MLFPM Publications

Peer-reviewed publications

  1. Duroux Diane, Climente-González Héctor, Wienbrandt Lars, and Van Steen Kristel. (2020). Network Aggregation to Enhance Results Derived from Multiple Analytics. In Artificial Intelligence Applications and Innovations. AIAI 2020. IFIP Advances in Information and Communication Technology, vol 583. Springer, Cham. 10.1007/978-3-030-49161-1_12
  2. Michal Chorev, Yoel Shoshan, Adam Spiro, Shaked Naor, Alon Hazan, Vesna Barros, Iuliana Weinstein, Esma Herzel, Varda Shalev, Michal Guind, and Michal Rosen-Zvi. (2020). The Case of Missed Cancers: Applying AI as a Radiologist’s Safety Net. In: Martel A.L. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science, vol 12266. Springer, Cham. 10.5281/zenodo.4076798
  3. Giulia Muzio*, Leslie O’Bray* and Karsten Borgwardt (* = equal contribution). (2020). Biological network analysis with deep learning. Briefings in Bioinformatics 2020, bbaa257. 10.1093/bib/bbaa257
  4. Emese Sükei, Agnes Norbury, M Mercedes Perez-Rodriguez, Pable M Olmos, and Antonio Artés. (2021). Predicting Emotional States Using Behavioral Markers Derived From Passively Sensed Data: Data-Driven Machine Learning Approach. JMIR Mhealth Uhealth 2021; 9(3): e24465. https://mhealth.jmir.org/2021/3/e24465
  5. 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, Divya Pathak, and Michal Rosen-Zvi. (2021). AI-assisted tracking of worldwide non-pharmaceutical interventions for COVID-19. Scientific Data 8, 94. 10.1038/s41597-021-00878-y
  6. Jihan Ryu, Emese Sükei, Agnes Norbury, Shelley H Liu, Juan José Campaña-Montes, Enrique Baca-Garcia, Antonio Artés, M Mercedes Perez-Rodriguez. (2021). Shift in Social Media App Usage During COVID-19 Lockdown and Clinical Anxiety Symptoms: Machine Learning–Based Ecological Momentary Assessment Study. JMIR Mental Health 2021; 8(9): e30833.
    https://mental.jmir.org/2021/9/e30833
  7. Lucas Miranda, Riya Paul , Benno Pütz, Nikolaos Koutsouleris and Bertram Müller-Myhsok. (2021). Systematic Review of Functional MRI Applications for Psychiatric Disease Subtyping. Frontiers in Psychiatry 2021, 12:665536. doi: 10.3389/fpsyt.2021.665536.
  8. Pradeep Eranti, Emmanuelle Bouzigon, Florence Demenais, The Egea Cooperative Group. Identification of Gene Modules Shared by Childhood-Onset Asthma and Immunoglobulin-E Levels by Integrated Network Analysis of Multi-Omics Data. 49th European Mathematical Genetics Meeting, Human Heredity 2021, 85: 76. DOI: 10.1159/000516194, Published abstract
  9. Tal Tlusty, Michal Ozery-Flato, Vesna Barros, Ella Barkan, Mika Amit, David Gruen, Michal Guindy, Tal Arazi, Mona Rozin, Michal Rosen-Zvi, and Efrat Hexter. Pre-Biopsy Multi-Class Classification of Breast Lesion Pathology in Mammograms. Machine Learning in Medical Imaging. MLMI 2021. Lecture Notes in Computer Science, vol 12966. https://doi.org/10.1007/978-3-030-87589-3_29
  10. Pelin Gundogdu, Carlos Loucera, Inmaculada Alamo-Alvarez, Joaquin Dopazo and Isabel Nepomuceno. Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data. BioData Mining 15, 1 (2022). 10.1186/s13040-021-00285-4
  11. Aditya Kashyap, Maria Anna Rapsomaniki, Vesna Barros, Anna Fomitcheva-Khartchenko, Adriano Luca Martinelli, Antonio Foncubierta Rodriguez, Maria Gabrani, Michal Rosen-Zvi, and Govind Kaigala. Quantification of tumor heterogeneity: from data acquisition to metric generation. Trends in Biotechnology 2021. 10.1016/j.tibtech.2021.11.006
