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CORDIS - EU research results
CORDIS

Human Exposome Assessment Platform

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Sensor pilot Documentation (opens in new window)

Prior to the enrollment of the first subject, we will submit (i) Final version of study protocol as submitted to regulators/ethics committee(s), (ii) Registration number of clinical study in a WHO-or ICMJE- approved registry (with the possibility to post results), (iii) Approvals (ethics committees and national competent authority if applicable) required for invitation/enrolment of first subject in at least one clinical centre.

Sustainability plan (opens in new window)

Plan to guarantee that the produced results from HEAP continue contributing to exposome research beyond the project’s lifetime.

Report on exposures which lead to epigenetic age acceleration or deceleration (opens in new window)

A list of exposures will be provided which either lead to an apparent increase of age compared to chronological age (i.e. age-acceleration) or a decrease (i.e. age-deceleration).

Exposure DNAme signatures (opens in new window)

A list of CpGs which collectively change as a function of exposure to a specific conditionfactor and which can be used to define an index eg smokingindex will be provided

List of Working Groups and ToR for the WGs - EXPANSE/HEAP (opens in new window)

A first set of working groups will be made and Term of Reference for the WGs will be specified including the selection of work group leaders coleads and members

Reference architecture (opens in new window)

Document describing the reference architecture for Information Commons and technical requirements.

Secure platform and recruitment (opens in new window)

Recruitment using secure electronic customer receipts analysis platform commenced Plan to recruit 10000 individuals

Report on secure data platform (opens in new window)

Documentation of the secure data platform and its integration into HEAP.

Ageing DNAme signatures (opens in new window)

A list of CpGs which collectively change as a function of age eg general age signature stem cell polycombgroup target signature replicative age etc will be provided

Report on databases mapped (opens in new window)

Report on databases mapped and how they contribute to the proper implementation of the GDPR and national legislation. Databases are mapped according to their legal bases, relevant other GDPR issues and options for 'further use' for research. The dataflows for the research, data protection by design, data security at the various in-between phases, controller-processor agreements and the final database(s) are mapped. The report will include recommendations for possible improvements from a GDPR perspective and include a DPIA on processing of data on the CSC platform.

Summary report about data governance (opens in new window)

Summary report about the legal and ethical challenges of managing and analysing exposome and outcomes data for public health and the HEAP experience of how these can be addressed. The report will address data protection issues and secure access rules as well as the procedure for processing data for research (how it will be decided that certain data may be processed for certain research questions).

Handover document to next coordinating team – EXPANSE/HEAP (opens in new window)

Document summarising network activities and ongoing activities to facilitate a smooth transition to the next team. This document will include concise reports from working groups.

Report on consumer receipts data and sample-derived data (opens in new window)

Special report about how data from a consenting cohort providing data from consumer receipts may be used for public health in an ethically and data protection compliant way In that context also a DPIA will be performed

Knowledge and information sharing - Phase II (opens in new window)

Report on learning and informational resources developed and activities implemented (including the HEAP symposium) to encourage and support European researcher beyond the consortium to use HEAP for research.

Knowledge and information sharing - Phase I (opens in new window)

Report from activities implemented and resources developed in order to support data providers within the consortium to effectively upload data to HEAP

Report on implementation for research use cases (opens in new window)

Report describing implementation and experiences from HEAP research use cases.

Report on consumer data (opens in new window)

Scientific report on consumer data’s potential as a tool for lifestyle assessment including methodology needed to facilitate evidence-based consumer-friendly lifestyle advice. Report on potential exposure to nutrients, chemicals, and additives as accessed by consumer data, and association to health-related outcomes, or absence of such outcomes.

Integrated personal exposome and metabolomics profile (opens in new window)

A complete report of personal exposome and metabolomics profile, and how these factors may impact the health of the participant, and potential risk for certain diseases. The report may be integrated with findings from WP8 and WP9 to provide a fuller vision of the health of a particular participant.

