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CORDIS - Resultados de investigaciones de la UE
CORDIS

Common Infrastructure for National Cohorts in Europe, Canada, and Africa

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

DMP - Data Management Plan (se abrirá en una nueva ventana)

CINECA is part of the Open Research Data Pilot (ORDP) and the consortium will therefore submit a first version of a Data Management Plan (DMP) as a deliverable within the first 6 months of the project. The DMP will be updated over the course of the project whenever significant changes arise, such as (but not limited to): - new data - changes in consortium policies (e.g. new innovation potential, decision to file for a patent) - changes in consortium composition and external factors (e.g. new consortium members joining or old members leaving). The DMP will be prepared using the template provided by the Commission (http://ec.europa.eu/research/participants/docs/h2020-funding-guide/cross-cutting-issues/open-access-data-management/data-management_en.htm).

First recommendations needed for implementation implemented in IT Framework (incl. a Data Management Plan) (se abrirá en una nueva ventana)

First recommendations needed for implementation implemented in IT Framework We will provide recommendations for the longterm cooperation between European African and Canadian cohorts to intensify collaboration as well as sharing and reuse of data56 ethical and legal recommendations IT solutions such as machine readable solutions to meet ethical and legal requirements and vice versa

Training Programme, detailed (se abrirá en una nueva ventana)

Training Programme a detailed plan of the training programme for the final two years of the project

Training Programme - annual report (se abrirá en una nueva ventana)

Training Programme Brief annual report on the training delivered shortterm reach and impact

Report of main achievements, impacts, sustainability and exploitation (se abrirá en una nueva ventana)

Report of main achievements impacts sustainability and exploitation

Meta-analysis of splicing and expression QTLs across three cohorts (se abrirá en una nueva ventana)

A Metaanalysis of splicing and expression QTLs across three cohorts We willdevelop a federated metaanalysis protocol that complies with the data sharing and privacy requirements of the individual cohorts and apply it to the three cohorts participating in the implementation study BIOS EGCUT TwinsUK Finally in collaboration with the eQTL Catalog currently being developed at EMBLEBI and UTartu we will make summary statistics from the federated eQTL metaanalysis available via public APIs

Report of impact and key results (se abrirá en una nueva ventana)

Development of a sustainability plan of each project result for maximum longterm impact

Training programme (se abrirá en una nueva ventana)

Brief annual reports on the training delivered shortterm reach and impact for the first three years of the project Report at mo 24 to provide a detailed plan of the training programme for the final two years of the project

CINECA Risk Management Registry (se abrirá en una nueva ventana)

The CINECA Risk Management Registry.The Project Management team will develop a risk management and contingency plan. Risks in CINECA will be assessed in the areas of data security, ethics, dissemination, innovation, and scientific quality. The contingency plan will ensure that items at risk will be closely monitored and if needed followed-up and controlled.

Catalog of Canada, European and African ethical and legal gaps identified (se abrirá en una nueva ventana)

A catalog of Canada European and African ethical and legal gaps to identify the legal and ethical gaps and roadblocks impairing future collaborations among the cohorts participating in this consortium We will focus on the legal and ethical requirementsrelated to informed consent secondary use of data and cross border exchanges of data between Europe and third countries We will base our analysis on the potential application of the GDPR to transnational datasamples exchanges on the Canadian domestic laws PIPEDA and H3Africa governance and on the respect on the ethical values stated byinternational policies

A report on how the GA4GH researcher ID specifications have been implemented in the ELIXIR AAI (se abrirá en una nueva ventana)

A report on how ELIXIR and CanDIG AAI systems will be upgraded to support the GA4GH Library Card concept

Semantic and harmonisation best practice (se abrirá en una nueva ventana)

A report on Semantic and harmonisation best practice to identify the current coding standards for each cohort and the variables recorded for each of the projects cohort

Catalogue on ELSI Issues V1.0 (se abrirá en una nueva ventana)

A catalogue of the ethical, legal and social issues for international collaboration of cohorts with a special focus on Europe, Canada and Africa noting the cloud context. The mapping exercise will be achieved by literature as well as legal and policy documents.

