER | Consortia: Connected Health Cities North East North Cumbria | Study: ALSPAC | Type: data governance | Type: proof of concept | Type: software engineering

DataSHIELD – New Directions and Dimensions
Wilson, Rebecca C.; Butters, Oliver W.; Avraam, Demetris; Baker, James; Tedds, Jonathan A.; Turner, Andrew; Murtagh, Madeleine; Burton, Paul R.
Data Science Journal, Volume 16 (2017)
DOI: 10.5334/dsj-2017-021 
Citations: 54 (Scopus)
Tags: Consortia: BBMRI-LPC | Consortia: BioSHaRE-EU | Consortia: Welsh and Scottish Farr Institutes | Type: data systems | Type: software engineering

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination.
Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent
Int J Epidemiol, Volume 46, Issue 5 (2017)
PMID: 29025122 DOI: 10.1093/ije/dyx180 
Citations: 70 (Scopus)
Tags: Consortia: BioSHaRE-EU | Consortia: InterConnect | Consortia: Maelstrom Research | Study: CLSA | Study: CPTP | Type: data harmonization | Type: software engineering

What Does Anonymization Mean? DataSHIELD and the Need for Consensus on Anonymization Terminology.
Wallace, Susan E
Biopreserv Biobank, Volume 14, Issue 3 (2016)
PMID: 27219861 DOI: 10.1089/bio.2015.0119 
Citations: 6 (Scopus)
Tags: Consortia: BioSHaRE-EU | Type: data systems | Type: software engineering

International Data Sharing in Practice: New Technologies Meet Old Governance.
Murtagh, Madeleine J; Turner, Andrew; Minion, Joel T; Fay, Michaela; Burton, Paul R
Biopreserv Biobank, Volume 14, Issue 3 (2016)
PMID: 27200470 DOI: 10.1089/bio.2016.0002 
Citations: 22 (Scopus)
Tags: Consortia: BBMRI-LPC | Consortia: BioSHaRE-EU | Consortia: Welsh and Scottish Farr Institutes | Type: data governance | Type: software engineering

The Biomedical Research Infrastructure Software as a Service Kit (BRISSKit): technical description
Butters, Oliver W.; Issa, Shajid; Lusted, Jeff; Newbury, Malcolm; Parsloe, Russ; Holden, Nick; Free, Robert C.; Beck, Tim; Wilson, Rebecca C.; Burton, Paul R.; Tedds, Jonathan A.
F1000Research, Volume 5 (2016)
DOI: 10.12688/f1000research.8736.1 
Citations: -
Tags: Consortia: BBMRI-LPC | Consortia: BioSHaRE-EU | Consortia: Welsh and Scottish Farr Institutes | Type: data systems | Type: software engineering

Genomic cloud computing: legal and ethical points to consider.
Dove, Edward S; Joly, Yann; Tassé, Anne-Marie; Knoppers, Bartha M
Eur J Hum Genet, Volume 23, Issue 10 (2015)
PMID: 25248396 DOI: 10.1038/ejhg.2014.196 
Citations: 76 (Scopus)
Tags: Consortia: International Cancer Genome Consortium | Consortia: P3G | Type: data governance | Type: software engineering

DataSHIELD: an ethically robust solution to multiple-site individual-level data analysis.
Budin-Ljøsne, Isabelle; Burton, Paul; Isaeva, Julia; Gaye, Amadou; Turner, Andrew; Murtagh, Madeleine J; Wallace, Susan; Ferretti, Vincent; Harris, Jennifer R
Public Health Genomics, Volume 18, Issue 2 (2015)
PMID: 25532061 DOI: 10.1159/000368959 
Citations: 31 (Scopus)
Tags: Consortia: BioSHaRE-EU | Consortia: ENGAGE | Consortia: Welsh and Scottish Farr Institutes | Type: data governance | Type: review | Type: software engineering

Protecting personal data in epidemiological research: DataSHIELD and UK law.
Wallace, Susan E; Gaye, Amadou; Shoush, Osama; Burton, Paul R
Public Health Genomics, Volume 17, Issue 3 (2014)
PMID: 24685519 DOI: 10.1159/000360255 
Citations: 24 (Scopus)
Tags: Consortia: BioSHaRE-EU | Type: data governance | Type: software engineering