  12. Diane Duroux, Héctor Climente-González, Chloé-Agathe Azencott, Kristel Van Steen. Interpretable network-guided epistasis detection, GigaScience, Volume 11, 2022, giab093, 10.1093/gigascience/giab093
  13. Andrew Walakira, Junior Ocira, Diane Duroux, Ramouna Fouladi, Miha Moškon, Damjana Rozman, and Kristel Van Steen. Detecting gene–gene interactions from GWAS using diffusion kernel principal components. BMC Bioinformatics 23, 57 (2022). 10.1186/s12859-022-04580-7
  14. Kadri Künnapuu, Solomon Ioannou, Kadri Ligi, Raivo Kolde, Sven Laur, Jaak Vilo, Peter R. Rijnbeek, Sulev Reisberg. (2021). Trajectories: a framework for detecting temporal clinical event sequences from health data standardized to the OMOP Common Data Model. JAMIA Open 2022 5, 1: ooac021. (2022). 10.1093/jamiaopen/ooac021
  15. 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, and Karsten M. Borgwardt. Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients. International Conference on Intelligent Systems for Molecular Biology (ISMB 2022) and Bioinformatics 2022, 38 (Supplement_1): i101–i108. 10.1093/bioinformatics/btac229
  16. Vesna Barros, Itay Manes, Victor Akinwande, Celia Cintas, Osnat Bar-Shira, Michal Ozery-Flato, Yishai Shimoni, and Michal Rosen-Zvi. A causal inference approach for estimating effects of non-pharmaceutical interventions during Covid-19 pandemic. PLOS ONE 17, 9: e0265289 (2022). 10.1371/journal.pone.0265289
  17. Vesna Barros, Tal Tlusty, Ella Barkan, Efrat Hexter, David Gruen, Michal Guindy, and Michal Rosen-Zvi. Virtual Biopsy by Using Artificial Intelligence–based Multimodal Modeling of Binational Mammography Data. Radiology, 2022. 10.1148/radiol.220027
  18. Renzo J. M. Riemens, Gunter Kenis, Jennifer Nolz, Sonia C. Susano Chaves, Diane Duroux, Ehsan Pishva, Diego Mastroeni, Kristel Van Steen, Thomas Haaf, and Daniël L. A. van den Hove. Targeted Methylation Profiling of Single Laser-Capture Microdissected Post-Mortem Brain Cells by Adapted Limiting Dilution Bisulfite Pyrosequencing (LDBSP). International Journal of Molecular Sciences. 2022; 23(24):15571. 10.3390/ijms232415571
  19. Joeri Bordes, Lucas Miranda, Bertram Müller-Myhsok, and Mathias V. Schmidt. Advancing social behavioral neuroscience by integrating ethology and comparative psychology methods through machine learning. Neuroscience & Biobehavioral Reviews 2023, 151: 105243, https://doi.org/10.1016/j.neubiorev.2023.105243
  20. 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. Leveraging Comprehensive Health Records for Breast Cancer Risk Prediction: A Binational Assessment. In AMIA Annual Symposium 2022 Proceedings. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10148351/
  21. Lucas Miranda, Joeri Bordes, Serena Gasperoni, and Juan Pablo Lopez. Increasing resolution in stress neurobiology: from single cells to complex group behaviors. Stress 2022, 26(1). 10.1080/10253890.2023.2186141
  22. Pradeep Eranti, Raphaël Vernet, Emmanuelle Bouzigon, Florence Demenais on behalf of the EGEA, EVADA and RESET-AID Consortia. Network analysis of multi-omics data identifies shared genes and pathways underlying the risk of allergic diseases and IgE production. The 2022 Annual Meeting of the International Genetic Epidemiology Society. Genetic Epidemiology 2022, 46: 475-551. DOI: 10.1002/gepi.22503, Published abstract.
