Human Exposome Assessment Platform

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

Sensor pilot Documentation

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

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

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

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

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

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

Secure platform and recruitment

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

Report on secure data platform

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

Ageing DNAme signatures

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

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

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

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

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

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

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

Report describing implementation and experiences from HEAP research use cases.

Report on consumer data

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

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

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

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

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

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

Assessment of Interoperability and Data Quality

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

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

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

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

HEAP Knowledge Engine

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

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

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

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

Metadata Catalogue and Access Procedures

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

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

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

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

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

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

Searchable database

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.

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

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

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

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

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

Data management plan

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.

Publicaciones

Challenges and recommendations for the translation of biomarkers of aging

Autores: 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
Publicado en: Nature Aging, Edición 4, 2024, Página(s) 1372-1383, ISSN 2662-8465
Editor: 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

Autores: Chiara M. S. Herzog, Elisa Redl, James Barrett, Sepideh Aminzadeh-Gohari, Daniela D. Weber, Julia Tevini, Roland Lang, Barbara Kofler, Martin Widschwendter
Publicado en: Communications Medicine, Edición 5, 2025, ISSN 2730-664X
Editor: 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

Autores: Daniela Skalt, Ting Chen, Ahmad Abbadi, Anna Lantz, Andrea Discacciati, Martin Eklund, Mark Clements, Tobias Nordström, Shuang Hao
Publicado en: European Urology Oncology, 2025, ISSN 2588-9311
Editor: Elsevier BV
DOI: 10.1016/j.euo.2025.05.015

Provenance of specimen and data – A prerequisite for AI development in computational pathology

Autores: Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Müller, Jörg Geiger
Publicado en: New Biotechnology, 2023, ISSN 1871-6784
Editor: Elsevier BV
DOI: 10.1016/j.nbt.2023.09.006

Improving Species Level‐taxonomic Assignment from 16S rRNA Sequencing Technologies

Autores: 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
Publicado en: Current Protocols, Edición 3, 2024, ISSN 2691-1299
Editor: Wiley
DOI: 10.1002/cpz1.930

Overweight in childhood and consumer purchases in a Danish cohort

Autores: Kathrine Kold Sørensen, Mikkel Porsborg Andersen, Frederik Trier Møller, Rikke Wiingreen, Marcella Broccia, Emil L. Fosbøl, Bochra Zareini, Thomas Alexander Gerds, Christian Torp-Pedersen
Publicado en: PLOS ONE, Edición 19, 2024, Página(s) e0297386, ISSN 1932-6203
Editor: 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

Autores: 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
Publicado en: BMC Genomics, Edición 25, 2024, ISSN 1471-2164
Editor: BioMed Central
DOI: 10.1186/s12864-024-10621-7

Assessing household lifestyle exposures from consumer purchases, the My Purchases cohort

Autores: 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
Publicado en: Scientific Reports, 2023, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-47534-6

BIBBOX, a FAIR toolbox and App Store for life science research

Autores: 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
Publicado en: New Biotechnology, 2023, ISSN 1871-6784
Editor: 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

Autores: 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
Publicado en: Genome Biology, Edición 27, 2022, Página(s) 52, ISSN 1474-760X
Editor: BMC SpringerNature
DOI: 10.1186/s13059-022-02603-3

Cervical cancer microbiome analysis: comparing HPV 16 and 18 with other HPV types

Autores: Maire Hidjo, Dhananjay Mukhedkar, Collen Masimirembwa, Jiayao Lei, Laila Sara Arroyo Mühr
Publicado en: Scientific Reports, Edición 14, 2024, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-024-73317-8

Toward Human–AI Interfaces to Support Explainability and Causability in Medical AI

Autores: Andreas Holzinger; Heimo Müller
Publicado en: Computer, Edición 28, 2021, Página(s) 78-86, ISSN 1558-0814
Editor: IEEE Computer Society
DOI: 10.1109/mc.2021.3092610

The Ten Commandments of Ethical Medical AI

Autores: H. Muller, M. Mayrhofer, E. Van Veen and A. Holzinger
Publicado en: Computer, Edición 54, 2021, Página(s) 119-123, ISSN 1558-0814
Editor: IEEE Computer Society
DOI: 10.1109/mc.2021.3074263

Spatio-temporal variation in prostate cancer testing in Stockholm: A population-based study

Autores: Balram Rai, Tobias Nordström, Anna Lantz, Rolf Lyneborg Lund, Ralf Kuja-Halkola, Marta Rado, Sara Öberg, Shuang Hao, Xiaoyang Du, Mark Clements
Publicado en: PLOS ONE, Edición 19, 2024, Página(s) e0308254, ISSN 1932-6203
Editor: 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

Autores: Heimo Müller, Andreas Holzinger, Markus Plass, Luka Brcic, Cornelia Stumptner, Kurt Zatloukal
Publicado en: New Biotechnology, Edición 70, 2022, Página(s) 67-72, ISSN 1871-6784
Editor: Elsevier BV
DOI: 10.1016/j.nbt.2022.05.002

