Machine Learning Frontiers in Precision Medicine

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

Closing conference
Software implementing the method developed

ESR 9: Software implementing the method developed

1st summer school
Publication of all research results
Software implementing methods for heterogeneous data integration

ESR 9: Software implementing methods for heterogeneous data integration

Systematic review on existing methods

ESR 9: Systematic review on existing methods

Software implementation of the models

ESR 10: Software implementation of the models

Sequential decision-making

ESR 2: Sequential decision-making

Identification, development and im

ESR 4: Identification, development and im

2nd summer school
Software implementation of Network GWAS approaches

ESR 1: Software implementation of Network GWAS approaches

3rd summer school
Defining patient states

ESR 2: Defining patient states

Methodology to embed sparse somatic genetic profiles

ESR 5: Methodology to embed sparse somatic genetic profiles

Software and report for learning prognosis and response to treatment from multimodal clinical records

ESR 11: Software and report for learning prognosis and response to treatment from multimodal clinical records

Implementation + publication of tools for large-scale, accurate causal inference

ESR 14: Implementation + publication of tools for large-scale, accurate causal inference

Implementation and publication of tool to compare networks with uncertainty; networks comprising results from studies addressing the same problem

ESR 3: Implementation and publication of tool to compare networks with uncertainty; networks comprising results from studies addressing the same problem

A framework for discovery and validation of omics-based predictors for follow-up data in large population-based biobanks

ESR 7: A framework for discovery and validation of omics-based predictors for follow-up data in large population-based biobanks.

Analysis of germline/somatic interactions and association with phenotype information

ESR 5: Analysis of germline/somatic interactions and association with phenotype information

Comparison of methods for network analysis of individual omics data

ESR 12: Comparison of methods for network analysis of individual comics data

Publication of results

ESR 10: Publication of results

Developing polygenic risk models with rich full medical profiles

ESR 8: Developing polygenic risk models with rich full medical profiles

Implementation of Qlucore visualizations of deep learning techniques

ESR 13: Implementation of Qlucore visualizations of deep learning techniques

Implementation and publication of tool to construct and combine statistical epistasis networks, ignoring network uncertainty or heterogeneity

ESR 3: Implementation and publication of tool to construct and combine statistical epistasis networks, ignoring network uncertainty or heterogeneity

Publication describing the application of current causal inference tools to a representative use-case

ESR 14: Publication describing the application of current causal inference tools to a representative use-case

Development and implementation of methods for integrated network analysis of multi-omics data

ESR 12: Development and implementation of methods for integrated network analysis of multi-omics data

Deep learning methods to find molecular components relevant for signaling that define functions that can be related to phenotypes (disease, drug response, etc.)

ESR 9: Deep learning methods to find molecular components relevant for signaling that define functions that can be related to phenotypes (disease, drug response, etc.)

Methodology to embed dense germline mutations

ESR 5: Methodology to embed dense germline mutations

Models for the integration of phenotypic and genomic data with precision prognostic purposes

ESR 9: Models for the integration of phenotypic and genomic data with precision prognostic purposes

e-ETN: Setup of homepage

Central Data Repository for Open Research Data Pilot

Publicaciones

Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients

Autores: Bowen Fan, Juliane Klatt, Michael M. Moor, Latasha A. Daniels, Swiss Pediatric Sepsis Study, Lazaro N. Sanchez-Pinto, Philipp K. A. Agyeman, Luregn J. Schlapbach, Karsten M. Borgwardt
Publicado en: Bioinformatics, Edición 38 (Supplement_1), 2022, Página(s) i101–i108, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btac229

Machine-Learning-Aided Prediction Of Brain Metastases Development In Non-Small Cell Lung Cancers

Autores: Giovanni Visonà, Lisa M. Spiller, Sophia Hahn, Elke Hattingen, Thomas J. Vogl, Gabriele Schweikert, Katrin Bankov, Melanie Demes, Henning Reis, Peter Wild, Pia S. Zeiner, Fabian Acker, Martin Sebastian, and Katharina J. Wenger
Publicado en: Clinical Lung Cancer, 2023, ISSN 1938-0690
Editor: Elsevier
DOI: 10.1016/j.cllc.2023.08.002

Persistent complement dysregulation with signs of thromboinflammation in active Long Covid