Report of CINECA kick off meeting (se abrirá en una nueva ventana)

A report of CINECA kick off meeting.

Data interoperability documentation (se abrirá en una nueva ventana)

An important use case of the federated discovery services is to discover cohorts of relevant samples or patients across data providers either programmatically or with interactive tools such as the portal of T141 and run uniform pipelines across those items for further analysis with the tools of T42

Integration of new cohort infrastructures to the ELIXIR AAI (se abrirá en una nueva ventana)

A report with the status of integration of new service providers to the ELIXIR AAI Due to the federated nature of human data each infrastructure has their own processes and procedures for granting access to datasets hosted We are proposing to harmonise AAI across the CINECA consortium by ensuring that all of the cohort infrastructures are integrated with either ELIXIR or CanDIG AAI or H3Africa

Curation-support for care planning (se abrirá en una nueva ventana)

Curationsupport for care planning with the aim to add clinical actionability beyond pathogenicity scales

Report on trust model for partner sites, and between sites and controlled-access researchers (se abrirá en una nueva ventana)

A report on trust model for partner sites, and between sites and controlled-access researchers. A machine readable consent ontology mapping of individual cohorts will be used as input to determine the appropriate trust model for partner sites, and between sites and controlled-access researchers.

Outreach and dissemination plan (se abrirá en una nueva ventana)

A report summarising the outcome of our stakeholder analysis (including training needs analysis), highest priority stakeholder groups and plan for engaging with them throughout the project. This will incorporate a detailed training plan for the first two years of the project and an outline plan for the second two years.

Development and application of optimised polygenic risk scores (se abrirá en una nueva ventana)

A report on the development and application of optimised polygenic risk scores We will focus on the development and implementation of methods to generate polygenic risk scores for traits of mutual interest and to use them both for trait prediction and causal inference in a Mendelian randomisation framework The methods developed will generate novel biological and translational insights including polygenic risk scores for medically relevant traits such as type 2 diabetes and coronary artery disease that are optimised for use across multiple samples andor populations

Final report and impact analysis (se abrirá en una nueva ventana)

A final report and impact analysis Summary report of all outreach dissemination and training activities including impact analysis

Text mining processing pipeline for semi structured data (se abrirá en una nueva ventana)

A text mining processing pipeline to extract meta data content from semi or unstructured text in documents

Access representation ontology developed for project's cohorts (se abrirá en una nueva ventana)

Access representation ontology developed for projects cohorts D35 will refine extend and integrate access representations for cohorts based on feedback from WP17 prior work DUO ADAM and user requirements for the cohort access representation

Cohort minimal meta data model (se abrirá en una nueva ventana)

The common minimal metadata model is intended to function supporting the analytical translational and federation use cases described in WP124 and 5 There are several nascent models in existence in this space though many of these as yet are untested in a HTP production environment of the type to be delivered by CINECA eg EDMI from EOSC and the GA4GH Clinical and Phenotypic Model Therefore we will locate merge and test the models for the use cases coming from the implementation work packages to ensure they are fit for purpose for CINECA

Populated minimal meta data model for project cohorts (se abrirá en una nueva ventana)

A minimal meta data model will provide a common for data discovery WP1 and will be populated by data from each cohort enabling federated analyses WP4 and clinical applications WP5

Framework and APIs for executing federated genomics analyses (se abrirá en una nueva ventana)

Framework and APIs for executing federated genomics analyses We will coordinate with an existing ELIXIR Compute platform project to establish interoperable execution platforms at CSC and EMBLEBI using the Toil framework We will collaborate with the ELIXIR Compute platform environments at CSC and EBI to implement new APIs

Universal FAIR Data Compliant Federated Biomarker Discovery Service (se abrirá en una nueva ventana)

Universal FAIR Data Compliant Federated Biomarker Discovery Service. In this task (T5.2) myFAIR will be developed to use federated data (T5.1) from the Catalog of FAIR data (T1.2) available via the interactive query portals developed in T1.4. Secure access to these data will be managed with the ELIXIR AAI service delivered in T2.3 and the trust model from T4.1. Federated workflows used to analyse these data from T4.2, T4.3and part of existing Galaxy services for cancer genomics including fusion gene detection (Teles et al., 2015, Hiltemann et al., 2015, Albuquerque et al., 2017).