DataSHIELD: taking the analysis to the data, not the data to the analysis.
Gaye, Amadou; Marcon, Yannick; Isaeva, Julia; LaFlamme, Philippe; Turner, Andrew; Jones, Elinor M; Minion, Joel; Boyd, Andrew W; Newby, Christopher J; Nuotio, Marja-Liisa; Wilson, Rebecca; Butters, Oliver; Murtagh, Barnaby; Demir, Ipek; Doiron, Dany; Giepmans, Lisette; Wallace, Susan E; Budin-Ljøsne, Isabelle; Oliver Schmidt, Carsten; Boffetta, Paolo; Boniol, Mathieu; Bota, Maria; Carter, Kim W; deKlerk, Nick; Dibben, Chris; Francis, Richard W; Hiekkalinna, Tero; Hveem, Kristian; Kvaløy, Kirsti; Millar, Sean; Perry, Ivan J; Peters, Annette; Phillips, Catherine M; Popham, Frank; Raab, Gillian; Reischl, Eva; Sheehan, Nuala; Waldenberger, Melanie; Perola, Markus; van den Heuvel, Edwin; Macleod, John; Knoppers, Bartha M; Stolk, Ronald P; Fortier, Isabel; Harris, Jennifer R; Woffenbuttel, Bruce H R; Murtagh, Madeleine J; Ferretti, Vincent; Burton, Paul R
Int J Epidemiol, Volume 43, Issue 6 (2014)
PMID: 25261970 DOI: 10.1093/ije/dyu188 
Citations: 207 (Scopus)
Tags: Consortia: BBMRI-LPC | Consortia: BioSHaRE-EU | Consortia: Welsh and Scottish Farr Institutes | Study: CHRIS | Study: FINRISK 2007 | Study: HUNT | Study: KORA | Study: Lifelines | Study: MICROS | Study: Mitchelstown | Study: NCDS | Study: PREVEND | Type: data systems | Type: proof of concept | Type: software engineering

Data harmonization and federated analysis of population-based studies: the BioSHaRE project.
Doiron, Dany; Burton, Paul; Marcon, Yannick; Gaye, Amadou; Wolffenbuttel, Bruce H R; Perola, Markus; Stolk, Ronald P; Foco, Luisa; Minelli, Cosetta; Waldenberger, Melanie; Holle, Rolf; Kvaløy, Kirsti; Hillege, Hans L; Tassé, Anne-Marie; Ferretti, Vincent; Fortier, Isabel
Emerg Themes Epidemiol, Volume 10, Issue 1 (2013)
PMID: 24257327 DOI: 10.1186/1742-7622-10-12 
Citations: 115 (Scopus)
Tags: Consortia: BioSHaRE-EU | Study: CHRIS | Study: FINRISK 2007 | Study: HUNT | Study: KORA | Study: Lifelines | Study: MICROS | Study: NCDS | Study: PREVEND | Type: data governance | Type: data harmonization | Type: software engineering

Data sharing across biobanks: epistemic values, data mutability and data incommensurability
Demir, Ipek; Murtagh, Madeleine J.
New Genetics and Society, Volume 32, Issue 4 (2013)
DOI: 10.1080/14636778.2013.846582 
Citations: 15 (Scopus)
Tags: Consortia: BioSHaRE-EU | Type: data systems | Type: software engineering

Navigating the perfect [data] storm
Murtagh, M.J.; Thorisson, G.A.; Wallace, S.E.; Kaye, J.; Demir, I.; Fortier, I.; Harris, J.R.; Cox, D.; Deschênes, M.; Laflamme, P.; Ferretti, V.; Sheehan, N.A.; Hudson, T.J.; Thomsen, A. Cambon; Stolk, R.P.; Knoppers, B.M.; Brookes, A.J.; Burton, P.R.
Norsk Epidemiologi, Volume 21, Issue 2 (2012)
DOI: 10.5324/nje.v21i2.1495 
Citations: 15 (Scopus)
Tags: Consortia: BioSHaRE-EU | Consortia: ENGAGE | Consortia: GEN2PHEN | Consortia: P3G | Type: software engineering

Securing the data economy: translating privacy and enacting security in the development of DataSHIELD.
Murtagh, M J; Demir, I; Jenkings, K N; Wallace, S E; Murtagh, B; Boniol, M; Bota, M; Laflamme, P; Boffetta, P; Ferretti, V; Burton, P R
Public Health Genomics, Volume 15, Issue 5 (2012)
PMID: 22722688 DOI: 10.1159/000336673 
Citations: 20 (Scopus)
Tags: Consortia: BioSHaRE-EU | Consortia: P3G | Consortia: PHOEBE | Type: | Type: child health | Type: cohort study | Type: data governance | Type: software engineering

DataSHIELD – shared individual-level analysis without sharing the data: a biostatistical perspective
Jones, E.M.; Sheehan, N.A.; Masca, N.; Wallace, S.E.; Murtagh, M.J.; Burton, P.R.
Norsk Epidemiologi, Volume 21, Issue 2 (2012)
DOI: 10.5324/nje.v21i2.1499 
Citations: 38 (Scopus)
Tags: Consortia: BioSHaRE-EU | Consortia: P3G | Consortia: PHOEBE | Type: data systems | Type: software engineering

DataSHIELD: resolving a conflict in contemporary bioscience--performing a pooled analysis of individual-level data without sharing the data.
Wolfson, Michael; Wallace, Susan E; Masca, Nicholas; Rowe, Geoff; Sheehan, Nuala A; Ferretti, Vincent; LaFlamme, Philippe; Tobin, Martin D; Macleod, John; Little, Julian; Fortier, Isabel; Knoppers, Bartha M; Burton, Paul R
Int J Epidemiol, Volume 39, Issue 5 (2010)
PMID: 20630989 DOI: 10.1093/ije/dyq111 
Citations: 145 (Scopus)
Tags: Consortia: P3G | Consortia: PHOEBE | Type: data systems | Type: software engineering