MO
Mhaned Oubounyt
bioinformaticsGene Regulatory NetworksMultiple SclerosisSoftwaredeep learningGene Expression Profilingq-bio.MNSingle-cell RNA sequencingSolanum lycopersicumAlgorithms
On Valency
published · living versionsW_hk8japdy·v1 · currentpublished
Quantum Optimisation for Protein-Protein Interaction Network Alignment
with Merle Stahl, Robert J. Banks, Matthias Traube, Josua Unger +2
1 version
Preprints & journals
24 papers in the corpus · 2019–2026Concurrent de novo inference of cell types and gene regulatory networks with NetMap10.64898/2026.10.04.756614v1 · Hartebrodt, A., Oubounyt, M., de Almeida, G. P. et al.2026 · 0 citationsbioRxiv
Integrating network medicine and foundation models reveals cell-type-specific regulatory alterations in Alzheimer's disease.42840584 · Álvarez-Pérez, Andrea, Rodríguez-González, Alejandro, Baumbach, Jan et al.2026 · 0 citationsNAR genomics and bioinformatics. 2026;8(4):lqag116
Quantum Optimisation for Protein-Protein Interaction Network Alignment2609.05238v1 · Merle Stahl, Robert J. Banks, Matthias Traube et al.2026 · 0 citationsarXivon Valency
Clifti-GPT: privacy-preserving federated fine-tuning and transferable inference of foundation models on clinical single-cell data.42557585 · Bakhtiari, Mohammad, Elkjaer, Maria Louise, Can, Ali Oğuz et al.2026 · 0 citationsBioData mining. 2026;19(1)
An integrated skin cell atlas decodes the pilosebaceous unit.42392254 · Düz, Tolga, Torocsik, Daniel, Momnougui, Sonia M E et al.2026 · 0 citationsThe Journal of investigative dermatology. 2026
Astrocyte-specific FoxF2 modulates immune and myelin repair: Evidence from multiple sclerosis lesions and an animal model.41785663 · Damsbo, Karina, Reyahi, Azadeh, Nik, Ali M et al.2026 · 0 citationsJournal of neuroimmunology. 2026;415:578896
Deletion of cardiac fibroblast growth factor-23 beneficially impacts myocardial energy metabolism in left ventricular hypertrophy.41152461 · Latic, Nejla, Lari, Arezou, Sun, Na et al.2025 · 5 citationsnpj metabolic health and disease. 2025;3(1):42
Development of an Integrated Single-Cell and Spatial Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit10.1101/2025.09.09.675235v1 · Duz, T., Torocsik, D., Momnougui, S. M. E. et al.2025 · 0 citationsbioRxiv
Phenotypic Changes in a Monocyte Cluster with High Interleukin-1 Beta Expression during Long-Term Anti-CD20 Therapy.40879186 · Waede, Mie, Kingo, Christina, Damsbo, Karina et al.2025 · 1 citationAnnals of neurology. 2025;98(6):1283-1298
DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics.40419963 · Delgado-Chaves, Fernando M, Spurny, Ferdinand, Laske, Tanja et al.2025 · 0 citationsBMC bioinformatics. 2025;26(1):137
Network analyses predict major regulators of resistance to early blight disease complex in tomato.38971719 · Tominello-Ramirez, Christopher S, Muñoz Hoyos, Lina, Oubounyt, Mhaned et al.2024 · 16 citationsBMC plant biology. 2024;24(1):641
Ablation of Vitamin D Signaling in Cardiomyocytes Leads to Functional Impairment and Stimulation of Pro-Inflammatory and Pro-Fibrotic Gene Regulatory Networks in a Left Ventricular Hypertrophy Model in Mice.38892126 · Zupcic, Ana, Latic, Nejla, Oubounyt, Mhaned et al.2024 · 5 citationsInternational journal of molecular sciences. 2024;25(11)
Heat-stress-induced ROS in maize silks cause late pollen tube growth arrest and sterility.38979009 · Gong, Wen, Oubounyt, Mhaned, Baumbach, Jan et al.2024 · 35 citationsiScience. 2024;27(7):110081
Single-Cell Multi-Omics Map of Cell Type-Specific Mechanistic Drivers of Multiple Sclerosis Lesions.38564686 · Elkjaer, Maria L, Hartebrodt, Anne, Oubounyt, Mhaned et al.2024 · 30 citationsNeurology(R) neuroimmunology & neuroinflammation. 2024;11(3):e200213
Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet.37862243 · Oubounyt, Mhaned, Adlung, Lorenz, Patroni, Fabio et al.2023 · 13 citationsBioinformatics (Oxford, England). 2023;39(11)
Network analyses reveal D clade ethylene response factors as major regulators of jasmonic acid-mediated resistance to early blight disease complex in tomato10.1101/2023.10.14.562343v1 · Tominello-Ramirez, C., Munoz Hoyos, L., Oubounyt, M. et al.2023 · 1 citationbioRxiv
Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing.37332567 · Maier, Andreas, Hartung, Michael, Abovsky, Mark et al.2024 · 34 citationsArXiv. 2023
Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense.36880316 · Kahlon, Parvinderdeep S, Förner, Andrea, Muser, Michael et al.2023 · 21 citationsJournal of experimental botany. 2023;74(10):3240-3254
De-novo reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters.36879901 · Oubounyt, Mhaned, Elkjaer, Maria L, Laske, Tanja et al.2024 · 8 citationsNAR genomics and bioinformatics. 2023;5(1):lqad018
Enabling single-cell trajectory network enrichment.38217228 · Grønning, Alexander G B, Oubounyt, Mhaned, Kanev, Kristiyan et al.2024 · 6 citationsNature computational science. 2021;1(2):153-163
Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing2004.12420v1 · Sepideh Sadegh, Julian Matschinske, David B. Blumenthal et al.2020 · 192 citationsNat Commun 11, 3518 (2020)
Comparative single-cell trajectory network enrichment identifies pseudo-temporal systems biology patterns in hematopoiesis and CD8 T-cell development10.1101/2020.04.02.021295v3 · Groenning, A. G. B., Oubounyt, M., Kanev, K. et al.2020 · 0 citationsbioRxiv
Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning.31374967 · Louadi, Zakaria, Oubounyt, Mhaned, Tayara, Hilal et al.2020 · 32 citationsGenes. 2019;10(8)
DeePromoter: Robust Promoter Predictor Using Deep Learning.31024615 · Oubounyt, Mhaned, Louadi, Zakaria, Tayara, Hilal et al.2020 · 191 citationsFrontiers in genetics. 2019;10:286
Career total: 55 works. 24 are in this corpus.
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