  | Touahri, Y.* , Hanna, J., Tachibana, N., OKAWA, S., Liu, H., David, L. A., Olender, T., Vasan, L., Pak, A., Mehta, D. N., Chinchalongporn, V., Balakrishnan, A., Cantrup, R., Dixit, R., Mattar, P., Saleh, F., Ilnytskyy, Y., Murshed, M., Mains, P. E., ... Schuurmans, C.*. (27 March 2024). Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina. Cell Reports, 43 (4), 114005. doi:10.1016/j.celrep.2024.114005  Peer Reviewed verified by ORBi |
 | BARVAUX, S.* , OKAWA, S., & DEL SOL MESA, A.*. (2024). SinCMat: A single-cell-based method for predicting functional maturation transcription factors. Stem Cell Reports. doi:10.1016/j.stemcr.2023.12.006 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2023). Epi-Impute: Single-Cell RNA-seq Imputation via Integration with Single-Cell ATAC-seq. International Journal of Molecular Sciences. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2023). Transcriptional and Chromatin Accessibility Profiling of Neural Stem Cells Differentiating into Astrocytes Reveal Dynamic Signatures Affected under Inflammatory Conditions. Cells. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2023). Measuring biological age using a functionally interpretable multi-tissue RNA clock. Aging Cell. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2022). Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration. Nature. doi:10.1038/s41586-022-05535-x Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2022). A single cell-based computational platform to identify chemical compounds targeting desired sets of transcription factors for cellular conversion. Stem Cell Reports. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2022). ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells. Nucleic Acids Research. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2022). Neural network learning defines glioblastoma features to be of neural crest perivascular or radial glia lineages. Science Advances. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2022). Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients. Cell Reports Medicine. Peer reviewed |
 | DEL SOL MESA, A. (January 2022). Fostering experimental and computational synergy to modulate hyperinflammation. Trends in Immunology, 43 (1). Peer Reviewed verified by ORBi |
DEL SOL MESA, A. (2022). Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research. In Methods in Molecular Biology. Springer. doi:10.1007/978-1-0716-2193-6_4 Peer reviewed |
 | DEL SOL MESA, A. (2021). A Catalogus Immune Muris of the mouse immune responses to diverse pathogens. Cell Death and Disease. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2021). Proneural genes define ground-state rules to regulate neurogenic patterning and cortical folding. Neuron. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2021). A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion. Nature Communications. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2021). A computer-guided design tool to increase the efficiency of cellular conversions. Nature Communications. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2021). Altered sphingolipid function in Alzheimer's disease; a gene regulatory network approach. Neurobiology of Aging. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2021). Computational modelling of stem cell‐niche interactions facilitates discovery of strategies to enhance tissue regeneration and counteract aging. FEBS Journal. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2021). Leveraging systems biology for predicting modulators of inflammation in patients with COVID-19. Science Advances. Peer Reviewed verified by ORBi |
  | DEL SOL MESA, A. (2021). Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2020). FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. Briefings in Bioinformatics. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2020). FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age. Nature Cell Biology. doi:10.1038/s41556-020-00593-7 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2020). TransSynW: A single‐cell RNA‐sequencing based web application to guide cell conversion experiments. Stem Cells Translational Medicine. Peer Reviewed verified by ORBi |