An established setting for evaluation (opens in new window)

An established setting for evaluation of the extent of exposures to the populations in 2 EU countries with consecutive time-windows (continuous population-based enrolment ongoing for 10 to 35 years) allows access to bio-specimens taken at any calendar year of interest for evaluating impact of naturally occurring and iatrogenic exposures to the population. This deliverable is linked to task 3.2.

Knowledge and information-sharing plan (opens in new window)

Report from the mapping of key topics to be addressed as well as the mapping of target audiences including a plan for the elaboration and implementation of learning and informational resources and events

Data availability confirmation (opens in new window)

An explicit confirmation that the data used in the project is publicly available and can be freely used for the purposes of the project. (KI, M6)

Ontology and semantic metadata (opens in new window)

Ontology and semantic metadata for metagenomic profiles and tools for NGS data management

Assessment of Interoperability and Data Quality (opens in new window)

Assessment of Interoperability and Data Quality - Report on assessment and validation of quality and interoperability of data from all the partners providing data to the HEAP.

Advanced statistics analysis on Finnish Maternity Cohort and Swedish Cervical Screening Cohort (opens in new window)

Test the methods and decision support module implemented in Task 6.6 on the Finnish Maternity Cohort and the Swedish Cervical Screening Cohort.

HEAP Data Warehouse (opens in new window)

Complete configuration of Hopswork for the requirements of HEAP including data management, analysis, and sharing and the integration with IC and analysis providers. We will create a Hopsworks HEAP repo in GitHub.

Demonstrator of integration of wearable sensors (opens in new window)

Data from the pilot for testing the workflow for data streaming from to data analysis in close collaboration with WP5.

HEAP Knowledge Engine (opens in new window)

In collaboration with WP8, WP9, WP3, WP4, implementation and integration of deep learning and the main analysis pipelines provided by the partners. Updating of Hopsworks HEAP repo in GitHub.

Integration in IC and DFW (opens in new window)

In collaboration with WP6 and WP10, develop approaches to integrate exposure to nutrients, chemicals, and additives in HEAP’s Information Commons and Knowledge Network. Explore approaches to personalized prevention using continuously collected consumer data.

Improved wearable PEMs (opens in new window)

A wearable and durable PEM that enables everyday monitoring of environmental exposure at the personal level and provides data for streaming and real-time monitoring implemented by WP6.

Integration of analysis results into HEAP Data & Feature Warehouse (opens in new window)

The produced knowledge from the DNAme analyses, will be available through HEAP DFW.

Metadata Catalogue and Access Procedures (opens in new window)

Metadata Catalogue and Access Procedures – The web service will include explicit information regarding metadata availability and the possibility of free use of all this data for the purposes of the project

AI based alignment free (agnostic) taxonomic classification (opens in new window)

AI based alignment free (agnostic) taxonomic classification algorithm able to classify virus-related sequences in metagenomic sequencing datasets, fully integrated in the bioinformatics workflow from D9.1.

FAIR Toolbox and BYOD workshops (opens in new window)

FAIR Toolbox and BYOD workshops - This deliverable provides a Findable, Accessible, Interoperable and Reusable and Bring Your Own Data (BYOD) workshops where HEAP data provider will get a hands-on training (hackathon) and can improve and evaluate the interoperability and FAIRness of their data sets.

Formalise Knowledge in HEAP (opens in new window)

A continuously expanding, comprehensive, population-level exposure assessment over time based on high-throughput laboratory analyses of the consecutive sample sets. In collaboration with WP6, this data will be formalised to be integrated into the HEAP IC and Data & Feature Warehouse.

Massively parallel Bioinformatics pipeline (opens in new window)

Bioinformatics pipeline, an ecosystem of bioinformatics tools, for complete analysis of metagenomic data generated from human biospecimens using NGS technologies, optimised for Hadoop and HPC ecosystems and, in collaboration with WP6, integrated to be used through the graphical user interface of the HEAP platform.

Exposome and metabolomics analysis pipelines (opens in new window)

Analysis pipelines for both exposome and metabolomics will be streamlined for integration with WP8 and WP9, and implementation with WP6.

