imAIgene-lab (Machine learning for Biomedical Imaging analysis and multi-omics integration)

Institution: Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM)

Members (researchers): Miguel Molina Moreno, Alejandra Rubio Muñoz, Emilio Ríos Jiménez, Jorge Aurelio Zamora Berna, Lupe Ivette Villegas López, Maria Alieva

Home page: www.imaigene-lab.com
Contact email: malieva@iib.uam.es

Tools: BEHAV3D, BEHAVIORAL GUIDED TRANSCRIPTOMICS, MorphoTrack-merger, BEHAV3D Tumor Profiler

There are no service units associated with this research group.

Research topics:

Bioinformatics education, Cloud Computing, Data Visualization, Deep Learning in Biology, Functional annotation, Image analysis, Integrative Analysis, Machine Learning in Biology, Model organisms, Multivariate statistics, Web-service

Publications

Alieva, M., Barrera Román, M., de Blank, S., Petcu, D., Zeeman, A. L., Dautzenberg, N. M. M., Cornel, A. M., van de Ven, C., Pieters, R., den Boer, M. L., Nierkens, S., Calkoen, F. G. J., Clevers, H., Kuball, J., Sebestyén, Z., Wehrens, E. J., Dekkers, J. F., & Rios, A. C. (2024). BEHAV3D: a 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response. Nature Protocols, 19(7), 2052–2084. https://doi.org/10.1038/s41596-024-00972-6

Acosta-Iborra, B., Gil-Acero, A. I., Sanz-Gómez, M., Berrouayel, Y., Puente-Santamaría, L., Alieva, M., del Peso, L., & Jiménez, B. (2024). Bhlhe40 Regulates Proliferation and Angiogenesis in Mouse Embryoid Bodies under Hypoxia. International Journal of Molecular Sciences, 25(14), 7669. https://doi.org/10.3390/ijms25147669

Alieva, M., Wezenaar, A. K. L., Wehrens, E. J., & Rios, A. C. (2023). Bridging live-cell imaging and next-generation cancer treatment. Nature Reviews Cancer, 23(11), 731–745. https://doi.org/10.1038/s41568-023-00610-5

van Ineveld, R. L., van Vliet, E. J., Wehrens, E. J., Alieva, M., & Rios, A. C. (2022). 3D imaging for driving cancer discovery. The EMBO Journal, 41(10). Portico. https://doi.org/10.15252/embj.2021109675

Dekkers, J. F., Alieva, M., Cleven, A., Keramati, F., Wezenaar, A. K. L., van Vliet, E. J., Puschhof, J., Brazda, P., Johanna, I., Meringa, A. D., Rebel, H. G., Buchholz, M.-B., Barrera Román, M., Zeeman, A. L., de Blank, S., Fasci, D., Geurts, M. H., Cornel, A. M., Driehuis, E., … Rios, A. C. (2022). Uncovering the mode of action of engineered T cells in patient cancer organoids. Nature Biotechnology, 41(1), 60–69. https://doi.org/10.1038/s41587-022-01397-w

Chen, N., Alieva, M., van der Most, T., Klazen, J. A. Z., Vollmann-Zwerenz, A., Hau, P., & Vrisekoop, N. (2022). Neutrophils Promote Glioblastoma Tumor Cell Migration after Biopsy. Cells, 11(14), 2196. https://doi.org/10.3390/cells11142196

van Ineveld, R. L., Collot, R., Román, M. B., Pagliaro, A., Bessler, N., Ariese, H. C. R., Kleinnijenhuis, M., Kool, M., Alieva, M., Chuva de Sousa Lopes, S. M., Wehrens, E. J., & Rios, A. C. (2022). Multispectral confocal 3D imaging of intact healthy and tumor tissue using mLSR-3D. Nature Protocols, 17(12), 3028–3055. https://doi.org/10.1038/s41596-022-00739-x

BEHAV3D: an imaging and transcriptomics platform that unravels T cell antitumor activity. (2022). Nature Biotechnology, 41(1), 31–32. https://doi.org/10.1038/s41587-022-01398-9

