Deliverables Other (4) Software implementing the method developed ESR 9: Software implementing the method developed 1st summer school 1st summer school Systematic review on existing methods ESR 9: Systematic review on existing methods 2nd summer school 2nd summer school Documents, reports (4) Methodology to embed sparse somatic genetic profiles ESR 5: Methodology to embed sparse somatic genetic profiles Comparison of methods for network analysis of individual omics data ESR 12: Comparison of methods for network analysis of individual comics data 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 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.) Websites, patent fillings, videos etc. (1) e-ETN: Setup of homepage e-ETN: Setup of homepage Open Research Data Pilot (1) Central Data Repository for Open Research Data Pilot Central Data Repository for Open Research Data Pilot Publications Peer reviewed articles (18) Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients Author(s): 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 Published in: Bioinformatics, Issue 38 (Supplement_1), 2022, Page(s) i101–i108, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btac229 Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data Author(s): Pelin Gundogdu, Carlos Loucera, Inmaculada Alamo-Alvarez, Joaquin Dopazo, Isabel Nepomuceno Published in: BioData Mining, Issue 15, 2022, ISSN 1756-0381 Publisher: BioMed Central DOI: 10.1186/s13040-021-00285-4 Systematic Review of Functional MRI Applications for Psychiatric Disease Subtyping Author(s): Lucas Miranda, Riya Paul, Benno Pütz, Nikolaos Koutsouleris, Bertram Müller-Myhsok Published in: Frontiers in Psychiatry, Issue 12, 2021, ISSN 1664-0640 Publisher: Frontiers Research Foundation DOI: 10.3389/fpsyt.2021.665536 Biological network analysis with deep learning Author(s): Giulia Muzio, Leslie O’Bray, Karsten Borgwardt Published in: Briefings in Bioinformatics, 2020, ISSN 1467-5463 Publisher: Oxford University Press DOI: 10.1093/bib/bbaa257 netANOVA: novel graph clustering technique with significance assessment via hierarchical ANOVA Author(s): Diane Duroux, Kristel Van Steen Published in: Briefings in Bioinformatics, Issue Volume 24, Issue 2,, 2023, Page(s) bbad029, ISSN 1477-4054 Publisher: Oxford University Press DOI: 10.1093/bib/bbad029 Virtual Biopsy by Using Artificial Intelligence–based Multimodal Modeling of Binational Mammography Data Author(s): Vesna Barros, Tal Tlusty, Ella Barkan, Efrat Hexter, David Gruen, Michal Guindy, Michal Rosen-Zvi Published in: Radiology, Issue 00338419, 2022, ISSN 0033-8419 Publisher: Radiological Society of North America DOI: 10.1148/radiol.220027 AI-assisted tracking of worldwide non-pharmaceutical interventions for COVID-19 Author(s): 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 Published in: Scientific Data, Issue 8/1, 2021, ISSN 2052-4463 Publisher: Springer DOI: 10.1038/s41597-021-00878-y Interpretable network-guided epistasis detection Author(s): Diane Duroux; Héctor Climente-González; Chloé-Agathe Azencott; Kristel Van Steen Published in: Gigascience, Issue 11, 2022, Page(s) giab093, ISSN 2047-217X Publisher: Oxford University Press DOI: 10.1101/2020.09.24.310136 Detecting gene–gene interactions from GWAS using diffusion kernel principal components Author(s): Andrew Walakira, Junior Ocira, Diane Duroux, Ramouna Fouladi, Miha Moškon, Damjana Rozman, Kristel Van Steen Published in: BMC Bioinformatics, Issue 23, 2022, ISSN 1471-2105 Publisher: BioMed Central DOI: 10.1186/s12859-022-04580-7 Increasing resolution in stress neurobiology: from single cells to complex group behaviors Author(s): Lucas Miranda, Joeri Bordes, Serena Gasperoni, Juan Pablo Lopez Published in: Stress, Issue 26(1), 2023, ISSN 1607-8888 Publisher: 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 Author(s): Jihan Ryu, Emese