 | RIBEIRO, M., OKAWA, S., & DEL SOL MESA, A. (2020). TransSynW: A single‐cell RNA‐sequencing based web application to guide cell conversion experiments. Stem Cells Translational Medicine. doi:10.1002/sctm.20-0227 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2020). The Importance of Computational Modeling in Stem Cell Research. Trends in Biotechnology. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2020). Multiomics data integration unveils core transcriptional regulatory networks governing cell-type identity. NPJ systems biology and applications. Peer reviewed |
 | DEL SOL MESA, A. (2020). HuR/ELAVL1 drives malignant peripheral nerve sheath tumour growth and metastasis. Journal of Clinical Investigation. Peer reviewed |
 | GOMEZ GIRO, G., Arias-Fuenzalida, J., JARAZO, J., Zeuschner, D., ALI, M., Possemis, N., BOLOGNIN, S., HALDER, R., Jäger, C., Kuper, W., van Hasselt, P., Zaehres, H., DEL SOL MESA, A., van der Putten, H., Schoeler, H., & SCHWAMBORN, J. C. (2020). Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis. Acta Neuropathologica Communications. doi:10.1186/s40478-019-0871-7 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2019). Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and blood. Clinical Epigenetics. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2019). SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies. Bioinformatics. Peer reviewed |
 | DEL SOL MESA, A. (2019). Integrative and perturbation based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors. Stem Cells. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2019). Assessment of network module identification across complex diseases. Nature Methods. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2019). Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects. Nature. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2019). Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks. In Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks. Springer. |
 | DEL SOL MESA, A. (2019). A general computational approach to predicting synergistic transcriptional cores that determine cellsubpopulation identities. Nucleic Acids Research. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., & RAVICHANDRAN, S. (2019). Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain. Cell. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2019). Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapy. Trends in Biotechnology. Peer reviewed |
 | ZAFFARONI, G., OKAWA, S., Morales-Ruiz, M., & DEL SOL MESA, A. (2019). An integrative method to predict signallingperturbations for cellular transitions. Nucleic Acids Research. doi:10.1093/nar/gkz232 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., OKAWA, S., & RAVICHANDRAN, S. (2019). Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapy. Trends in Biotechnology. Peer reviewed |
 | OKAWA, S., & DEL SOL MESA, A. (2019). A general computational approach to predicting synergistic transcriptional cores that determine cell subpopulation identities. Nucleic Acids Research. doi:10.1093/nar/gkz147 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2019). Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis. Acta Neuropathologica. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2018). Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift. Nature Communications. Peer Reviewed verified by ORBi |
ALI, M., & DEL SOL MESA, A. (2018). Modeling of Cellular Systems: Application in Stem Cell Research and Computational Disease Modeling. Springer International Publishing. doi:10.1007/978-3-319-74974-7_7 |