Dekkers, J. F., Alieva, M., Cleven, A., Keramati, F., Brazda, P., Rebel, H. G., Wezenaar, A. K. L., Puschhof, J., Buchholz, M.-B., Román, M. B., Johanna, I., Meringa, A. D., Fasci, D., Geurts, M. H., Ariese, H. C. R., van Vliet, E. J., van Ineveld, R. L., Karaiskaki, E., Kopper, O., … Rios, A. C. (2021). Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids. https://doi.org/10.1101/2021.05.05.442764

van Ineveld, R. L., Kleinnijenhuis, M., Alieva, M., de Blank, S., Barrera Roman, M., van Vliet, E. J., Martínez Mir, C., Johnson, H. R., Bos, F. L., Heukers, R., Chuva de Sousa Lopes, S. M., Drost, J., Dekkers, J. F., Wehrens, E. J., & Rios, A. C. (2021). Revealing the spatio-phenotypic patterning of cells in healthy and tumor tissues with mLSR-3D and STAPL-3D. Nature Biotechnology, 39(10), 1239–1245. https://doi.org/10.1038/s41587-021-00926-3

Kluiver, T. A., Alieva, M., van Vuurden, D. G., Wehrens, E. J., & Rios, A. C. (2020). Invaders Exposed: Understanding and Targeting Tumor Cell Invasion in Diffuse Intrinsic Pontine Glioma. Frontiers in Oncology, 10. https://doi.org/10.3389/fonc.2020.00092

Alieva, M., & Rios, A. C. (2019). Longitudinal Intravital Imaging of Brain Tumor Cell Behavior in Response to an Invasive Surgical Biopsy. Journal of Visualized Experiments, 147. https://doi.org/10.3791/59278

Dekkers, J. F., Alieva, M., Wellens, L. M., Ariese, H. C. R., Jamieson, P. R., Vonk, A. M., Amatngalim, G. D., Hu, H., Oost, K. C., Snippert, H. J. G., Beekman, J. M., Wehrens, E. J., Visvader, J. E., Clevers, H., & Rios, A. C. (2019). High-resolution 3D imaging of fixed and cleared organoids. Nature Protocols, 14(6), 1756–1771. https://doi.org/10.1038/s41596-019-0160-8

Alieva, M., Leidgens, V., Riemenschneider, M. J., Klein, C. A., Hau, P., & van Rheenen, J. (2019). Intravital imaging of glioma border morphology reveals distinctive cellular dynamics and contribution to tumor cell invasion. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-38625-4

Alieva, M., van Rheenen, J., & Broekman, M. L. D. (2018). Potential impact of invasive surgical procedures on primary tumor growth and metastasis. Clinical & Experimental Metastasis, 35(4), 319–331. https://doi.org/10.1007/s10585-018-9896-8

Leidgens, V. J., Alieva, M., Lu, X., Patwary, N., Kerkhoff, E., Proescholdt, M. J. M., Vollmann-Zwerenz, A., van Rheenen, J., Klein, C. A., & Hau, P. (2017). OS06.3 Characterisation of human brain tumour initiating cells leading invasion. Neuro-Oncology, 19(suppl_3), iii11–iii11. https://doi.org/10.1093/neuonc/nox036.037

Leidgens, V., Alieva, M., Lu, X., Patwary, N., Kerkhoff, E., Proescholdt, M., Vollmann-Zwerenz, A., van Rheenen, J., Klein, C., & Hau, P. (2017). ANGI-06. CHARACTERISATION OF INVASION OF HUMAN BRAIN TUMOUR INITIATING CELLS IN HUMAN GLIOBLASTOMA. Neuro-Oncology, 19(suppl_6), vi22–vi23. https://doi.org/10.1093/neuonc/nox168.085

Alieva, M., Margarido, A. S., Wieles, T., Abels, E. R., Colak, B., Boquetale, C., Jan Noordmans, H., Snijders, T. J., Broekman, M. L., & van Rheenen, J. (2017). Preventing inflammation inhibits biopsy-mediated changes in tumor cell behavior. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-07660-4