  23. Dexiong Chen, Bowen Fan, Carlos Oliver, and Karsten Borgwardt. Unsupervised Manifold Alignment with Joint Multidimensional Scaling. Accepted at The Eleventh International Conference on Learning Representations ICLR 2023. 10.48550/arXiv.2207.02968  
  24. Diane Duroux, Kristel Van Steen. netANOVA: novel graph clustering technique with significance assessment via hierarchical ANOVA. Briefings in Bioinformatics 2023, 24(2). doi: 10.1093/bib/bbad029
  25. Giulia Muzio, Leslie O’Bray, Laetitia Meng-Papaxanthos, Juliane Klatt, Krista Fischer, and Karsten Borgwardt. networkGWAS: A network-based approach to discover genetic associations. Bioinformatics. 2023; 10.1093/bioinformatics/btad370
  26. Paolo Pellizzoni, Giulia Muzio and Karsten Borgwardt. Higher-order genetic interaction discovery with network-based biological priors, Bioinformatics 2023, Volume 39, Issue Supplement_1, Pages i523–i533. doi: 10.1093/bioinformatics/btad273
  27. Alex Hawkins-Hooker, Giovanni Visonà, Tanmayee Narendra, Mateo Rojas-Carulla, Bernhard Schölkopf, and Gabriele Schweikert. Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning. Nature Communications 2023, 14(1). doi: 10.1038/s41467-023-40211-2
  28. 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. Machine-Learning-Aided Prediction of Brain Metastases Development in Non–Small-Cell Lung Cancers, Clinical Lung Cancer 2023. doi: 10.1016/j.cllc.2023.08.002.
  29. Emese Sükei, Lorena Romero-Medrano, Santiago de Leon-Martinez, Jesús Herrera López, Juan José Campaña-Montes, Pablo M Olmos, Enrique Baca-Garcia , Antonio Artés. Continuous Assessment of Function and Disability via Mobile Sensing: Real-World Data-Driven Feasibility Study. JMIR Formative Research 2023, 7:e47167. doi: 10.2196/47167
  30. Pelin Gundogdu, Inmaculada Alamo, Isabel A. Nepomuceno-Chamorro, Joaquin Dopazo, and Carlos Loucera. 2023. “SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types” Biology 12, no. 4: 579. https://doi.org/10.3390/biology12040579
  31. Diane Duroux, Christian Wohlfart, Kristel Van Steen, Antoaneta Vladimirova, and Michael King. Graph-based multi-modality integration for prediction of cancer subtype and severity. Scientific Reports 2023, 13: 19653. https://doi.org/10.1038/s41598-023-46392-6
  32. Lucas Miranda, Joeri Bordes, Benno Pütz, Mathias V. Schmidt, and Bertram Müller-Myhsok. DeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking data. Journal of Open Source Software 2023, 8(86): 5394, https://doi.org/10.21105/joss.05394
  33. Pelin Gundogdu, Miriam Payá-Milans, Inmaculada Alamo-Alvarez, Isabel A. Nepomuceno-Chamorro, Joaquin Dopazo, Carlos Loucera. Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder. In: Pang, J., Niehren, J. (eds) Computational Methods in Systems Biology. CMSB 2023. Lecture Notes in Computer Science 2023, vol 14137. Springer, Cham. https://doi.org/10.1007/978-3-031-42697-1_5
  34. 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. Automatically annotated motion tracking identifies a distinct social behavioral profile following chronic social defeat stress. Nature Communications 2023; 14: 4319 doi: https://doi.org/10.1038/s41467-023-40040-3
  35. Emese Sükei, Santiago de Leon-Martinez, Pablo M. Olmos, Antonio Artés. Automatic patient functionality assessment from multimodal data using deep learning techniques–Development and feasibility evaluation. Internet Interventions 2023;33:100657. https://doi.org/10.1016/j.invent.2023.100657
  36. 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. A historical perspective of biomedical explainable AI research. Patterns 2023, 4(9): 100830. https://doi.org/10.1016/j.patter.2023.100830.