 | DEL SOL MESA, A. (2018). Loss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients. Oncotarget. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., RAVICHANDRAN, S., & MICHELUCCI, A. (2018). Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease. Frontiers in Physiology. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2018). The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity. Cell Reports. Peer Reviewed verified by ORBi |
 | Nicklas, S., Hillje, A.-L., OKAWA, S., Rudolph, I.-M., Collmann, F. M., VAN WÜLLEN, T. M., DEL SOL MESA, A., & SCHWAMBORN, J. C. (2018). A complex of the ubiquitin ligase TRIM32 and the deubiquitinase USP7 balances the level of c-Myc ubiquitination and thereby determines neural stem cell fate specification. Cell Death and Differentiation. doi:10.1038/s41418-018-0144-1 Peer reviewed |
 | Medelnik, J.-P., Roensch, K., OKAWA, S., DEL SOL MESA, A., Chara, O., Mchedlishvili, L., & Tanaka, E. M. (2018). Signaling-Dependent Control of Apical Membrane Size and Self-Renewal in Rosette-Stage Human Neuroepithelial Stem Cells. Stem Cell Reports. doi:10.1016/j.stemcr.2018.04.018 Peer Reviewed verified by ORBi |
 | OKAWA, S., Saltó, C., RAVICHANDRAN, S., Yang, S., Toledo, E. M., Arenas, E., & DEL SOL MESA, A. (2018). Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift. Nature Communications. doi:10.1038/s41467-018-05016-8 Peer Reviewed verified by ORBi |
 | HARTMANN, A., OKAWA, S., ZAFFARONI, G., & DEL SOL MESA, A. (2018). SeesawPred: A Web Application for Predicting Cell-fate Determinants in Cell Differentiation. Scientific Reports. doi:10.1038/s41598-018-31688-9 Peer Reviewed verified by ORBi |
 | ASHRAFI, A., GARCIA, P., Kollmus, H., Schughart, K., DEL SOL MESA, A., BUTTINI, M., & GLAAB, E. (October 2017). Absence of regulator of G-protein signaling 4 does not protect against dopamine neuron dysfunction and injury in the mouse 6-hydroxydopamine lesion model of Parkinson's disease. Neurobiology of Aging, 58, 30-33. doi:10.1016/j.neurobiolaging.2017.06.008 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2017). Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons. Genome Research. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., & ZICKENROTT, S. (2017). Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data. Scientific Reports. doi:10.1038/s41598-017-04929-6 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2017). Absence of regulator of G-protein signaling 4 does not protect against dopamine neuron dysfunction and injury in the mouse 6-hydroxydopamine lesion model of Parkinson’s disease. Neurobiology of Aging. Peer reviewed |
DEL SOL MESA, A. (2017). Bioinformatics Tools for Genome-Wide Epigenetic Research. In Neuroepigenomics in Aging and Disease. Springer International Publishing. doi:10.1007/978-3-319-53889-1_25 Peer reviewed |
 | DEL SOL MESA, A. (2017). Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus. PLoS Genetics. doi:10.1371/journal.pgen.1006682 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., JUNG GEB. ZICKENROTT, S., & HARTMANN, A. (2017). RefBool: a reference-based algorithm for discretizing gene expression data. Bioinformatics. Peer reviewed |
 | DEL SOL MESA, A. (2017). Big-data-driven stem cell science and tissue engineering: vision and unique opportunities. Cell Stem Cell. Peer Reviewed verified by ORBi |
 | RAVICHANDRAN, S., & DEL SOL MESA, A. (2017). Identifying niche mediated regulatory factors of stem cell phenotypic state: a systems biology approach. FEBS Letters. doi:10.1002/1873-3468.12559 Peer Reviewed verified by ORBi |
 | Frejo, L., Requena, T., OKAWA, S., Gallego-Martinez, A., Martinez-Bueno, M., Aran, I., Batuecas-Caletrio, A., Benitez-Rosario, J., Espinosa-Sanchez, J. M., Fraile-Rodrigo, J. J., García-Arumi, A. M., González-Aguado, R., Marques, P., Martin-Sanz, E., Perez-Fernandez, N., Pérez-Vázquez, P., Perez-Garrigues, H., Santos-Perez, S., Soto-Varela, A., ... Lopez-Escamez, J. A. (2017). Regulation of Fn14 Receptor and NF-κB Underlies Inflammation in Meniere’s Disease. Frontiers in Immunology. doi:10.3389/fimmu.2017.01739 Peer Reviewed verified by ORBi |