Alieva, M., Colak, B., Boquetale, C., & Van Rheenen, J. (2015). Abstract A84: Intravital microscopy reveals biopsy induced local wound-healing response. Molecular Cancer Therapeutics, 14(12_Supplement_2), A84–A84. https://doi.org/10.1158/1535-7163.targ-15-a84

Alieva, M., Ritsma, L., Giedt, R. J., Weissleder, R., & van Rheenen, J. (2014). Imaging windows for long-term intravital imaging. IntraVital, 3(2), e29917. https://doi.org/10.4161/intv.29917

Aguilar, E., Bagó, J. R., Soler-Botija, C., Alieva, M., Rigola, M. A., Fuster, C., Vila, O. F., Rubio, N., & Blanco, J. (2014). Fast-Proliferating Adipose Tissue Mesenchymal-Stromal-Like Cells for Therapy. Stem Cells and Development, 23(23), 2908–2920. https://doi.org/10.1089/scd.2014.0231

Bagó, J. R., Aguilar, E., Alieva, M., Soler-Botija, C., Vila, O. F., Claros, S., Andrades, J. A., Becerra, J., Rubio, N., & Blanco, J. (2013). In VivoBioluminescence Imaging of Cell Differentiation in Biomaterials: A Platform for Scaffold Development. Tissue Engineering Part A, 19(5–6), 593–603. https://doi.org/10.1089/ten.tea.2012.0073

Bagó, J. R., Alieva, M., Soler, C., Rubio, N., & Blanco, J. (2013). Endothelial Differentiation of Adipose Tissue-Derived Mesenchymal Stromal Cells in Glioma Tumors: Implications for Cell-Based Therapy. Molecular Therapy, 21(9), 1758–1766. https://doi.org/10.1038/mt.2013.145

Bagó, J. R., Soler-Botija, C., Casaní, L., Aguilar, E., Alieva, M., Rubio, N., Bayes-Genis, A., & Blanco, J. (2013). Bioluminescence imaging of cardiomyogenic and vascular differentiation of cardiac and subcutaneous adipose tissue-derived progenitor cells in fibrin patches in a myocardium infarct model. International Journal of Cardiology, 169(4), 288–295. https://doi.org/10.1016/j.ijcard.2013.09.013

Alieva, M., Bagó, J. R., Aguilar, E., Soler-Botija, C., Vila, O. F., Molet, J., Gambhir, S. S., Rubio, N., & Blanco, J. (2012). Glioblastoma Therapy with Cytotoxic Mesenchymal Stromal Cells Optimized by Bioluminescence Imaging of Tumor and Therapeutic Cell Response. PLoS ONE, 7(4), e35148. https://doi.org/10.1371/journal.pone.0035148

Alieva, M., Bago, J. R., Aguilar, E., Rubio, N., & Blanco, J. (2012). 911 Bioluminescence Imaging of Glioblastoma Therapy with Cytotoxic Human Mesenchymal Stroma Cells that Differentiate to Endothelial Lineage. European Journal of Cancer, 48, S220. https://doi.org/10.1016/s0959-8049(12)71540-x

Vila, O. F., Bagó, J. R., Navarro, M., Alieva, M., Aguilar, E., Engel, E., Planell, J., Rubio, N., & Blanco, J. (2012). Calcium phosphate glass improves angiogenesis capacity of poly(lactic acid) scaffolds and stimulates differentiation of adipose tissue‐derived mesenchymal stromal cells to the endothelial lineage. Journal of Biomedical Materials Research Part A, 101A(4), 932–941. Portico. https://doi.org/10.1002/jbm.a.34391

Montero-Pedrazuela, A., Fernández-Lamo, I., Alieva, M., Pereda-Pérez, I., Venero, C., & Guadaño-Ferraz, A. (2011). Adult-Onset Hypothyroidism Enhances Fear Memory and Upregulates Mineralocorticoid and Glucocorticoid Receptors in the Amygdala. PLoS ONE, 6(10), e26582. https://doi.org/10.1371/journal.pone.0026582

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