  37. 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. netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity. Frontiers in Genetics 2023, 14:1286800. doi: 10.3389/fgene.2023.1286800
  38. Giovanni Visonà, Diane Duroux, Lucas Miranda, Emese Sükei, Yiran Li, Karsten Borgwardt, Carlos Oliver, Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information, Bioinformatics, Volume 39, Issue 12, December 2023, btad717, https://doi.org/10.1093/bioinformatics/btad717
  39. 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. Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus. Science Advances 2023, 9: eadj3793(2023). doi:10.1126/sciadv.adj3793
  40. Tatjana Meister, Anastassia Kolde, Krista Fischer, Heti Pisarev, Raivo Kolde, Ruth Kalda, Kadri Suija, Anna Tisler, Anneli Uusküla. A retrospective cohort study of incidence and risk factors for severe SARS-CoV-2 breakthrough infection among fully vaccinated people. Scientific Reports 2023, 13: 8531. https://doi.org/10.1038/s41598-023-35591-w
  41. Giovanni Visonà, Emmanuelle Bouzigon, Florence Demenais, and Gabriele Schweikert. Network propagation for GWAS analysis: a practical guide to leveraging molecular networks for disease gene discovery, Briefings in Bioinformatics, Volume 25, Issue 2, March 2024, bbae014, https://doi.org/10.1093/bib/bbae014
  42. Carlo Cervia-Hasler, Sarah C. Brüningk, Tobias Hoch, Bowen Fan, Giulia Muzio, Ryan C. Thompson, Laura Ceglarek, Roman Meledin, Patrick Westermann, Marc Emmenegger, Patrick Taeschler, Yves Zurbuchen, Michele Pons, Dominik Menges, Tala Ballouz, Sara Cervia-Hasler, Sarah Adamo, Miriam Merad, Alexander W. Charney, Milo Puhan, Petter Brodin, Jakob Nilsson, Adriano Aguzzi, Miro E. Raeber, Christoph B. Messner, Noam D. Beckmann, Karsten Borgwardt, and Onur Boyman. Persistent complement dysregulation with signs of thromboinflammation in active Long Covid. Science 2024. 383: eadg7942. DOI:10.1126/science.adg7942

Preprints

  1. Fernando Moreno-Pino, Emese Sükei, Pablo M. Olmos, Antonio Artés-Rodríguez. (2022). PyHHMM: A Python Library for Heterogeneous Hidden Markov Models. arXiv:2201.06968; doi:https://doi.org/10.48550/arXiv.2201.06968
  2. Dexiong Chen, Bowen Fan, Carlos Oliver, and Karsten Borgwardt. (2022). Unsupervised Manifold Alignment with Joint Multidimensional Scaling. arXiv:2207.02968; doi: https://doi.org/10.48550/arXiv.2207.02968  
  3. Tanmayee Narendra, Giovanni Visonà, Crhistian de Jesus Cardona, Gabriele Schweikert. (2022). Multi-histone ChIP-Seq Analysis with DecoDen. bioRxiv 2022.10.18.512665; doi: https://doi.org/10.1101/2022.10.18.512665
  4. Vesna Barros, Nour Abdallah, Moshiko Raboh, Nicholas Heller, Simona Rabinovici-Cohen, Alex Golts, Amilcare Gentili, Daniel Lang, Suman Chaudhary, Varsha Satish, Resha Tejpaul, Ivan Eggel, Henning Müller, Efrat Hexter, Michal Rosen-Zvi, and Christopher Weight. Preoperative Kidney Tumor Risk Estimation from CT Imaging for Adjuvant Treatment Prediction. SSRN, 2024. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4779677
  5. Xinrui Lyu, Bowen Fan, Matthias Hüser, Philip Hartout, Thomas Gumbsch, MartinFaltys, Tobias M. Merz, Gunnar Rätsch, Karsten Borgwardt. An Empirical Study on KDIGO-Defined Acute Kidney Injury Prediction in the Intensive Care Unit. medRxiv 2024.02.01.24302063; doi: https://doi.org/10.1101/2024.02.01.24302063
  6. Arno van Hilten, Federico Melograna, Bowen Fan, Wiro Niessen, Kristel van Steen, Gennady Roshchupkin. Detecting Genetic Interactions with Visible Neural Networks. bioRxiv 2024.02.27.582086. doi: https://doi.org/10.1101/2024.02.27.582086
  7. Emese Sükei, Lorena Romero-Medrano, Santiago de Leon-Martinez, Jesús Herrera López, Juan José Campaña-Montes, Pablo M. Olmos, Enrique Baca-Garcia, Antonio Artés. Assessing WHODAS 2.0 Scores from Behavioral Biomarkers: a Data-driven Approach; JMIR Preprints 2022: 38231 https://doi.org/10.2196/preprints.38231