Publications

(For a full list see below)

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Blomquist, M. R. et al. Glioblastoma resistance to EGFR antibody-drug conjugate is driven by transcriptional reprogramming and TEK-induced EGFR suppression. J Transl Med 23, 1153 (2025). Cite
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De Falco, A. et al. Knowledge-informed multimodal cfDNA analysis improves sensitivity and generalization in cancer detection. Preprint at https://doi.org/10.1101/2025.10.20.683167 (2025). Cite
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Ciervo, E. et al. Transposable Elements and Homotypic Niches Drive Immune Dynamics and Resistance in Melanoma Epigenetic-based immunotherapy. Preprint at https://doi.org/10.1101/2025.10.09.679175 (2025). Cite
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Anichini, A. et al. Integrated multi-omics profiling reveals the role of the DNA methylation landscape in shaping biological heterogeneity and clinical behaviour of  metastatic melanoma. J Exp Clin Cancer Res 44, 212 (2025). Cite
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Kołodziejczak-Guglas, I. et al. Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets. Cell Genom 5, 100851 (2025). Cite
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Martins Rodrigues, F. et al. Precision proteogenomics reveals pan-cancer impact of germline variants. Cell 188, 2312-2335.e26 (2025). Cite
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Yan, F. et al. Genome-wide methylome modeling via generative AI incorporating long- and short-range interactions. Sci. Adv. 11, eadt4152 (2025). Cite
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Guo, Y. et al. A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector. Nat Protoc https://doi.org/10.1038/s41596-025-01149-5 (2025) doi:10.1038/s41596-025-01149-5. Cite
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Seetharam, D. et al. Activating antiviral immune responses potentiates immune checkpoint inhibition in glioblastoma models. J Clin Invest 135, e183745 (2025). Cite
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Lofiego, M. F. et al. DNA methylation status classifies pleural mesothelioma cells according to their immune profile: implication for precision epigenetic therapy. J Exp Clin Cancer Res 44, 58 (2025). Cite Download
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Floudas, C. S., Sarkizova, S., Ceccarelli, M. & Zheng, W. Leveraging mRNA technology for antigen based immuno-oncology therapies. J Immunother Cancer 13, e010569 (2025). Cite
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Guo, Y. et al. A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector. Nat Protoc 20, 2845–2864 (2025). Cite
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Migliozzi, S. et al. Restraint of cancer cell plasticity by spatial homotypic clustering. Cancer Cell S1535610825003666 (2025) http://doi.org/10.1016/j.ccell.2025.08.009. Cite
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Huyghe, N. et al. Impact of the tumor immune contexture in microsatellite-stable metastatic colorectal cancer treated with avelumab, cetuximab, and irinotecan. Cell Reports Medicine 6, 102201 (2025). Cite
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Huyghe, N. et al. Impact of the tumor immune contexture in microsatellite-stable metastatic colorectal cancer treated with avelumab, cetuximab, and irinotecan. Cell Reports Medicine 102201 (2025) http://doi.org/10.1016/j.xcrm.2025.102201. Cite
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Kołodziejczak-Guglas, I. et al. Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets. Cell Genomics 5, 100851 (2025). Cite
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Brandi, A. et al. MiDNE a tool for Multi-omics genes and drugs interactions discovery. Computational and Structural Biotechnology Journal 27, 4469–4475 (2025). Cite
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Scala, G. et al. MoNETA: MultiOmics Network Embedding for SubType Analysis. NAR Genomics and Bioinformatics 6, lqae141 (2024). Cite Download
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White, B. S. et al. Community assessment of methods to deconvolve cellular composition from bulk gene expression. Nat Commun 15, 7362 (2024). Cite
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Yan, F., Jiang, L., Chen, D., Ceccarelli, M. & Guo, Y. Reinventing gene expression connectivity through regulatory and spatial structural empowerment via principal node aggregation graph neural network. Nucleic Acids Research 52, e60–e60 (2024). Cite Download
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Yan, F., Jiang, L., Chen, D., Ceccarelli, M. & Guo, Y. Reinventing gene expression connectivity through regulatory and spatial structural empowerment via principal node aggregation graph neural network. Nucleic Acids Research 52, e60–e60 (2024). Cite
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Falco, M. et al. Identification and bioinformatic characterization of a serum miRNA signature for early detection of laryngeal squamous cell carcinoma. J Transl Med 22, 647 (2024). Cite
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Bertucci, F. et al. Mutational landscape of inflammatory breast cancer. J Transl Med 22, 374 (2024). Cite
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Wang, L. et al. Quantifying intra-tumoral genetic heterogeneity of glioblastoma toward precision medicine using MRI and a data-inclusive machine learning algorithm. PLoS ONE 19, e0299267 (2024). Cite Download
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Costa, M. C. et al. Identification of therapeutic targets in osteoarthritis by combining heterogeneous transcriptional datasets, drug-induced expression profiles, and known drug-target interactions. J Transl Med 22, 281 (2024). Cite Download