Cervical cancer screening using DNA methylation triage in a real-world population

Autores: Lena Schreiberhuber, James E. Barrett, Jiangrong Wang, Elisa Redl, Chiara Herzog, Charlotte D. Vavourakis, Karin Sundström, Joakim Dillner, Martin Widschwendter
Publicado en: Nature Medicine, Edición 30, 2024, Página(s) 2251-2257, ISSN 1078-8956
Editor: Nature Publishing Group
DOI: 10.1038/s41591-024-03014-6

Creating personas for exposome research: the experience from the HEAP project

Autores: Heather Coombs; Tracy Wootton; Joakim Dillner; Heimo Müller; Anouk Berger; Zisis Kozlakidis
Publicado en: Open Research Europe, 2023, ISSN 2732-5121
Editor: EU
DOI: 10.12688/openreseurope.15474.1

HPV-induced host epigenetic reprogramming is lost upon progression to high-grade cervical intraepithelial neoplasia

Autores: Herzog C, Vavourakis CD, Barrett JE, Karbon G, Villunger A, Wang J, Sundström K, Dillner J, Widschwendter M
Publicado en: International Journal of Cancer, 2023, ISSN 0020-7136
Editor: John Wiley & Sons Inc.
DOI: 10.1002/ijc.34477

The European health data space: Too big to succeed?

Autores: 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
Publicado en: Health Policy, 2023, ISSN 0168-8510
Editor: 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

Autores: Evert-Ben Van Veen, Martin Boeckhout, Irene Schlünder, Jan Willem Boiten, Vasco Dias
Publicado en: Open Research Europe, Edición 2, 2024, Página(s) 80, ISSN 2732-5121
Editor: 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

Autores: Evert-Ben Van Veen; Martin Boeckhout; Irene Schlünder; Jan Willem Boiten; Vasco Dias
Publicado en: Open Research Europe, Edición 28, 2022, ISSN 2732-5121
Editor: European Comission
DOI: 10.12688/openreseurope.14825.1

Ecological diversity profiles of non-vaccine-targeted HPVs after gender-based community vaccination efforts

Autores: Ville N. Pimenoff, Penelope Gray, Karolina Louvanto, Tiina Eriksson, Camilla Lagheden, Anna Söderlund-Strand, Joakim Dillner, Matti Lehtinen
Publicado en: Cell Host & Microbes, 2023, ISSN 1931-3128
Editor: Cell Press
DOI: 10.1016/j.chom.2023.10.001

Technical and biological sources of unreliability of Infinium probes on Illumina methylation microarrays

Autores: 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
Publicado en: Clinical Epigenetics, Edición 16, 2024, ISSN 1868-7083
Editor: Springer Science and Business Media LLC
DOI: 10.1186/s13148-024-01739-2

HPV-KITE: sequence analysis software for rapid HPV genotype detection

Autores: Marek Nowicki, Magdalena Mroczek, Dhananjay Mukhedkar, Piotr Bała, Ville Nikolai Pimenoff, Laila Sara Arroyo Mühr
Publicado en: Briefings in Bioinformatics, Edición 26, 2025, ISSN 1467-5463
Editor: Oxford University Press
DOI: 10.1093/bib/bbaf155

Is human oversight to AI systems still possible?

Autores: Andreas Holzinger, Kurt Zatloukal, Heimo Müller
Publicado en: New Biotechnology, Edición 85, 2025, Página(s) 59-62, ISSN 1871-6784
Editor: 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

Autores: Shuang Hao, Andrea Discacciati, Martin Eklund, Emelie Heintz, Ellinor Östensson, K. Miriam Elfström, Mark S. Clements, Tobias Nordström
Publicado en: JAMA Oncology, Edición 9, 2023, Página(s) 88, ISSN 2374-2437
Editor: 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

Autores: Jenny Rydén; Mark Clements; Agneta Wikman; Eva Hellström‐Lindberg; Gustaf Edgren; Petter Höglund
Publicado en: Transfusion, 2023, ISSN 2080-1505
Editor: Wiley
DOI: 10.1111/trf.17562

Noncancer-Related Mortality in Randomized Clinical Trials

Autores: Jiayao Lei, Yunyang Deng, Mark Clements, Stephen Duffy, Peter Sasieni
Publicado en: JAMA Network Open, Edición 8, 2025, Página(s) e2526990, ISSN 2574-3805
Editor: American Medical Association (AMA)
DOI: 10.1001/jamanetworkopen.2025.26990

Personas for Artificial Intelligence (AI) an Open Source Toolbox

Autores: Andreas Holzinger; Michaela Kargl; Bettina Kipperer; Peter Regitnig; Markus Plass; Heimo Muller
Publicado en: IEEE Access, Edición 27, 2022, Página(s) 23732-23747, ISSN 2169-3536
Editor: 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

Autores: 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
Publicado en: International Journal of Molecular Sciences, Edición 25, 2025, Página(s) 10988, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms252010988

Explainability and causability in digital pathology

Autores: Markus Plass; Michaela Kargl; Tim‐Rasmus Kiehl; Peter Regitnig; Christian Geißler; Theodore Evans; Norman Zerbe; Rita Carvalho; Andreas Holzinger; Heimo Müller
Publicado en: The Journal of Pathology Clinical Research, Edición 22, 2023, ISSN 2056-4538
Editor: Wiley
DOI: 10.1002/cjp2.322

Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes.