Autores: Cervia, Carlo; Brüningk, sarah; Hoch, Tobias; Fan, Bowen; Muzio, Giulia; Thompson, Ryan; Ceglarek, Laura; Meledin, Roman; Westermann, Patrick; Emmenegger, Marc; Taeschler, Patrick; Zurbuchen, Yves; Pons, Michele; Menges, Dominik; Ballouz, Tala; Hasler, Sara; Adamo, Sarah; Merad, Miriam; Charney, Alexander; Puhan, Milo; Brodin, Petter; Nilsson, Jakob; Aguzzi, Adriano; Miro, Raeber; Messner, Christ
Publicado en: Science, Edición Vol 383, Edición 6680, 2024, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.adg7942

Graph-based multi-modality integration for prediction of cancer subtype and severity

Autores: Diane Duroux, Christian Wohlfart, Kristel Van Steen, Antoaneta Vladimirova, Michael King
Publicado en: Scientific Reports, Edición 13, 2023, Página(s) 19653, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-46392-6

Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data

Autores: Pelin Gundogdu, Carlos Loucera, Inmaculada Alamo-Alvarez, Joaquin Dopazo, Isabel Nepomuceno
Publicado en: BioData Mining, Edición 15, 2022, ISSN 1756-0381
Editor: BioMed Central
DOI: 10.1186/s13040-021-00285-4

Systematic Review of Functional MRI Applications for Psychiatric Disease Subtyping

Autores: Lucas Miranda, Riya Paul, Benno Pütz, Nikolaos Koutsouleris, Bertram Müller-Myhsok
Publicado en: Frontiers in Psychiatry, Edición 12, 2021, ISSN 1664-0640
Editor: Frontiers Research Foundation
DOI: 10.3389/fpsyt.2021.665536

Biological network analysis with deep learning

Autores: Giulia Muzio, Leslie O’Bray, Karsten Borgwardt
Publicado en: Briefings in Bioinformatics, 2020, ISSN 1467-5463
Editor: Oxford University Press
DOI: 10.1093/bib/bbaa257

netANOVA: novel graph clustering technique with significance assessment via hierarchical ANOVA

Autores: Diane Duroux, Kristel Van Steen
Publicado en: Briefings in Bioinformatics, Edición Volume 24, Edición 2,, 2023, Página(s) bbad029, ISSN 1477-4054
Editor: Oxford University Press
DOI: 10.1093/bib/bbad029

Virtual Biopsy by Using Artificial Intelligence–based Multimodal Modeling of Binational Mammography Data

Autores: Vesna Barros, Tal Tlusty, Ella Barkan, Efrat Hexter, David Gruen, Michal Guindy, Michal Rosen-Zvi
Publicado en: Radiology, Edición 00338419, 2022, ISSN 0033-8419
Editor: Radiological Society of North America
DOI: 10.1148/radiol.220027

DeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking data

Autores: Lucas Miranda, Joeri Bordes, Benno Pütz, Mathias V. Schmidt, Bertram Müller-Myhsok
Publicado en: Journal of Open Source Software, Edición 8(86), 2023, Página(s) 5394, ISSN 2475-9066
Editor: Open Journals
DOI: 10.21105/joss.05394

AI-assisted tracking of worldwide non-pharmaceutical interventions for COVID-19

Autores: Parthasarathy Suryanarayanan, Ching-Huei Tsou, Ananya Poddar, Diwakar Mahajan, Bharath Dandala, Piyush Madan, Anshul Agrawal, Charles Wachira, Osebe Mogaka Samuel, Osnat Bar-Shira, Clifton Kipchirchir, Sharon Okwako, William Ogallo, Fred Otieno, Timothy Nyota, Fiona Matu, Vesna Resende Barros, Daniel Shats, Oren Kagan, Sekou Remy, Oliver Bent, Pooja Guhan, Shilpa Mahatma, Aisha Walcott-Bryant, Div
Publicado en: Scientific Data, Edición 8/1, 2021, ISSN 2052-4463
Editor: Springer
DOI: 10.1038/s41597-021-00878-y

Identification of Gene Modules Shared by Childhood-Onset Asthma and Immunoglobulin-E Levels by Integrated Network Analysis of Multi-Omics Data

Autores: Eranti, Pradeep; Bouzigon, Emmanuelle; Demenais, Florence; The EGEA Cooperative Group
Publicado en: Human Heredity, Edición 85 (2), 2021, Página(s) 69–100, ISSN 0001-5652
Editor: S. Karger AG
DOI: 10.1159/000516194

Interpretable network-guided epistasis detection

Autores: Diane Duroux; Héctor Climente-González; Chloé-Agathe Azencott; Kristel Van Steen
Publicado en: Gigascience, Edición 11, 2022, Página(s) giab093, ISSN 2047-217X
Editor: Oxford University Press
DOI: 10.1101/2020.09.24.310136

Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information

Autores: Giovanni Visonà, Diane Duroux, Lucas Miranda, Emese Sükei, Yiran Li, Karsten Borgwardt, Carlos Oliver
Publicado en: Bioinformatics, Edición Volume 39, Edición 12, 2023, Página(s) btad717, ISSN 1367-4811
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btad717

Detecting gene–gene interactions from GWAS using diffusion kernel principal components

Autores: Andrew Walakira, Junior Ocira, Diane Duroux, Ramouna Fouladi, Miha Moškon, Damjana Rozman, Kristel Van Steen
Publicado en: BMC Bioinformatics, Edición 23, 2022, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-022-04580-7

Automatic patient functionality assessment from multimodal data using deep learning techniques – Development and feasibility evaluation

Autores: Emese Sükei, Santiago de Leon-Martinez, Pablo M. Olmos, Antonio Artés
Publicado en: Internet Interventions, Edición 33, 2023, Página(s) 100657, ISSN 2214-7829
Editor: Elsevier BV
DOI: 10.1016/j.invent.2023.100657

Increasing resolution in stress neurobiology: from single cells to complex group behaviors

Autores: Lucas Miranda, Joeri Bordes, Serena Gasperoni, Juan Pablo Lopez
Publicado en: Stress, Edición 26(1), 2023, ISSN 1607-8888
Editor: Taylor & Francis
DOI: 10.1080/10253890.2023.2186141

Shift in Social Media App Usage During COVID-19 Lockdown and Clinical Anxiety Symptoms: Machine Learning–Based Ecological Momentary Assessment Study

Autores: Jihan Ryu, Emese Sükei, Agnes Norbury, Shelley H Liu, Juan José Campaña-Montes, Enrique Baca-Garcia, Antonio Artés, M Mercedes Perez-Rodriguez
Publicado en: JMIR Mental Health, Edición 8/9, 2021, Página(s) e30833, ISSN 2368-7959
Editor: JMIR Publications
DOI: 10.2196/30833

Automatically annotated motion tracking identifies a distinct social behavioral profile following chronic social defeat stress

Autores: Joeri Bordes; Lucas Miranda; Maya Reinhardt; Sowmya Narayan; Jakob Hartmann; Emily L. Newman; Lea Maria Brix; Lotte van Doeselaar; Clara Engelhardt; Larissa Dillmann; Shiladitya Mitra; Kerry J. Ressler; Benno Pütz; Felix Agakov; Bertram Müller-Myhsok; Mathias V. Schmidt
Publicado en: Nature Communications, Edición Vol 14, Iss 1, 2023, Página(s) 1, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-40040-3

Continuous Assessment of Function and Disability via Mobile Sensing: Real-World Data-Driven Feasibility Study

Autores: Emese Sükei, Lorena Romero-Medrano, Santiago de Leon-Martinez, Jesús Herrera López, Juan José Campaña-Montes, Pablo M Olmos, Enrique Baca-Garcia, Antonio Artés
Publicado en: JMIR Formative Research, 2023, Página(s) e47167, ISSN 2561-326X
Editor: JMIR Publications
DOI: 10.2196/47167

Higher-order genetic interaction discovery with network-based biological priors

Autores: Paolo Pellizzoni, Giulia Muzio, Karsten Borgwardt
Publicado en: Bioinformatics, Edición Volume 39, Edición Supplement_1, 2023, Página(s) i523–i533, ISSN 1367-4811
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btad273

Quantification of tumor heterogeneity: from data acquisition to metric generation

Autores: Aditya Kashyap, Maria Anna Rapsomaniki, Vesna Barros, Anna Fomitcheva-Khartchenko, Adriano Luca Martinelli, Antonio Foncubierta Rodriguez, Maria Gabrani, Michal Rosen-Zvi, Govind Kaigala
Publicado en: Trends in Biotechnology, Edición Volume 40, Edición 6, 2022, Página(s) 647-676, ISSN 0968-0004
Editor: Elsevier BV
DOI: 10.1016/j.tibtech.2021.11.006

Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus

Autores: Aron Kos, Juan Pablo Lopez, Joeri Bordes, Carlo de Donno, Julien Dine, Elena Brivio, Stoyo Karamihalev, Malte D. Luecken, Suellen Almeida-Correa, Serena Gasperoni, Alec Dick, Lucas Miranda, Maren Büttner, Rainer Stoffel, Cornelia Flachskamm, Fabian J. Theis, Mathias V. Schmidt, Alon Chen
Publicado en: Science Advances, Edición 9, 2023, Página(s) eadj3793, ISSN 2375-2548
Editor: American Association for the Advancement of Science
DOI: 10.1126/sciadv.adj3793