 | RAVICHANDRAN, S., OKAWA, S., MARTINEZ ARBAS, S., & DEL SOL MESA, A. (2016). A systems biology approach to identify niche determinants of cellular phenotypes. Stem Cell Research. doi:10.1016/j.scr.2016.09.006 Peer reviewed |
 | ESPINOSA ANGARICA, V., & DEL SOL MESA, A. (August 2016). Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation. BioEssays, 38 (8). doi:10.1002/bies.201600103 Peer Reviewed verified by ORBi |
 | ANTONY, P., TALLAM, A., PERUMAL, T. M., Jäger, C., FRITZ, J., BALLING, R., DEL SOL MESA, A., MICHELUCCI, A., & Vallar, L. (2016). Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages. PLoS ONE. doi:10.1371/journal.pone.0149050 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., ZICKENROTT, S., & ESPINOSA ANGARICA, V. (14 January 2016). Prediction of disease-gene-drug relationships following a differential network analysis. Cell Death and Disease, 7, 2040. doi:10.1038/cddis.2015.393 Peer Reviewed verified by ORBi |
 | OKAWA, S., NICKLAS, S., ZICKENROTT, S., SCHWAMBORN, J. C., & DEL SOL MESA, A. (2016). A generalized gene regulatory network model of stem cell differentiation for predicting lineage specifiers. Stem Cell Reports. doi:10.1016/j.stemcr.2016.07.014 Peer Reviewed verified by ORBi |
 | Ashrafi, A., BUTTINI, M., GARCIA, P., DEL SOL MESA, A., & GLAAB, E. (2016). Exploring therapeutic viability of a non-dopaminergic target for Parkinson’s disease. Movement Disorders, 31 (2), 630. Peer Reviewed verified by ORBi |
 | Bunk, E., Ertaylan, G., Ortega, F., PAVLOU, M. A., GONZALEZ CANO, L., Stergiopoulos, A., Safaiyan, S., Voels, S., van Cann, M., Politis, P., Berninger, B., DEL SOL MESA, A., & SCHWAMBORN, J. C. (2016). Prox1 is required for oligodendrocyte cell identity in adult neural stem cells of the subventricular zone. Stem Cells. doi:10.1002/stem.2374 Peer Reviewed verified by ORBi |
 | OKAWA, S., & DEL SOL MESA, A. (2015). A computational strategy for predicting lineage specifiers in stem cell subpopulations. Stem Cell Research. doi:10.1016/j.scr.2015.08.006 Peer Reviewed verified by ORBi |
 | KILLCOYNE, S., & DEL SOL MESA, A. (2015). Identification of large-scale genomic variation in cancer genomes using in silico reference models. Nucleic Acids Research. doi:10.1093/nar/gkv828 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., & Mummery, C. (2015). Transcriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells. Development. Peer reviewed |
 | Rodriguez, A.* , CRESPO, I.* , ANDROSOVA, G., & DEL SOL MESA, A. (09 June 2015). Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET. PLoS ONE, 10 (6), 0127216. doi:10.1371/journal.pone.0127216 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | DEL SOL MESA, A. (2015). Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET. PLoS ONE. Peer Reviewed verified by ORBi |
 | Grosse-Wilde, A., FOUQUIER DU0027HÉROUËL, A., McIntosh, E., ERTAYLAN, G., SKUPIN, A., Kuestner, R. E., DEL SOL MESA, A., Walters, K.-A., & Huang, S. (28 May 2015). Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival. PLoS ONE, 10 (5), 0126522. doi:10.1371/journal.pone.0126522 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2015). The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs. Nucleic Acids Research. Peer Reviewed verified by ORBi |
 | NICKLAS, S., OKAWA, S., HILLJE, A.-L., GONZALEZ CANO, L., DEL SOL MESA, A., & SCHWAMBORN, J. C. (2015). The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs. Nucleic Acids Research. doi:10.1093/nar/gkv138 Peer Reviewed verified by ORBi |
 | Bahnassawy, L. A., Perumal, T., GONZALEZ CANO, L., HILLJE, A.-L., Taher, L., Makalowski, W., Suzuki, Y., Fuellen, G., DEL SOL MESA, A., & SCHWAMBORN, J. C. (2015). TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability. Scientific Reports. doi:10.1038/srep13456 Peer Reviewed verified by ORBi |