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Lofiego, M. F. et al. Epigenetic remodeling to improve the efficacy of immunotherapy in human glioblastoma: pre-clinical evidence for development of new immunotherapy approaches. J Transl Med 22, 223 (2024). Cite Download
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Mason, M. et al. A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer. J Transl Med 22, 190 (2024). Cite
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Cossu, A. M. et al. MiR-449a ANTAGONIZES EMT THROUGH IL-6-MEDIATED TRANS- SIGNALING IN LARYNGEAL SQUAMOUS CANCER. Molecular Therapy - Nucleic Acids 102140 (2024) http://doi.org/10.1016/j.omtn.2024.102140. Cite
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Petralia, F. et al. Pan-cancer proteogenomics characterization of tumor immunity. Cell S0092867424000643 (2024) http://doi.org/10.1016/j.cell.2024.01.027. Cite Download
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Feng, S. et al. Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution. Cell Reports Methods 4, 100708 (2024). Cite
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Ramsoomair, C. K., Ceccarelli, M., Heiss, J. D. & Shah, A. H. The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses. J Transl Med 21, 893 (2023). Cite Download
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Ramsoomair, C. K., Ceccarelli, M., Heiss, J. D. & Shah, A. H. The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses. J Transl Med 21, 893 (2023). Cite
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Hu, L. S. et al. Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures. Nat Commun 14, 6066 (2023). Cite Download
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Hu, L. S. et al. Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures. Nat Commun 14, 6066 (2023). Cite
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Noviello, T. M. R. et al. Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial. Nat Commun 14, 5914 (2023). Cite Download
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Mogenet, A. et al. Immunologic constant of rejection as a predictive biomarker of immune checkpoint inhibitors efficacy in non-small cell lung cancer. J Transl Med 21, 637 (2023). Cite Download
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Jethalia, M., Jani, S. P., Ceccarelli, M. & Mall, R. Pancancer network analysis reveals key master regulators for cancer invasiveness. J Transl Med 21, 558 (2023). Cite Download
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Ferraro, L., Scala, G., Cerulo, L., Carosati, E. & Ceccarelli, M. MOViDA: multiomics visible drug activity prediction with a biologically informed neural network model. Bioinformatics 39, btad432 (2023). Cite Download
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Besharat, Z. M. et al. Circulating miR-26b-5p and miR-451a as diagnostic biomarkers in medullary thyroid carcinoma patients. J Endocrinol Invest https://doi.org/10.1007/s40618-023-02115-2 (2023) doi:10.1007/s40618-023-02115-2. Cite
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De Falco, A., Caruso, F., Su, X.-D., Iavarone, A. & Ceccarelli, M. A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data. Nature Communications 14, 1074 (2023). Cite Download
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Rosaria Noviello, T. M. et al. Guadecitabine plus Ipilimumab in Unresectable Melanoma: Five-Year Follow-up and Correlation with Integrated, Multiomic Analysis in the NIBIT-M4 Trial. http://medrxiv.org/lookup/doi/10.1101/2023.02.09.23285227 (2023) http://doi.org/10.1101/2023.02.09.23285227. Cite Download
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Migliozzi, S. et al. Integrative multi-omics networks identify PKCδ and DNA-PK as master kinases of glioblastoma subtypes and guide targeted cancer therapy. Nat Cancer https://doi.org/10.1038/s43018-022-00510-x (2023) doi:10.1038/s43018-022-00510-x. Cite Download
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Simeone, I. & Ceccarelli, M. Pan-cancer onco-signatures reveal a novel mitochondrial subtype of luminal breast cancer with specific regulators. J Transl Med 21, 55 (2023). Cite Download
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McLaughlin, R. T. et al. Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning. npj Precis. Onc. 7, 4 (2023). Cite Download
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Feng, S. et al. Decomprolute: A Benchmarking Platform Designed for Multiomics-Based Tumor Deconvolution. http://biorxiv.org/lookup/doi/10.1101/2023.01.05.522902 (2023) http://doi.org/10.1101/2023.01.05.522902. Cite Download
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Wang, J. M. et al. Deep learning integrates histopathology and proteogenomics at a pan-cancer level. Cell Reports Medicine 101173 (2023) http://doi.org/10.1016/j.xcrm.2023.101173. Cite Download
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Liang, W.-W. et al. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin. Cancer Cell S1535610823002532 (2023) http://doi.org/10.1016/j.ccell.2023.07.013. Cite
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Li, Y. et al. Proteogenomic data and resources for pan-cancer analysis. Cancer Cell 41, 1397–1406 (2023). Cite Download
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Li, Y. et al. Pan-cancer proteogenomics connects oncogenic drivers to functional states. Cell 186, 3921-3944.e25 (2023). Cite Download
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Geffen, Y. et al. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation. Cell 186, 3945-3967.e26 (2023). Cite Download