Institution: IIBM

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

Position: Group Leader

Home page: https://www.imaigene-lab.com/

Contact email: malieva@iib.uam.es

ORCID: https://orcid.org/0000-0002-1425-9908

BCB Committee: No committees assigned.

BCB Community: Bioinformatics tools, benchmarks and data visualization

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

BCB Services:

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

Biography: I am an interdisciplinary scientist with dual expertise in experimental biology and computational analysis, focusing on the cellular and molecular mechanisms that drive tumor behavior and therapeutic response.
My scientific journey began with a specialization in advanced imaging techniques, developing and applying non-invasive, single-cell resolution approaches to track tumor and therapeutic cell dynamics in vivo. During my PhD with Prof. Jeronimo Blanco (CSIC-ICCC, Barcelona), I investigated cellular therapeutic vehicles against brain tumors, earning my doctorate in 2012 with “cum laude” distinction. In 2013, I joined Prof. Jacco van Rheenen’s group (Hubrecht Institute, The Netherlands), where I studied how surgical interventions influence the progression of brain cancer using intravital microscopy.
Realizing that the field of imaging research was often hampered by the lack of tools to extract meaningful information from the data, I started to specialize in the development of new computational methods for the analysis of complex imaging data. In 2017, I joined the group of Dr. Anne Rios (Princess Máxima Center, The Netherlands), where I focused on the development of computational techniques to study cellular behavior and perform large-scale tissue phenotyping in order to understand and improve the functionality of cell therapies against cancer. One of the highlights of my recent research was the development of a novel methodological approach that integrates single cell sequencing and single cell spatio-temporal 3D imaging (BEHAV3D) of T cell cancer immunotherapy targeting patient-derived tumor organoids. Confirming the relevance of this work, I have was awarded the Jon van Rood award for the best paper of 2022 that significantly contributed to the field of cellular transplantation. It should be noted that this scientific contribution is not an isolated impact and has led to numerous collaborations with international and national academic groups and industrial partners (HubOrganoid Merck).
In 2023 I was granted a tenure track position by the “Programa de Atraccion de Talento de la Comunidad de Madrid” allowing me to start my independent research group at the Instituto de Investigaciones Biomedicas Sols-Morreale (IIBM), where I am focused on the development of analytical approaches for biomedical imaging, integration of different data types to discover biological patterns in the context of tumor progression and immunotherapy targeting. Moreover, I was granted the prestigious Beca Leonardo by the Fundacion BBVA to pursue my work in the field of artificial intelligence (AI) application to imaging. As part of my institutional responsibilities, I serve as an ambassador for the CSIC’s Computational Biology and Bioinformatics Connection, and I am a member of the Internationalization Committee at the IIBM.
I am deeply committed to democratizing access to AI tools for biomedical research. To this end, I co-developed user-friendly data analysis tools and step-by-step protocols tailored for researchers with no coding experience, promoting reproducibility and wider adoption of deep learning tools.
Throughout my career, I have taken part in various teaching and training activities, including leading seminars and workshops such as those at the European Molecular Imaging Meeting. I also engage in scientific outreach through school presentations, contributions to written media (La Vanguardia, El Espanol, etc), and occasional participation in radio programs (A Golpe de Bit and En la Cresta de la Onda). In 2021, I was honored with the Scientific Art Prize for a short scientific narrative that was beautifully transformed into a captivating graphical representation as an award. And in 2023 I won the second prize for Best Scientific Image at the ASEICA 40th conference.
In short, my interdisciplinary expertise drives research in translational oncology and strengthens the connection between biological researchers and computational scientists, unlocking our collective potential to advance life sciences knowledge.

Publications
Displayed publications: 28

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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Doctoral Programs: HORIZON-MSCA-2024-DN-01-01