GDPR and FAIR compliant Diagnostic Services (se abrirá en una nueva ventana)

GDPR and FAIR compliant Diagnostic Services. We will develop a proof of concept open source diagnostic NGS services.

Query expansion services (se abrirá en una nueva ventana)

As part of the Discovery portal T141 we will deliver services for expanding interactive user queries for phenotype and genotype metadata WP3

CanDIG and ELIXIR AAI interoperability demonstration (se abrirá en una nueva ventana)

A public demonstration of showing technical integration and interoperability between Europe and Canada AAI systems

Discovery service catalog (se abrirá en una nueva ventana)

A discovery service catalog by which users will be able to search the datasets by genomic information as well as using the variable related metadata standards developed as part of WP4. The unique contribution of CINECA will be the first unified multidimensional cohort discovery platform that can perform real-time search across a disparate set of cohort infrastructures in Canada, Europe, and Africa.

Federated discovery across registry services (se abrirá en una nueva ventana)

An important use case of the federated discovery services is to discover cohorts of relevant samples or patients across data providers either programmatically or with interactive tools such as the portal of T141 and run uniform pipelines across those items for further analysis with the tools of T42

Federated Data Analytics for European Biobanks (se abrirá en una nueva ventana)

A report outlining the federated data analytics developed by CINECA for European Biobanks.

Publicaciones

CINECA - Meta-analysis of splicing and expression QTLs across three cohorts D4.4 (se abrirá en una nueva ventana)

Autores: Alasoo, Kaur; Warmerdam, Robert; Westra, Harm-Jan
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7464116

Training Programme, Detailed D6.4 (se abrirá en una nueva ventana)

Autores: Nicola Mulder, Mamana Mbiyavanga, Saskia Hiltemann, Vera Matser
Publicado en: 2020
Editor: Zenodo
DOI: 10.5281/zenodo.6223125

CINECA Report of main achievements, impacts, sustainability and exploitation D8.4 (se abrirá en una nueva ventana)

Autores: Garcia, Carles
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8099739

CINECA: Catalogue of ELSI issues_D7.1 (se abrirá en una nueva ventana)

Autores: Gennet, Éloïse; Goisauf, Melanie
Publicado en: 2019
Editor: Zenodo
DOI: 10.5281/zenodo.3943732

CINECA Catalogue of Canadian, European and African ethical and legal gaps D7.2 (se abrirá en una nueva ventana)

Autores: Gennet, Éloïse; Goisauf, Melanie; Pichereau, Delphine; Rial-Sebbag, Emmanuelle
Publicado en: 2020
Editor: Zenodo
DOI: 10.5281/zenodo.6256295

Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci (se abrirá en una nueva ventana)

Autores: Nurlan Kerimov, Ralf Tambets, James D. Hayhurst, Ida Rahu, Peep Kolberg, Uku Raudvere, Ivan Kuzmin, Anshika Chowdhary, Andreas Vija, Hans J. Teras, Masahiro Kanai, Jacob Ulirsch, Mina Ryten, John Hardy, Sebastian Guelfi, Daniah Trabzuni, Sarah Kim-Hellmuth, Will Rayner, Hilary Finucane, Hedi Peterson, Abayomi Mosaku, Helen Parkinson, Kaur Alasoo
Publicado en: BioRxiv, 2023
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.04.06.535816

CINECA Data interoperability documentation D1.4 (se abrirá en una nueva ventana)

Autores: Spalding, Dylan
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8093973

CINECA_D6.1_Outreach and Dissemination Plan (se abrirá en una nueva ventana)

Autores: Mulder, Nicola; Mbiyavanga, Mamana; Mendonca, Michelle; Matser, Vera; Hiltemann, Saskia
Publicado en: Edición 1, 2019
Editor: Zenodo
DOI: 10.5281/zenodo.4562406

CINECA: Common Infrastructure for National Cohorts in Europe, Canada, and Africa - Kick Off Report (se abrirá en una nueva ventana)