Autores: 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.
Publicado en: Cancers, 2022, ISSN 2072-6694
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14174214

Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis

Autores: Chiara Herzog, Allison Jones, Iona Evans, Janhavi R. Raut, Michal Zikan, David Cibula, Andrew Wong, Hermann Brenner, Rebecca C. Richmond, Martin Widschwendter
Publicado en: Cancer Research, Edición 84, 2024, Página(s) 1898-1914, ISSN 0008-5472
Editor: 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

Autores: Ainhoa Garcia‐Serrano; Dhananjay Mukhedkar; Emilie Hultin; Ulla Rudsander; Yvonne Wettergren; Agustín Enrique Ure; Joakim Dillner; Laila Sara Arroyo‐Mühr
Publicado en: Cancer Medicine, Edición 17, 2023, ISSN 2045-7634
Editor: 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

Autores: 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.
Publicado en: BMJ Open, Edición 12(6), 2022, Página(s) e055779, ISSN 2044-6055
Editor: BMJ Publishing Group
DOI: 10.1136/bmjopen-2021-055779

AI for life: Trends in artificial intelligence for biotechnology

Autores: Andreas Holzinger, Katharina Keiblinger, Petr Holub, Kurt Zatloukal, Heimo Müller
Publicado en: New Biotechnology, 2023, ISSN 1871-6784
Editor: Elsevier BV
DOI: 10.1016/j.nbt.2023.02.001

Using HPV-meta for human papillomavirus RNA quality detection

Autores: Agustin Ure; Dhananjay Mukhedkar; Laila Sara Arroyo Mühr
Publicado en: Scientific Reports, Edición 10, 2022, Página(s) 13058, ISSN 2045-2322
Editor: 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

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

Human exposome assessment platform

Autores: 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
Publicado en: Environmental Epidemiology, Edición 13, 2021, Página(s) e182, ISSN 2474-7882
Editor: Wolters Kluwer
DOI: 10.1097/ee9.0000000000000182

The Swedish Cervical Screening Cohort

Autores: Joakim Dillner, Laila Sara Arroyo Mühr, Sara Nordqvist Kleppe, Jiangrong Wang, Helena Andersson, Miriam Elfström, Roxana Merino, Karin Sundström
Publicado en: Scientific Data, Edición 11, 2024, ISSN 2052-4463
Editor: 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

Autores: Kathrine Kold Sørensen, Mikkel Porsborg Andersen, Frederik Trier Møller, Caroline Eves, Thor Grønborg Junker, Bochra Zareini, Christian Torp-Pedersen
Publicado en: BMJ Open, Edición 14, 2024, Página(s) e078773, ISSN 2044-6055
Editor: 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

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Publicado en: Infection Ecology & Epidemiology, Edición 12, 2022, ISSN 2000-8686
Editor: Informa UK Limited
DOI: 10.1080/20008686.2021.2007828

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

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Publicado en: Proceedings of the 21st International Middleware Conference Industrial Track, 2020, Página(s) 23-30, ISBN 978-1-4503-8201-4
Editor: ACM

The Hopsworks Feature Store for Machine Learning

Autores: 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
Publicado en: Companion of the 2024 International Conference on Management of Data, 2025, Página(s) 135-147
Editor: ACM
DOI: 10.1145/3626246.3653389

Time Travel and Provenance for Machine Learning Pipelines

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Publicado en: Proceedings of the 2020 USENIX Conference on Operational Machine Learning (OpML ’20), 2020, Página(s) 13-15, ISBN 978-1-939133-15-1
Editor: USENIX Association

Cost-effectiveness of human papillomavirus self-sampling in the Swedish cervical screening program

Autores: Ellinor Östensson, Christer Borgfeldt, Kine Pedersen, Kristina Hellman, Stephen Sy, Jiayao Lei, Emily A. Burger, Mark S. Clements
Publicado en: MedRxiv, 2025, ISSN 2475-9066
Editor: openRxiv
DOI: 10.1101/2025.02.12.25322120

Modelling the potential contributions of polygenic risk stratification to cost-effective screening for prostate cancer

Autores: Padraig Dixon, Jonathan Aning, Richard Martin, Mark Clements
Publicado en: MedRxiv, 2025, ISSN 2475-9066
Editor: OpenRxiv
DOI: 10.1101/2025.05.19.25327897

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