Searchable database (opens in new window)

Searchable database with data on all the donors (age, sex) and registry-derived data on all the disease endpoints that have developed in the three cohorts. The software for the database is developed by partner 2 (SSI) and allows integrity-assured, yet flexible searches that will allow easy design of maximally informative research studies based on the biospecimens and data from these cohorts. In Collaboration with WP10, data from the database will be available to the IC.

Bacterial and viral metagenomics. (opens in new window)

High performance bioinformatics workflow for mining bacterial de novo analysis of viral genomes in metagenomic sequencing datasets genomes in NGS metagenomic sequencing datasets.

Online platform and tools (opens in new window)

An online platform combining informational and educational material, enriched with learning management and newsletter functionalities.

Demonstrator of the data analysis and data sharing on HEAP (opens in new window)

This deliverable will provide a test environment for curating, uploading, managing, analysing and sharing data. Partners providing data and analysis pipelines will use the environment to produce the first results from the cohorts. Shareable data and results will available through the Data & Feature Warehouse.

Project Website (opens in new window)

The HEAP website with information on exposome research in general and the project in particular, with sections targeted either to the scientific community or to the general public.

Network website - HEAP (opens in new window)

Website with network activities and links to all individual network websites.

Data management plan (opens in new window)

Data Management Plan - This deliverable will provide the governance and HEAP policies regarding the access, management and sharing of all the used and produced data during and after the project is completed. The plan will cover the generation of metadata from the different data sources of the project including all the cohorts, the raw and processed data and the results to be stored, preserved and shared for future exposome research.

Publications

Challenges and recommendations for the translation of biomarkers of aging (opens in new window)

Author(s): null null, Chiara M. S. Herzog, Ludger J. E. Goeminne, Jesse R. Poganik, Nir Barzilai, Daniel W. Belsky, Joe Betts-LaCroix, Brian H. Chen, Michelle Chen, Alan A. Cohen, Steven R. Cummings, Peter O. Fedichev, Luigi Ferrucci, Alexander Fleming, Kristen Fortney, David Furman, Vera Gorbunova, Albert Higgins-Chen, Lee Hood, Steve Horvath, Jamie N. Justice, Douglas P. Kiel, George A. Kuchel, Jessica Las
Published in: Nature Aging, Issue 4, 2024, Page(s) 1372-1383, ISSN 2662-8465
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s43587-024-00683-3

Functionally enriched epigenetic clocks reveal tissue-specific discordant aging patterns in individuals with cancer (opens in new window)

Author(s): Chiara M. S. Herzog, Elisa Redl, James Barrett, Sepideh Aminzadeh-Gohari, Daniela D. Weber, Julia Tevini, Roland Lang, Barbara Kofler, Martin Widschwendter
Published in: Communications Medicine, Issue 5, 2025, ISSN 2730-664X
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s43856-025-00739-4

Prostate Cancer Testing Between Screening Rounds: Evidence from the STHLM3-MRI Trial (opens in new window)

Author(s): Daniela Skalt, Ting Chen, Ahmad Abbadi, Anna Lantz, Andrea Discacciati, Martin Eklund, Mark Clements, Tobias Nordström, Shuang Hao
Published in: European Urology Oncology, 2025, ISSN 2588-9311
Publisher: Elsevier BV
DOI: 10.1016/j.euo.2025.05.015

Provenance of specimen and data – A prerequisite for AI development in computational pathology (opens in new window)

Author(s): Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Müller, Jörg Geiger
Published in: New Biotechnology, 2023, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2023.09.006

Improving Species Level‐taxonomic Assignment from 16S rRNA Sequencing Technologies (opens in new window)

Author(s): David Bars‐Cortina, Ferran Moratalla‐Navarro, Ainhoa García‐Serrano, Núria Mach, Lois Riobó‐Mayo, Jordi Vea‐Barbany, Blanca Rius‐Sansalvador, Silvia Murcia, Mireia Obón‐Santacana, Victor Moreno
Published in: Current Protocols, Issue 3, 2024, ISSN 2691-1299
Publisher: Wiley
DOI: 10.1002/cpz1.930