Autores: Keane, Thomas; Glass, Leslie
Publicado en: 2019
Editor: Zenodo
DOI: 10.5281/zenodo.3908145

CINECA Integration of new cohort infrastructures to the ELIXIR AAI - D2.3 (se abrirá en una nueva ventana)

Autores: Licehammer; Bučík; Broncová; Spalding
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8056340

CINECA Federated Data Analytics for European Biobanks D5.1 (se abrirá en una nueva ventana)

Autores: Ruch; Mottin; Michel; Pasche; Mottaz; Naderi
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/zenodo.6783295

CINECA_Query expansion service_D1.2 (se abrirá en una nueva ventana)

Autores: Tanzer, Romain; Naderi, Nona; Teodoro, Douglas; Mottaz, Anais; Ruch, Patrick; Dursi, Jonathan; Rambla de Argila, Jordi
Publicado en: Edición 4, 2020
Editor: Zenodo
DOI: 10.5281/zenodo.4609334

CINECA Cohort Level metadata Representation D3.1 (se abrirá en una nueva ventana)

Autores: Jin, Vivian; Brinkman, Fiona
Publicado en: Edición 8, 2020
Editor: Zenodo
DOI: 10.5281/zenodo.4575460

CINECA Populated minimal metadata model for project cohorts - D3.4 (se abrirá en una nueva ventana)

Autores: Brinkman, Fiona
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8297040

CINECA_Semantic and harmonisation best practice_D3.2 (se abrirá en una nueva ventana)

Autores: Courtot, Melanie; Liyanage, Isuru
Publicado en: Edición 8, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.5055308

CINECA Federated discovery across registry services D1.3 (se abrirá en una nueva ventana)

Autores: Fromont; Milla
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8099693

CINECA Report on GA4GH Researcher ID D2.2 (se abrirá en una nueva ventana)

Autores: Linden, Mikael; Kuba, Martin; Izquierdo, Jorge; Mbiyavanga, Mamana
Publicado en: Edición 2, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.5795408

CINECA D7.3 First recommendations for implementation in IT Framework (Incl. a Data Management Plan) (se abrirá en una nueva ventana)

Autores: Goisauf, Melanie; Fériol, Lisa; Rial-Sebbag, Emmanuelle
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7680755

Text mining processing pipeline for semi structured data D3.3 (se abrirá en una nueva ventana)

Autores: Copara, Jenny; Naderi, Nona; Kellmann, Alexander; Gosal, Gurinder; Hsiao, William; Teodoro, Douglas
Publicado en: Edición 4, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.5795432

Access representation ontology developed for project's cohorts D3.5 (se abrirá en una nueva ventana)

Autores: Courtot, Melanie; Dursi, Jonathan; Mulder, Nicola; Swertz, Morris
Publicado en: Edición 2, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.5795448

CINECA GDPR and FAIR compliant Diagnostic Services D5.3 (se abrirá en una nueva ventana)

Autores: Johansson, Lennart; Been, Gerieke; Michie, Alex; Binsl, Thomas
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7925804

CINECA_Discovery Service Catalogue_D1.1 (se abrirá en una nueva ventana)

Autores: Dursi, Jonathan; Rambla de Argila, Jordi; de la Torre, Sabela; Tanzer, Romain; Naderi, Nona; Mbiyavanga, Mamana; Agarwal, Samarth
Publicado en: 2020
Editor: Zenodo
DOI: 10.5281/zenodo.3908397

CINECA_Training Programme_D6.2a (se abrirá en una nueva ventana)

Autores: Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Matser, Vera
Publicado en: 2019
Editor: Zenodo
DOI: 10.5281/zenodo.3952621

CINECA Universal FAIR Data Compliant Federated Biomarker Discovery Service D5.2 (se abrirá en una nueva ventana)

Autores: Hiltemann, Saskia; Ouwerkerk, Jasper; Stubbs, Andrew
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7925781

CINECA Data Management Plan v2 (se abrirá en una nueva ventana)

Autores: Glass, Leslie; Spalding, Dylan; Mulder, Nicola; Courtot, Melanie; Brinkman, Fiona; Ruch, Patrick
Publicado en: 2021
Editor: Zenodo
DOI: 10.5281/zenodo.4683415