 | OKAWA, S., ESPINOSA ANGARICA, V., Lemischka, I., Moore, K., & DEL SOL MESA, A. (2015). A differential network analysis approach for lineage specifier prediction in stem cell subpopulations. NPJ Systems Biology and Applications. doi:10.1038/npjsba.2015.12 Peer reviewed |
 | ERTAYLAN, G., OKAWA, S., SCHWAMBORN, J. C., & DEL SOL MESA, A. (2014). Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain. Frontiers in Cellular Neuroscience. doi:10.3389/fncel.2014.00437 Peer Reviewed verified by ORBi |
 | Liu, G.-H., Suzuki, K., Li, M., Qu, J., Montserrat, N., Tarantino, C., Gu, Y., Yi, F., Xu, X., Zhang, W., Ruiz, S., Plongthongkum, N., Zhang, K., Masuda, S., Nivet, E., Tsunekawa, Y., Soligalla, R. D., Goebl, A., Aizawa, E., ... Izpisua Belmonte, J. C. (2014). Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs. Nature Communications, 5, 4330. doi:10.1038/ncomms5330 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2014). A population shift view of cellular reprogramming. Stem Cells. Peer reviewed |
 | DEL SOL MESA, A. (2014). sorting signal targeting mRNA into hepatic extracellular vesicles. RNA Biology. Peer Reviewed verified by ORBi |
 | Fujita, K. A., OSTASZEWSKI, M., Matsuoka, Y., Ghosh, S., GLAAB, E., TREFOIS, C., CRESPO, I., PERUMAL, T. M., JURKOWSKI, W., ANTONY, P., DIEDERICH, N., BUTTINI, M., Kodama, A., SATAGOPAM, V., EIFES, S., DEL SOL MESA, A., SCHNEIDER, R., Kitano, H., & BALLING, R. (2014). Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map. Molecular Neurobiology. doi:10.1007/s12035-013-8489-4 Peer Reviewed verified by ORBi |
 | KILLCOYNE, S., & DEL SOL MESA, A. (2014). FIGG: Simulating populations of whole genome sequences for heterogeneous data analyses. BMC Bioinformatics, 15 (1). doi:10.1186/1471-2105-15-149 Peer Reviewed verified by ORBi |
 | Vegh, M. J., Rausell, A., Loos, M., Heldring, C. M., JURKOWSKI, W., van Nierop, P., Paliukovich, I., Li, K. W., DEL SOL MESA, A., Smit, A. B., Spijker, S., & van Kesteren, R. E. (2014). Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline. Molecular and Cellular Proteomics. doi:10.1074/mcp.M113.032086 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2014). Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein and Cell. doi:10.1007/s13238-013-0016-x Peer Reviewed verified by ORBi |
 | OSTASZEWSKI, M., Fujita, K., Matsuoka, Y., Ghosh, S., GLAAB, E., TREFOIS, C., CRESPO, I., PERUMAL, T. M., JURKOWSKI, W., ANTONY, P., DIEDERICH, N., BUTTINI, M., KOLODKIN, A., Kodama, A., SATAGOPAM, V., BIRYUKOV, M., EIFES, S., DEL SOL MESA, A., SCHNEIDER, R., ... BALLING, R. (09 March 2013). The Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways [Poster presentation]. The 11th International Conference on Alzheimer's & Parkinson's Diseases, Florence, Italy. |
 | DEL SOL MESA, A. (2013). Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networks. BMC Systems Biology. Peer Reviewed verified by ORBi |
 | CRESPO, I., KRISHNA, A., LE BÉCHEC, A., DEL SOL MESA, A., & *Co-first-authors. (2013). Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states. Nucleic Acids Research, 41 (1), 8. doi:10.1093/nar/gks785 Peer Reviewed verified by ORBi |
 | CRESPO, I., & DEL SOL MESA, A. (2013). A general strategy for cellular reprogramming: the importance of transcription factor cross-repression. Stem Cells. doi:10.1002/stem.1473 Peer Reviewed verified by ORBi |
TREFOIS, C., Fujita, A. K., OSTASZEWSKI, M., Matsuoka, Y., Ghosh, S., GLAAB, E., Crespo, I., Perumal, T. M., Jurkowski, W., ANTONY, P., DIEDERICH, N., BUTTINI, M., Kodama, A., SATAGOPAM, V., EIFES, S., DEL SOL MESA, A., SCHNEIDER, R., Kitano, H., & BALLING, R. (August 2012). Constructing a comprehensive map of Parkinson’s disease to elucidate underlying mechanisms of its multifaceted molecular pathology [Poster presentation]. The 13th International Conference on Systems Biology. |