Overweight in childhood and consumer purchases in a Danish cohort (opens in new window)

Author(s): Kathrine Kold Sørensen, Mikkel Porsborg Andersen, Frederik Trier Møller, Rikke Wiingreen, Marcella Broccia, Emil L. Fosbøl, Bochra Zareini, Thomas Alexander Gerds, Christian Torp-Pedersen
Published in: PLOS ONE, Issue 19, 2024, Page(s) e0297386, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0297386

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota (opens in new window)

Author(s): David Bars-Cortina, Elies Ramon, Blanca Rius-Sansalvador, Elisabet Guinó, Ainhoa Garcia-Serrano, Núria Mach, Olfat Khannous-Lleiffe, Ester Saus, Toni Gabaldón, Gemma Ibáñez-Sanz, Lorena Rodríguez-Alonso, Alfredo Mata, Ana García-Rodríguez, Mireia Obón-Santacana, Victor Moreno
Published in: BMC Genomics, Issue 25, 2024, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-024-10621-7

Assessing household lifestyle exposures from consumer purchases, the My Purchases cohort (opens in new window)

Author(s): Frederik T. Møller, Thor Grønborg Junker, Kathrine Kold Sørensen, Caroline Eves, Jan Wohlfahrt, Joakim Dillner, Christian Torp-Pedersen, Bartlomiej Wilkowski, Steven Chong, Tune H. Pers, Victor Yakimov, Heimo Müller, Steen Ethelberg & Mads Melbye
Published in: Scientific Reports, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-47534-6

BIBBOX, a FAIR toolbox and App Store for life science research (opens in new window)

Author(s): Heimo Müller, Catarina Lopes-Dias, Petr Holub, Markus Plass, Emilian Jungiwrth, Robert Reihs, Paul R. Torke, Apostolos Malatras, Anouk Berger, Heather Coombs, Joakim Dillner and Roxana Merino-Martinez
Published in: New Biotechnology, 2023, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2023.06.001

Susceptibility to hormone-mediated cancer is reflected by different tick rates of the epithelial and general epigenetic clock (opens in new window)

Author(s): James E. Barrett; Chiara Herzog; Yoo-Na Kim; Thomas E. Bartlett; Allison Jones; Iona Evans; David Cibula; Michal Zikan; Line Bjørge; Nadia Harbeck; Nicoletta Colombo; Sacha J. Howell; Angelique Flöter Rådestad; Kristina Gemzell-Danielsson; Martin Widschwendter
Published in: Genome Biology, Issue 27, 2022, Page(s) 52, ISSN 1474-760X
Publisher: BMC SpringerNature
DOI: 10.1186/s13059-022-02603-3

Cervical cancer microbiome analysis: comparing HPV 16 and 18 with other HPV types (opens in new window)

Author(s): Maire Hidjo, Dhananjay Mukhedkar, Collen Masimirembwa, Jiayao Lei, Laila Sara Arroyo Mühr
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-73317-8

Toward Human–AI Interfaces to Support Explainability and Causability in Medical AI (opens in new window)

Author(s): Andreas Holzinger; Heimo Müller
Published in: Computer, Issue 28, 2021, Page(s) 78-86, ISSN 1558-0814
Publisher: IEEE Computer Society
DOI: 10.1109/mc.2021.3092610

The Ten Commandments of Ethical Medical AI (opens in new window)

Author(s): H. Muller, M. Mayrhofer, E. Van Veen and A. Holzinger
Published in: Computer, Issue 54, 2021, Page(s) 119-123, ISSN 1558-0814
Publisher: IEEE Computer Society
DOI: 10.1109/mc.2021.3074263

Spatio-temporal variation in prostate cancer testing in Stockholm: A population-based study (opens in new window)

Author(s): Balram Rai, Tobias Nordström, Anna Lantz, Rolf Lyneborg Lund, Ralf Kuja-Halkola, Marta Rado, Sara Öberg, Shuang Hao, Xiaoyang Du, Mark Clements
Published in: PLOS ONE, Issue 19, 2024, Page(s) e0308254, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0308254