Network propagation for GWAS analysis: a practical guide to leveraging molecular networks for disease gene discovery

Autores: Visonà, Giovanni; Bouzigon, Emmanuelle; Demenais, Florence; Schweikert, Gabriele
Publicado en: Briefings in Bioinformatics, Edición Volume 25, Edición 2, 2024, Página(s) bbae014, ISSN 1477-4054
Editor: Oxford University Press
DOI: 10.1093/bib/bbae014

A retrospective cohort study of incidence and risk factors for severe SARS-CoV-2 breakthrough infection among fully vaccinated people

Autores: Tatjana Meister, Anastassia Kolde, Krista Fischer, Heti Pisarev, Raivo Kolde, Ruth Kalda, Kadri Suija, Anna Tisler, Anneli Uusküla
Publicado en: Scientific Reports, Edición 13: 8531, 2023, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-35591-w

Advancing social behavioral neuroscience by integrating ethology and comparative psychology methods through machine learning

Autores: Joeri Bordes, Lucas Miranda, Bertram Müller-Myhsok, and Mathias V. Schmidt
Publicado en: Neuroscience & Biobehavioral Reviews, Edición 151, 2023, Página(s) 105243, ISSN 1873-7528
Editor: Elsevier
DOI: 10.1016/j.neubiorev.2023.105243

Predicting Emotional States Using Behavioral Markers Derived From Passively Sensed Data: Data-Driven Machine Learning Approach

Autores: Emese Sükei, Agnes Norbury, M Mercedes Perez-Rodriguez, Pablo M Olmos, Antonio Artés
Publicado en: JMIR mHealth and uHealth, Edición 9/3, 2021, Página(s) e24465, ISSN 2291-5222
Editor: JMIR Publications
DOI: 10.2196/24465

Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning.

Autores: Hawkins-Hooker, Alex; Visonà, Giovanni; Narendra, Tanmayee; Rojas-Carulla, Mateo; Schölkopf, Bernhard; Schweikert, Gabriele
Publicado en: Nature Communications, Edición 14, 2023, Página(s) 4750, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-40211-2

Network Analysis of Multi-omics Data Identifies Shared Genes and Pathways Underlying the Risk of Allergic Diseases and IgE Production

Autores: Eranti, Pradeep; Vernet, Raphaël; Bouzigon, Emmanuelle; Demenais, Florence; on behalf of the EGEA, EVADA and RESET-AID Consortia
Publicado en: Genetic Epidemiology, Edición 46, 2022, Página(s) 475-551, ISSN 0741-0395
Editor: John Wiley & Sons Inc.
DOI: 10.1002/gepi.22503

netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity

Autores: Zuqi Li, Federico Melograna, Hanne Hoskens, Diane Duroux, Mary L. Marazita, Susan Walsh, Seth M. Weinberg, Mark D. Shriver, Bertram Müller-Myhsok, Peter Claes, Kristel Van Steen
Publicado en: Frontiers in Genetics, Edición Volume 14, 2023, Página(s) 1286800, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2023.1286800

A causal inference approach for estimating effects of non-pharmaceutical interventions during Covid-19 pandemic

Autores: Vesna Barros , Itay Manes, Victor Akinwande, Celia Cintas, Osnat Bar-Shira, Michal Ozery-Flato, Yishai Shimoni, Michal Rosen-Zvi
Publicado en: PLOS ONE, Edición 19326203, 2022, Página(s) e0265289, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0265289

Trajectories: a framework for detecting temporal clinical event sequences from health data standardized to the Observational Medical Outcomes Partnership (OMOP) Common Data Model

Autores: Kadri Künnapuu, Solomon Ioannou, Kadri Ligi, Raivo Kolde, Sven Laur, Jaak Vilo, Peter R Rijnbeek, Sulev Reisberg
Publicado en: JAMIA Open, Edición 25742531, 2022, Página(s) ooac021, ISSN 2574-2531
Editor: Oxford University Press
DOI: 10.1093/jamiaopen/ooac021

Targeted Methylation Profiling of Single Laser-Capture Microdissected Post-Mortem Brain Cells by Adapted Limiting Dilution Bisulfite Pyrosequencing (LDBSP)

Autores: Renzo J. M. Riemens, Gunter Kenis, Jennifer Nolz, Sonia C. Susano Chaves, Diane Duroux, Ehsan Pishva, Diego Mastroeni, Kristel Van Steen, Thomas Haaf, Daniël L. A. van den Hove
Publicado en: International Journal of Molecular Sciences, Edición 23(24), 2022, Página(s) 15571, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms232415571