 | MOES, M., LE BÉCHEC, A., CRESPO, I., LAURINI, C., HALAVATYI, A., Vetter, G., DEL SOL MESA, A., & Friederich, A. (2012). A Novel Network Integrating a miRNA-203/SNAI1 Feedback Loop which Regulates Epithelial to Mesenchymal Transition. PLoS ONE, 7 (4), 35440. doi:10.1371/journal.pone.0035440 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2012). PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells. Molecular Systems Biology. Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A. (2012). Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human. PLoS ONE. Peer Reviewed verified by ORBi |
 | CRESPO, I., RUMP, K., JURKOWSKI, W., Kitano, H., & DEL SOL MESA, A. (2012). Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease. BMC Systems Biology, 6 (132). doi:10.1186/1752-0509-6-132 Peer Reviewed verified by ORBi |
 | OSTASZEWSKI, M., EIFES, S., & DEL SOL MESA, A. (2012). Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human. PLoS ONE, 7 (5), 36488. doi:10.1371/journal.pone.0036488 Peer Reviewed verified by ORBi |
 | JURKOWSKI, W., ROOMP, K., CRESPO, I., SCHNEIDER, J., & DEL SOL MESA, A. (2011). PPARγ population shift produces disease-related changes in molecular networks associated with metabolic syndrome. Cell Death and Disease, 2 (8), 192. doi:10.1038/cddis.2011.74 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., BALLING, R., HOOD, L., & GALAS, D. J. (2010). Diseases as network perturbations. Current Opinion in Biotechnology, 21 (4), 566-571. doi:10.1016/j.copbio.2010.07.010 Peer Reviewed verified by ORBi |
 | Carbonell, P., Nussinov, R., & DEL SOL MESA, A. (2009). Energetic determinants of protein binding specificity: insights into protein interaction networks. Proteomics, 9 (7), 1744-53. doi:10.1002/pmic.200800425 Peer Reviewed verified by ORBi |
 | DEL SOL MESA, A., Fujihashi, H., Amoros, D., & Nussinov, R. (2009). Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Molecular Systems Biology, 2. Peer Reviewed verified by ORBi |
 | Tsai, C. J., DEL SOL MESA, A., & Nussinov, R. (2009). Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Molecular Biosystems, 5 (3), 207-16. doi:10.1039/b819720b Peer Reviewed verified by ORBi |
 | Carbonell, P., & DEL SOL MESA, A. (2009). Methyl side-chain dynamics prediction based on protein structure. Bioinformatics, 25 (19), 2552-8. doi:10.1093/bioinformatics/btp463 Peer reviewed |
 | DEL SOL MESA, A., Tsai, C.-J., Ma, B., & Nussinov, R. (2009). The origin of Allosteric Modulation: Multiple Pre-existing Pathways Selection. Structure, 17 (8), 1042-1050. Peer reviewed |
Tsai, C.-J., DEL SOL MESA, A., & Nussinov, R. (2008). Allostery: absence of a change in shape does not imply that allostery is not at play. Journal of Molecular Biology, 378 (1), 1-11. doi:10.1016/j.jmb.2008.02.034 Peer Reviewed verified by ORBi |
Hu, Z., Bowen, D., Southerland, W. M., DEL SOL MESA, A., Pan, Y., Nussinov, R., & Ma, B. (12 June 2007). Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Computational Biology, 3 (6), 117. doi:10.1371/journal.pcbi.0030117 Peer Reviewed verified by ORBi |
DEL SOL MESA, A., & Carbonell, P. (13 April 2007). The modular organization of domain structures: insights into protein-protein binding. PLoS Computational Biology, 3 (12), 239. doi:10.1371/journal.pcbi.0030239 Peer Reviewed verified by ORBi |
DEL SOL MESA, A., Arauzo-Bravo, M. J., Amoros, D., & Nussinov, R. (12 April 2007). Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages. Genome biology, 8 (5), 92. doi:10.1186/gb-2007-8-5-r92 Peer reviewed |
DEL SOL MESA, A., Fujihashi, H., Amoros, D., & Nussinov, R. (11 July 2006). Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Science: A Publication of the Protein Society, 15 (9), 2120-8. doi:10.1110/ps.062249106 Peer reviewed |
DEL SOL MESA, A., Fujihashi, H., Amoros, D., & Nussinov, R. (13 May 2006). Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Molecular Systems Biology, 2, 2006.0019. doi:10.1038/msb4100063 Peer Reviewed verified by ORBi |