Explainability and causability for artificial intelligence-supported medical image analysis in the context of the European In Vitro Diagnostic Regulation (opens in new window)

Author(s): Heimo Müller, Andreas Holzinger, Markus Plass, Luka Brcic, Cornelia Stumptner, Kurt Zatloukal
Published in: New Biotechnology, Issue 70, 2022, Page(s) 67-72, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2022.05.002

Cervical cancer screening using DNA methylation triage in a real-world population (opens in new window)

Author(s): Lena Schreiberhuber, James E. Barrett, Jiangrong Wang, Elisa Redl, Chiara Herzog, Charlotte D. Vavourakis, Karin Sundström, Joakim Dillner, Martin Widschwendter
Published in: Nature Medicine, Issue 30, 2024, Page(s) 2251-2257, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-024-03014-6

Creating personas for exposome research: the experience from the HEAP project (opens in new window)

Author(s): Heather Coombs; Tracy Wootton; Joakim Dillner; Heimo Müller; Anouk Berger; Zisis Kozlakidis
Published in: Open Research Europe, 2023, ISSN 2732-5121
Publisher: EU
DOI: 10.12688/openreseurope.15474.1

HPV-induced host epigenetic reprogramming is lost upon progression to high-grade cervical intraepithelial neoplasia (opens in new window)

Author(s): Herzog C, Vavourakis CD, Barrett JE, Karbon G, Villunger A, Wang J, Sundström K, Dillner J, Widschwendter M
Published in: International Journal of Cancer, 2023, ISSN 0020-7136
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/ijc.34477

The European health data space: Too big to succeed? (opens in new window)

Author(s): Luca Marelli , Marthe Stevens , Tamar Sharon , Ine Van Hoyweghen , Martin Boeckhout , Ilaria Colussi , Alexander Degelsegger-M ́ arquez , Seliem El-Sayed , Klaus Hoeyer , Robin van Kessel , Dorota Krekora Zaj Î ac , Mihaela Matei , Sara Roda , Barbara Prainsack , Irene Schl ̈ under , Mahsa Shabani , Tom Southerington
Published in: Health Policy, 2023, ISSN 0168-8510
Publisher: Elsevier BV
DOI: 10.1016/j.healthpol.2023.104861

Joint controllers in large research consortia: a funnel model to distinguish controllers in the sense of the GDPR from other partners in the consortium (opens in new window)

Author(s): Evert-Ben Van Veen, Martin Boeckhout, Irene Schlünder, Jan Willem Boiten, Vasco Dias
Published in: Open Research Europe, Issue 2, 2024, Page(s) 80, ISSN 2732-5121
Publisher: F1000 Research Ltd
DOI: 10.12688/openreseurope.14825.2

Joint controllers in large research consortia: a funnel model to distinguish controllers in the sense of the GDPR from other partners in the consortium (opens in new window)

Author(s): Evert-Ben Van Veen; Martin Boeckhout; Irene Schlünder; Jan Willem Boiten; Vasco Dias
Published in: Open Research Europe, Issue 28, 2022, ISSN 2732-5121
Publisher: European Comission
DOI: 10.12688/openreseurope.14825.1

Ecological diversity profiles of non-vaccine-targeted HPVs after gender-based community vaccination efforts (opens in new window)

Author(s): Ville N. Pimenoff, Penelope Gray, Karolina Louvanto, Tiina Eriksson, Camilla Lagheden, Anna Söderlund-Strand, Joakim Dillner, Matti Lehtinen
Published in: Cell Host & Microbes, 2023, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2023.10.001

Technical and biological sources of unreliability of Infinium probes on Illumina methylation microarrays (opens in new window)

Author(s): Tatiana Nazarenko, Charlotte Dafni Vavourakis, Allison Jones, Iona Evans, Lena Schreiberhuber, Christine Kastner, Isma Ishaq-Parveen, Elisa Redl, Anthony W. Watson, Kirsten Brandt, Clive Carter, Alexey Zaikin, Chiara Maria Stella Herzog, Martin Widschwendter
Published in: Clinical Epigenetics, Issue 16, 2024, ISSN 1868-7083
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s13148-024-01739-2