A historical perspective of biomedical explainable AI research

Autores: Luca Malinverno, Vesna Barros, Francesco Ghisoni, Giovanni Visonà, Roman Kern, Philip J. Nickel, Barbara Elvira Ventura, Ilija Šimić, Sarah Stryeck, Francesca Manni, Cesar Ferri, Claire Jean-Quartier, Laura Genga, Gabriele Schweikert, Mario Lovrić, Michal Rosen-Zvi
Publicado en: Patterns, Edición Volume 4, Edición 9, 2023, ISSN 2666-3899
Editor: Elsevier
DOI: 10.1016/j.patter.2023.100830

networkGWAS: a network-based approach to discover genetic associations

Autores: Giulia Muzio, Leslie O’Bray, Laetitia Meng-Papaxanthos, Juliane Klatt, Krista Fischer, Karsten Borgwardt
Publicado en: Bioinformatics, Edición Volume 39, Edición 6, 2023, Página(s) btad370, ISSN 1367-4811
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btad370

SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types

Autores: Gundogdu, Pelin; Álamo-Álvarez, Inmaculada; Nepomuceno-Chamorro, Isabel A.; Dopazo, Joaquin; Loucera, Carlos
Publicado en: Biology, Edición Volume 12, Edición 4, 2023, Página(s) 579, ISSN 2079-7737
Editor: MDPI
DOI: 10.3390/biology12040579

Unsupervised Manifold Alignment with Joint Multidimensional Scaling

Autores: Dexiong Chen, Bowen Fan, Carlos Oliver, Karsten Borgwardt
Publicado en: The Eleventh International Conference on Learning Representations, Edición 2023, 2023
Editor: International Conference on Learning Representations
DOI: 10.48550/arxiv.2207.02968

Leveraging Comprehensive Health Records for Breast Cancer Risk Prediction: A Binational Assessment

Autores: Michal Chorev, Vesna Barros, Adam Spiro, Ella Evron, Ella Barkan, Oren Kagan, Mika Amit, Michal Ozery-Flato, Ayelet Akselrod-Balin, Varda Shalev, Michal Rosen-Zvi, Michal Guindy
Publicado en: AMIA ... Annual Symposium proceedings. AMIA Symposium, 2022, Página(s) 385–394
Editor: AMIA

Pre-biopsy Multi-Class Classification of Breast Lesion Pathology in Mammograms

Autores: Tal Tlusty, Michal Ozery-Flato, Vesna Barros, Ella Barkan, Mika Amit, David Gruen, Michal Guindy, Tal Arazi, Mona Rozin, Michal Rosen-Zvi, Efrat Hexter
Publicado en: Machine Learning in Medical Imaging. MLMI 2021. Lecture Notes in Computer Science, Edición 12966, 2021, ISBN 978-3-030-87588-6
Editor: Springer
DOI: 10.1007/978-3-030-87589-3_29

The Case of Missed Cancers: Applying AI as a Radiologist's Safety Net

Autores: Michal Chorev, Yoel Shoshan, Ayelet Akselrod-Ballin, Adam Spiro, Shaked Naor, Alon Hazan, Vesna Barros, Iuliana Weinstein, Esma Herzel, Varda Shalev, Michal Guindy, Michal Rosen-Zvi
Publicado en: Medical Image Computing and Computer Assisted Intervention – MICCAI 2020, 2020, Página(s) 220-229
Editor: Springer
DOI: 10.5281/zenodo.4076797

Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder

Autores: Pelin Gundogdu, Miriam Payá-Milans, Inmaculada Alamo-Alvarez, Isabel A. Nepomuceno-Chamorro, Joaquin Dopazo, Carlos Loucera
Publicado en: Lecture Notes in Computer Science, Edición volume 14137, 2023, Página(s) 62–77, ISBN 978-3-031-42696-4
Editor: Springer
DOI: 10.1007/978-3-031-42697-1_5

Network Aggregation to Enhance Results Derived from Multiple Analytics

Autores: Diane Duroux, Héctor Climente-González, Lars Wienbrandt, Kristel Van Steen
Publicado en: Artificial Intelligence Applications and Innovations - 16th IFIP WG 12.5 International Conference, AIAI 2020, Neos Marmaras, Greece, June 5–7, 2020, Proceedings, Part I, Edición 583, 2020, Página(s) 128-140, ISBN 978-3-030-49160-4
Editor: Springer International Publishing
DOI: 10.1007/978-3-030-49161-1_12

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