CINECA_CanDIG and ELIXIR AAI interoperability demonstration_D2.1 (se abrirá en una nueva ventana)

Autores: Procházka, Michal; Linden, Mikael; Sethi, Amanjeev; Binsl, Thomas; Michie, Alex; Mbiyavanga, Mamana; Spalding, Dylan
Publicado en: 2020
Editor: Zenodo
DOI: 10.5281/zenodo.3938916

CINECA Framework and APIs for executing federated genomics analyses D4.2 (se abrirá en una nueva ventana)

Autores: Álvaro González, Shubham Kapoor, Kirill Tsukanov
Publicado en: 2020
Editor: Zenodo
DOI: 10.5281/zenodo.4609356

CINECA Curation-support application for care planning D5.4 (se abrirá en una nueva ventana)

Autores: Ruch, Patrick; Naderi, Nona; Mottin, Luc; Pasche, Emilie; Mottaz, Anais
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7925825

Catalogue of Canadian, European and African ethical and legal gaps (se abrirá en una nueva ventana)

Autores: Gennet, ��lo��se; Goisauf, Melanie; Pichereau, Delphine; Rial-Sebbag, Emmanuelle
Publicado en: Edición 1, 2020
Editor: Zenodo
DOI: 10.5281/zenodo.4298449

CINECA Risk Management Registry D8.2 (se abrirá en una nueva ventana)

Autores: Keane, Thomas
Publicado en: 2019
Editor: Zenodo
DOI: 10.5281/zenodo.7734061

CIENCA Final Report and Impact Analysis D6.3 (se abrirá en una nueva ventana)

Autores: Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Gurwitz, Kim; Lloret Llinares, Marta; Thomas Lopez, Daniel
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7925741

CINECA Report of impact and key results D8.3 (se abrirá en una nueva ventana)

Autores: Garcia, Carles
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8099814

CINECA: Data Management Plan v.1 (se abrirá en una nueva ventana)

Autores: Kerry, Giselle; Glass, Leslie; Keane, Thomas; Ruch, Patrick; Mulder, Nicola; Brinkman, Fiona
Publicado en: 2019
Editor: Zenodo
DOI: 10.5281/zenodo.3909577

Training Programme_Annual Report 2021 D6.5 (se abrirá en una nueva ventana)

Autores: Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Matser, Vera; Lloret Llinares, Marta
Publicado en: Edición 4, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.5795482

CINECA: Report on trust model for partner sites, and between sites and controlled-access researchers (se abrirá en una nueva ventana)

Autores: Cirillo, Elisa; Alasoo, Kaur; Michie, Alex; Binsl, Thomas; Törnroos, Juha; Kapoor, Shubham; Tsukanov, Kirill; Rayner, William; Mbiyavanga, Mamana; Rashid, Shaikh; Westra, Harm-Jan
Publicado en: 2020
Editor: Zenodo
DOI: 10.5281/zenodo.3909521

Reconciling the biomedical data commons and the GDPR: three lessons from the EUCAN ELSI collaboratory (se abrirá en una nueva ventana)

Autores: Alexander Bernier, Fruzsina Molnár-Gábor, Bartha M Knoppers, Pascal Borry, Priscilla M D G Cesar, Thijs Devriendt, Melanie Goisauf, Madeleine Murtagh, Pilar Nicolás Jiménez, Mikel Recuero, Emmanuelle Rial-Sebbag, Mahsa Shabani, Rebecca C Wilson, Davide Zaccagnini, Lauren Maxwell
Publicado en: European Journal of Human Genetics, 2023, ISSN 1476-5438
Editor: Nature
DOI: 10.1038/s41431-023-01403-y

International federation of genomic medicine databases using GA4GH standards (se abrirá en una nueva ventana)

Autores: Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla,Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, and Ewan Birney
Publicado en: Cell Genomics, 2021, ISSN 2666-979X
Editor: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100032

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants (se abrirá en una nueva ventana)

Autores: Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Publicado en: eLife, 2020, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.58705