HPV-KITE: sequence analysis software for rapid HPV genotype detection (opens in new window)

Author(s): Marek Nowicki, Magdalena Mroczek, Dhananjay Mukhedkar, Piotr Bała, Ville Nikolai Pimenoff, Laila Sara Arroyo Mühr
Published in: Briefings in Bioinformatics, Issue 26, 2025, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaf155

Is human oversight to AI systems still possible? (opens in new window)

Author(s): Andreas Holzinger, Kurt Zatloukal, Heimo Müller
Published in: New Biotechnology, Issue 85, 2025, Page(s) 59-62, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2024.12.003

Cost-effectiveness of Prostate Cancer Screening Using Magnetic Resonance Imaging or Standard Biopsy Based on the STHLM3-MRI Study (opens in new window)

Author(s): Shuang Hao, Andrea Discacciati, Martin Eklund, Emelie Heintz, Ellinor Östensson, K. Miriam Elfström, Mark S. Clements, Tobias Nordström
Published in: JAMA Oncology, Issue 9, 2023, Page(s) 88, ISSN 2374-2437
Publisher: American Medical Association (AMA)
DOI: 10.1001/jamaoncol.2022.5252

Red blood cell alloimmunization in myelodysplastic syndromes: Associations with sex, DAT‐positivity, and increased transfusion needs (opens in new window)

Author(s): Jenny Rydén; Mark Clements; Agneta Wikman; Eva Hellström‐Lindberg; Gustaf Edgren; Petter Höglund
Published in: Transfusion, 2023, ISSN 2080-1505
Publisher: Wiley
DOI: 10.1111/trf.17562

Noncancer-Related Mortality in Randomized Clinical Trials (opens in new window)

Author(s): Jiayao Lei, Yunyang Deng, Mark Clements, Stephen Duffy, Peter Sasieni
Published in: JAMA Network Open, Issue 8, 2025, Page(s) e2526990, ISSN 2574-3805
Publisher: American Medical Association (AMA)
DOI: 10.1001/jamanetworkopen.2025.26990

Personas for Artificial Intelligence (AI) an Open Source Toolbox (opens in new window)

Author(s): Andreas Holzinger; Michaela Kargl; Bettina Kipperer; Peter Regitnig; Markus Plass; Heimo Muller
Published in: IEEE Access, Issue 27, 2022, Page(s) 23732-23747, ISSN 2169-3536
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/access.2022.3154776

Metagenomic Study Reveals Phage–Bacterial Interactome Dynamics in Gut and Oral Microbiota in Pancreatic Diseases (opens in new window)

Author(s): Laura Vilà-Quintana, Esther Fort, Laura Pardo, Maria T. Albiol-Quer, Maria Rosa Ortiz, Montserrat Capdevila, Anna Feliu, Anna Bahí, Marc Llirós, Adelaida García-Velasco, Mireia Morell Ginestà, Berta Laquente, Débora Pozas, Victor Moreno, Librado Jesús Garcia-Gil, Eric Jeffrey Duell, Ville Nikolai Pimenoff, Robert Carreras-Torres, Xavier Aldeguer
Published in: International Journal of Molecular Sciences, Issue 25, 2025, Page(s) 10988, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms252010988

Explainability and causability in digital pathology (opens in new window)

Author(s): Markus Plass; Michaela Kargl; Tim‐Rasmus Kiehl; Peter Regitnig; Christian Geißler; Theodore Evans; Norman Zerbe; Rita Carvalho; Andreas Holzinger; Heimo Müller
Published in: The Journal of Pathology Clinical Research, Issue 22, 2023, ISSN 2056-4538
Publisher: Wiley
DOI: 10.1002/cjp2.322

Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes. (opens in new window)