Carro, A., Tress, M., de Juan, D., Pazos, F., Lopez-Romero, P., DEL SOL MESA, A., Valencia, A., & Rojas, A. M. (13 March 2006). TreeDet: a web server to explore sequence space. Nucleic Acids Research, 34 (Web Server issue), 110-5. doi:10.1093/nar/gkl203 Peer Reviewed verified by ORBi |
de Juan, D., Mellado, M., Rodriguez-Frade, J. M., Hernanz-Falcon, P., Serrano, A., DEL SOL MESA, A., Valencia, A., Martinez-A, C., & Rojas, A. M. (11 March 2005). A framework for computational and experimental methods: identifying dimerization residues in CCR chemokine receptors. Bioinformatics, 21 Suppl 2, 13-8. doi:10.1093/bioinformatics/bti1101 Peer reviewed |
DEL SOL MESA, A., & O'Meara, P. (2005). Small-world network approach to identify key residues in protein-protein interaction. Proteins, 58 (3), 672-82. doi:10.1002/prot.20348 Peer Reviewed verified by ORBi |
DEL SOL MESA, A., Fujihashi, H., & O'Meara, P. (2005). Topology of small-world networks of protein-protein complex structures. Bioinformatics, 21 (8), 1311-5. doi:10.1093/bioinformatics/bti167 Peer reviewed |
Hernanz-Falcon, P., Rodriguez-Frade, J. M., Serrano, A., Juan, D., DEL SOL MESA, A., Soriano, S. F., Roncal, F., Gomez, L., Valencia, A., Martinez-A, C., & Mellado, M. (2004). Identification of amino acid residues crucial for chemokine receptor dimerization. Nature immunology, 5 (2), 216-23. doi:10.1038/ni1027 Peer reviewed |
DEL SOL MESA, A., Pazos, F., & Valencia, A. (2003). Automatic methods for predicting functionally important residues. Journal of molecular biology, 326 (4), 1289-302. doi:10.1016/S0022-2836(02)01451-1 Peer reviewed |
DEL SOL MESA, A. (2002). Connection between type B (or C) and F factorizations and construction of algebras. Journal of Physics: A Mathematical and General. doi:10.1088/0305-4470/35/12/310 Peer reviewed |
DEL SOL MESA, A. (2000). Connection between type A and E factorizations and construction of satellite algebras. Journal of Physics: A Mathematical and General. doi:10.1088/0305-4470/33/22/309 Peer reviewed |
DEL SOL MESA, A. (1999). A class of exactly solvable matrix models. Journal of Mathematical Chemistry. doi:10.1023/A:1019109222477 Peer Reviewed verified by ORBi |
DEL SOL MESA, A. (1998). Generalized Morse potential: Symmetry and satellite potentials. Journal of Physics: A Mathematical and General. doi:10.1088/0305-4470/31/1/028 Peer reviewed |
DEL SOL MESA, A. (1997). Supermultiplicity and the relativistic coulomb problem with arbitrary spin. Foundations of Physics. doi:10.1007/BF02551438 Peer reviewed |
DEL SOL MESA, A. (1997). Ordering problems in fermionic relativistic quantum mechanics. International Journal of Modern Physics A. doi:10.1142/S0217751X97000359 Peer Reviewed verified by ORBi |
DEL SOL MESA, A. (1996). Fermionic anomalies in quantum-mechanical relativistic problems. Il Nuovo Cimento. Peer reviewed |
DEL SOL MESA, A. (1996). On some solutions of the Dirac equation. Journal of Physics: A Mathematical and General. doi:10.1088/0305-4470/29/11/016 Peer reviewed |
DEL SOL MESA, A. (1996). The dirac oscillator of arbitrary spin. Journal of Physics: A Mathematical and General. doi:10.1088/0305-4470/29/14/039 Peer reviewed |
DEL SOL MESA, A. (1995). Symmetry Lie algebra of the two body systems with a Dirac oscillator interaction. Revista Mexicana de Física. Peer reviewed |
DEL SOL MESA, A. (1994). On some aspects of a relativistic problem. Canadian Journal of Physics. Peer Reviewed verified by ORBi |
DEL SOL MESA, A. (1994). Relationship between different approaches to the relativistic two body problem. Journal of Physics: A Mathematical and General. Peer reviewed |
DEL SOL MESA, A. (1993). Quantum groups and the recovery of the U(3) symmetry in the hamiltonian of the nuclear shell model. Journal of Physics: A Mathematical and General. doi:10.1088/0305-4470/26/5/033 Peer reviewed |
DEL SOL MESA, A. (1992). Transformation from U(3) to a pseudo U(3) basis of the matrix representation of a deformed Nilsson hamiltonian. Revista Mexicana de Física. Peer reviewed |