Assessing the use of supplementary materials to improve genomic variant discovery (se abrirá en una nueva ventana)

Autores: Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch
Publicado en: Database, Edición Volume 2023, 2023, ISSN 1758-0463
Editor: Oxford University Press
DOI: 10.1093/database/baad017

Voices of GA4GH members: Collaborating in technology and policy development (se abrirá en una nueva ventana)

Autores: Bartha Maria Knoppers, Danya Vears, Calvin W.L. Ho, Anna Middleton, Jacob Shujui Hsu, Alex Handler Wagner, Mélanie Courtot, Melissa Haendel, Michael Baudis, Orion Buske, Andy Yates, Kathy Reinold, Jonathan Lawson, Melissa Cline, Tiffany Boughtwood, Alexander Kanitz, Jordi Rambla,
Publicado en: Cell Genomics, 2021, ISSN 2666-979X
Editor: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100036

GA4GH: International policies and standards for data sharing across genomic research and healthcare (se abrirá en una nueva ventana)

Autores: Heidi L.Rehm, Angela J.H.Page, Lindsay Smith, Jeremy B.Adams, Gil Alterovitz, Lawrence J.Babb, Maxmillian P.Barkley, Michael Baudis, Michael J.S.Beauvais, Tim Beck, Jacques S.Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K.Bonfield, Tiffany F.Boughtwood, Guillaume Bourque, Sarion R.Bowers… Ewan Birney
Publicado en: Cell Genonics, 2021, ISSN 2666-979X
Editor: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100029

The Data Use Ontology to streamline responsible access to human biomedical datasets (se abrirá en una nueva ventana)

Autores: Jonathan Lawson, Moran N.Cabili, Giselle Kerry, Tiffany Bought Wood, Adrian Thorogood, Pinar Alper, Sarion R.Bowers, Rebecca R.Boyles, Anthony J.Brookes, Matthew Brush, Tony Burdett, Hayley Clissold, Stacey Donnelly, Stephanie O.M.Dyke, Mallory A.Freeberg, Melissa A.Haendel, Chihiro Hata, Petr Holub, MélanieCourtot
Publicado en: Cell Genomics, 2021, ISSN 2666-979X
Editor: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100028

GA4GH Passport standard for digital identity and access permissions (se abrirá en una nueva ventana)

Autores: Craig Voisin, Mikael Linden, Stephanie O.M.Dyke, Sarion R.Bowers, Pinar Alper, Maxmillian P.Barkley, David Bernick, Jianpeng Chao, Mélanie Courtot, Francis Jeanson, Melissa A.Konopko, Martin Kuba, Jonathan Lawson, Jaakko Leinonen, Stephanie Li, Vivian Ota Wang, Anthony A.Philippakis, Kathy Reinold, Gregory A.Rushton, J. Dylan Spalding, Juha Törnroos, Ilya Tulchinsky, Jaime M.Guidry Auvil, Tommi
Publicado en: Cell Genomics, 2021, ISSN 2666-979X
Editor: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100030

Training Infrastructure as a Service (se abrirá en una nueva ventana)

Autores: Helena Rasche, Cameron Hyde, John Davis, Simon Gladman, Nate Coraor, Anthony Bretaudeau, Gianmauro Cuccuru, Wendi Bacon, Beatriz Serrano-Solano, Jennifer Hillman-Jackson, Saskia Hiltemann, Miaomiao Zhou, Björn Grüning, Andrew Stubbs
Publicado en: Gigascience, Edición 2022 Dec 28;12:giad048, 2023, ISSN 2047-217X
Editor: Oxford Academy
DOI: 10.1093/gigascience/giad048

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy. (se abrirá en una nueva ventana)

Autores: Willem de Koning; Milad Miladi; Saskia Hiltemann; Astrid P. Heikema; John P. Hays; Stephan Flemming; Marius van den Beek; Dana A M Mustafa; Rolf Backofen; Björn Grüning; Andrew P. Stubbs
Publicado en: GigaScience, Edición 2, 2020, ISSN 2047-217X
Editor: Oxford Academic
DOI: 10.1093/gigascience/giaa105