Author(s): Obón-Santacana M, Mas-Lloret J, Bars-Cortina D, Criado-Mesas L, Carreras-Torres R, Díez-Villanueva A, Moratalla-Navarro F, Guinó E, Ibáñez-Sanz G, Rodríguez-Alonso L, Mulet-Margalef N, Mata A, García-Rodríguez A, Duell EJ, Pimenoff VN, Moreno V.
Published in: Cancers, 2022, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14174214

Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis (opens in new window)

Author(s): Chiara Herzog, Allison Jones, Iona Evans, Janhavi R. Raut, Michal Zikan, David Cibula, Andrew Wong, Hermann Brenner, Rebecca C. Richmond, Martin Widschwendter
Published in: Cancer Research, Issue 84, 2024, Page(s) 1898-1914, ISSN 0008-5472
Publisher: American Association for Cancer Research
DOI: 10.1158/0008-5472.can-23-2957

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using <scp>RNA</scp> and <scp>DNA</scp> deep sequencing (opens in new window)

Author(s): Ainhoa Garcia‐Serrano; Dhananjay Mukhedkar; Emilie Hultin; Ulla Rudsander; Yvonne Wettergren; Agustín Enrique Ure; Joakim Dillner; Laila Sara Arroyo‐Mühr
Published in: Cancer Medicine, Issue 17, 2023, ISSN 2045-7634
Publisher: Wiley
DOI: 10.1002/cam4.6483

Influence of Genetics, Immunity and the Microbiome on the Prognosis of Inflammatory Bowel Disease (IBD Prognosis Study): the protocol for a Copenhagen IBD Inception Cohort Study (opens in new window)

Author(s): Attauabi M, Madsen GR, Bendtsen F, Wewer AV, Wilkens R, Ilvemark J, Vladimirova N, Jensen AB, Jensen FK, Hansen SB, Siebner HR, Nielsen YJW, Møller JM, Thomsen HS, Thomsen SF, Ingels HAS, Theede K, Boysen T, Bjerrum JT, Jakobsen C, Dorn-Rasmussen M, Jansson S, Yao Y, Burian EA, Møller FT, Fana V, Wiell C, Terslev L, Østergaard M, Bertl K, Stavropoulos A, Seidelin JB, Burisch J.
Published in: BMJ Open, Issue 12(6), 2022, Page(s) e055779, ISSN 2044-6055
Publisher: BMJ Publishing Group
DOI: 10.1136/bmjopen-2021-055779

AI for life: Trends in artificial intelligence for biotechnology (opens in new window)

Author(s): Andreas Holzinger, Katharina Keiblinger, Petr Holub, Kurt Zatloukal, Heimo Müller
Published in: New Biotechnology, 2023, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2023.02.001

Using HPV-meta for human papillomavirus RNA quality detection (opens in new window)

Author(s): Agustin Ure; Dhananjay Mukhedkar; Laila Sara Arroyo Mühr
Published in: Scientific Reports, Issue 10, 2022, Page(s) 13058, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-17318-5

Seroepidemiological assessment of the spread of SARS-CoV-2 among 25 and 28 year-old adult women in Finland between March 2020-June 2022 (opens in new window)

Author(s): Penelope Gray, Tiina Eriksson, Lovisa Skoglund, Camilla Lagheden, Ceke Hellström, Elisa Pin, Anna Suomenrinne-Nordvik, Ville N. Pimenoff, Peter Nilsson, Joakim Dillner, Matti Lehtinen
Published in: PLOS ONE, Issue 19, 2024, Page(s) e0305285, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0305285

Human exposome assessment platform (opens in new window)

Author(s): Merino Martinez, R. (Roxana); Müller, H. (Heimo); Negru, S. (Stefan); Ormenisan, A. (Alex); Arroyo Mühr, L. S. (Laila Sara); Zhang, X. (Xinyue); Trier Møller, F. (Frederik); Clements, M. S. (Mark S.); Kozlakidis, Z. (Zisis); Pimenoff, V. N. (Ville N.); Wilkowski, B. (Bartlomiej); Boeckhout, M. (Martin); Öhman, H. (Hanna); Chong, S. (Steven); Holzinger, A. (Andreas); Lehtinen, M. (Matti); van V
Published in: Environmental Epidemiology, Issue 13, 2021, Page(s) e182, ISSN 2474-7882
Publisher: Wolters Kluwer
DOI: 10.1097/ee9.0000000000000182