Sükei, Agnes Norbury, Shelley H Liu, Juan José Campaña-Montes, Enrique Baca-Garcia, Antonio Artés, M Mercedes Perez-Rodriguez Published in: JMIR Mental Health, Issue 8/9, 2021, Page(s) e30833, ISSN 2368-7959 Publisher: JMIR Publications DOI: 10.2196/30833 Higher-order genetic interaction discovery with network-based biological priors Author(s): Paolo Pellizzoni, Giulia Muzio, Karsten Borgwardt Published in: Bioinformatics, Issue Volume 39, Issue Supplement_1, 2023, Page(s) i523–i533, ISSN 1367-4811 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btad273 Quantification of tumor heterogeneity: from data acquisition to metric generation Author(s): Aditya Kashyap, Maria Anna Rapsomaniki, Vesna Barros, Anna Fomitcheva-Khartchenko, Adriano Luca Martinelli, Antonio Foncubierta Rodriguez, Maria Gabrani, Michal Rosen-Zvi, Govind Kaigala Published in: Trends in Biotechnology, Issue Volume 40, Issue 6, 2022, Page(s) 647-676, ISSN 0968-0004 Publisher: Elsevier BV DOI: 10.1016/j.tibtech.2021.11.006 Predicting Emotional States Using Behavioral Markers Derived From Passively Sensed Data: Data-Driven Machine Learning Approach Author(s): Emese Sükei, Agnes Norbury, M Mercedes Perez-Rodriguez, Pablo M Olmos, Antonio Artés Published in: JMIR mHealth and uHealth, Issue 9/3, 2021, Page(s) e24465, ISSN 2291-5222 Publisher: JMIR Publications DOI: 10.2196/24465 A causal inference approach for estimating effects of non-pharmaceutical interventions during Covid-19 pandemic Author(s): Vesna Barros , Itay Manes, Victor Akinwande, Celia Cintas, Osnat Bar-Shira, Michal Ozery-Flato, Yishai Shimoni, Michal Rosen-Zvi Published in: PLOS ONE, Issue 19326203, 2022, Page(s) e0265289, ISSN 1932-6203 Publisher: 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 Author(s): Kadri Künnapuu, Solomon Ioannou, Kadri Ligi, Raivo Kolde, Sven Laur, Jaak Vilo, Peter R Rijnbeek, Sulev Reisberg Published in: JAMIA Open, Issue 25742531, 2022, Page(s) ooac021, ISSN 2574-2531 Publisher: 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) Author(s): 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 Published in: International Journal of Molecular Sciences, Issue 23(24), 2022, Page(s) 15571, ISSN 1422-0067 Publisher: Multidisciplinary Digital Publishing Institute (MDPI) DOI: 10.3390/ijms232415571 networkGWAS: a network-based approach to discover genetic associations Author(s): Giulia Muzio, Leslie O’Bray, Laetitia Meng-Papaxanthos, Juliane Klatt, Krista Fischer, Karsten Borgwardt Published in: Bioinformatics, Issue Volume 39, Issue 6, 2023, Page(s) btad370, ISSN 1367-4811 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btad370 Conference proceedings (2) Unsupervised Manifold Alignment with Joint Multidimensional Scaling Author(s): Dexiong Chen, Bowen Fan, Carlos Oliver, Karsten Borgwardt Published in: The Eleventh International Conference on Learning Representations, Issue 2023, 2023 Publisher: International Conference on Learning Representations DOI: 10.48550/arxiv.2207.02968 The Case of Missed Cancers: Applying AI as a Radiologist's Safety Net Author(s): 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 Published in: Medical Image Computing and Computer Assisted Intervention – MICCAI 2020, 2020, Page(s) 220-229 Publisher: Springer DOI: 10.5281/zenodo.4076797 Book chapters (1) Network Aggregation to Enhance Results Derived from Multiple Analytics Author(s): Diane Duroux, Héctor Climente-González, Lars Wienbrandt, Kristel Van Steen Published in: Artificial Intelligence Applications and Innovations - 16th IFIP WG 12.5 International Conference, AIAI 2020, Neos Marmaras, Greece, June 5–7, 2020, Proceedings, Part I, Issue 583, 2020, Page(s) 128-140, ISBN 978-3-030-49160-4 Publisher: Springer International Publishing DOI: 10.1007/978-3-030-49161-1_12 Searching for OpenAIRE data... 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