Empirical validation of an automated approach to data use oversight (se abrirá en una nueva ventana)

Autores: Moran N.Cabili, Jonathan Lawson, Andrea Saltzman, Greg Rushton, Pearl O’Rourke, John Wilbanks, Laura Lyman Rodriguez, Tommi Nyronen, Mélanie Courtot, Stacey Donnelly, Anthony A.Philippakis
Publicado en: Cell Genomics, 2021, ISSN 2666-979X
Editor: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100031

Information Retrieval in an Infodemic: The Case of COVID-19 Publications (se abrirá en una nueva ventana)

Autores: Douglas Teodoro, Sohrab Ferdowsi, Nikolay Borissov, Elham Kashani, David Vicente Alvarez, Jenny Copara, Racha Gouareb, Nona Naderi, Poorya Amini
Publicado en: Journal of Medical Internet Research, 2021, ISSN 1438-8871
Editor: Journal of medical Internet Research
DOI: 10.2196/30161

A compendium of uniformly processed human gene expression and splicing quantitative trait loci (se abrirá en una nueva ventana)

Autores: Nurlan Kerimov, James D. Hayhurst, Kateryna Peikova, Jonathan R. Manning,Peter Walter, Liis Kolberg, Marija Samoviča, Manoj Pandian Sakthivel, Ivan Kuzmin, Stephen J. Trevanion, Tony Burdett, Simon Jupp, Helen Parkinson, Irene Papatheodorou,Andrew D. Yates, Daniel R. Zerbino and Kaur Alasoo
Publicado en: Nature Genetics, 2021, ISSN 1546-1718
Editor: Nature
DOI: 10.1038/s41588-021-00924-w

Galactic Circos: User-friendly Circos plots within the Galaxy platform (se abrirá en una nueva ventana)

Autores: Helena Rasche, Saskia Hiltemann
Publicado en: GigaScience, Edición 9/6, 2020, ISSN 2047-217X
Editor: Oxford Academic
DOI: 10.1093/gigascience/giaa065

Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature (se abrirá en una nueva ventana)

Autores: Julien Knafou, Quentin Haas, Nikolay Borissov, Michel Counotte , Nicola Low, Hira Imeri, Aziz Mert Ipekci, Diana Buitrago-Garcia, Leonie Heron, Poorya Amini, Douglas Teodoro
Publicado en: Systematic Reviews, Edición Systematic Reviews 12, Article number: 94 (2023), 2023, ISSN 2046-4053
Editor: BioMed Central
DOI: 10.1186/s13643-023-02247-9

Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond (se abrirá en una nueva ventana)

Autores: Jordi Rambla, Michael Baudis, Roberto Ariosa, Tim Beck, Lauren A Fromont, Arcadi Navarro, Rahel Paloots, Manuel Rueda, Gary Saunders, Babita Singh, John D Spalding, Juha Törnroos, Claudia Vasallo, Colin D Veal, Anthony J Brookes
Publicado en: Human Mutation, Edición 2022 Jun;43(6), 2022, Página(s) 791-799, ISSN 1098-1004
Editor: Wiley Online Library
DOI: 10.1002/humu.24369

Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora (se abrirá en una nueva ventana)

Autores: Nona Naderi, Julien Knafou, Jenny Copara, Patrick Ruch, Douglas Teodoro
Publicado en: Frontiers in Research Metrics and Analytics, 2021, ISSN 2504-0537
Editor: Lausanne: Frontiers Media S.A.
DOI: 10.3389/frma.2021.689803

Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service (se abrirá en una nueva ventana)

Autores: Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, Patrick Ruch
Publicado en: Studies in Health Technology and Informatics, Edición Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Página(s) 839 - 843
Editor: IOS Press
DOI: 10.3233/shti220603

Analyzing the Information Content of Text-Based Files in Supplementary Materials of Biomedical Literature (se abrirá en una nueva ventana)

Autores: Nona Naderi, Anaïs Mottaz, Douglas Teodoro, Patrick Ruch
Publicado en: Studies in Health Technology and Informatics, Edición Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Página(s) 876 - 877
Editor: IOS Press
DOI: 10.3233/shti220614

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