The Swedish Cervical Screening Cohort (opens in new window)

Author(s): Joakim Dillner, Laila Sara Arroyo Mühr, Sara Nordqvist Kleppe, Jiangrong Wang, Helena Andersson, Miriam Elfström, Roxana Merino, Karin Sundström
Published in: Scientific Data, Issue 11, 2024, ISSN 2052-4463
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41597-024-03519-2

Cohort profile: The Health, Food, Purchases and Lifestyle (SMIL) cohort – a Danish open cohort (opens in new window)

Author(s): Kathrine Kold Sørensen, Mikkel Porsborg Andersen, Frederik Trier Møller, Caroline Eves, Thor Grønborg Junker, Bochra Zareini, Christian Torp-Pedersen
Published in: BMJ Open, Issue 14, 2024, Page(s) e078773, ISSN 2044-6055
Publisher: BMJ Publishing Group
DOI: 10.1136/bmjopen-2023-078773

A common framework for using and reporting consumer purchase data (CPD) in foodborne outbreak investigations in Europe (opens in new window)

Author(s): Solveig Jore, Uffe Christian Braae, Frederik Trier Møller, Ingrid Friesema, Karthik Paranthaman, Katri Jalava, Nathalie Jourdan-DaSilva, Emma Löf, Moa Rehn, Steen Ethelberg
Published in: Infection Ecology &amp; Epidemiology, Issue 12, 2022, ISSN 2000-8686
Publisher: Informa UK Limited
DOI: 10.1080/20008686.2021.2007828

Extending Object Stores with POSIX-like Semantics and more (industry track)

Author(s): Mahmoud Ismail, Salman Niazi, Gautier Berthou , Mikael Ronström, Seif Haridi, Jim Dowling
Published in: Proceedings of the 21st International Middleware Conference Industrial Track, 2020, Page(s) 23-30, ISBN 978-1-4503-8201-4
Publisher: ACM

The Hopsworks Feature Store for Machine Learning (opens in new window)

Author(s): Javier de la Rúa Martínez, Fabio Buso, Antonios Kouzoupis, Alexandru A. Ormenisan, Salman Niazi, Davit Bzhalava, Kenneth Mak, Victor Jouffrey, Mikael Ronström, Raymond Cunningham, Ralfs Zangis, Dhananjay Mukhedkar, Ayushman Khazanchi, Vladimir Vlassov, Jim Dowling
Published in: Companion of the 2024 International Conference on Management of Data, 2025, Page(s) 135-147
Publisher: ACM
DOI: 10.1145/3626246.3653389

Time Travel and Provenance for Machine Learning Pipelines

Author(s): Alexandru A. Ormenisan, Moritz Meister, Fabio Buso, Robin Andersson, Seif Haridi, Jim Dowling
Published in: Proceedings of the 2020 USENIX Conference on Operational Machine Learning (OpML ’20), 2020, Page(s) 13-15, ISBN 978-1-939133-15-1
Publisher: USENIX Association

Cost-effectiveness of human papillomavirus self-sampling in the Swedish cervical screening program (opens in new window)

Author(s): Ellinor Östensson, Christer Borgfeldt, Kine Pedersen, Kristina Hellman, Stephen Sy, Jiayao Lei, Emily A. Burger, Mark S. Clements
Published in: MedRxiv, 2025, ISSN 2475-9066
Publisher: openRxiv
DOI: 10.1101/2025.02.12.25322120

Modelling the potential contributions of polygenic risk stratification to cost-effective screening for prostate cancer (opens in new window)

Author(s): Padraig Dixon, Jonathan Aning, Richard Martin, Mark Clements
Published in: MedRxiv, 2025, ISSN 2475-9066
Publisher: OpenRxiv
DOI: 10.1101/2025.05.19.25327897

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