Publications

(For a full list see below)

1.
Federico, A. et al. Integrated Network Pharmacology Approach for Drug Combination Discovery: A Multi-Cancer Case Study. Cancers 14, 2043 (2022). Cite Download
1.
Chan, S. et al. An anti-PD-1–GITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy. Nat Cancer (2022) http://doi.org/10.1038/s43018-022-00334-9. Cite Download
1.
Simeone, I. et al. Prediction and pan-cancer analysis of mammalian transcripts involved in target directed miRNA degradation. Nucleic Acids Research 50, 2019–2035 (2022). Cite Download
1.
D’Agostino, Y. et al. Loss of circadian rhythmicity in bdnf knock-out zebrafish larvae. iScience 104054 (2022) http://doi.org/10.1016/j.isci.2022.104054. Cite Download
1.
Saad, M. et al. Genetic predisposition to cancer across people of different ancestries in Qatar: a population-based, cohort study. The Lancet Oncology S147020452100752X (2022) http://doi.org/10.1016/S1470-2045(21)00752-X. Cite
1.
Bertucci, F. et al. Immunologic constant of rejection signature is prognostic in soft-tissue sarcoma and refines the CINSARC signature. J Immunother Cancer 10, e003687 (2022). Cite Download
1.
McLaughlin, R. T. et al. Attentive deep learning-based tumor-only somatic mutation classifier achieves high accuracy agnostic of tissue type and capture kit. http://biorxiv.org/lookup/doi/10.1101/2021.12.07.471513 (2021) doi:10.1101/2021.12.07.471513. Cite Download
1.
De Falco, A., Caruso, F. P., Su, X. D., Iavarone, A. & Ceccarelli, M. A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data. http://biorxiv.org/lookup/doi/10.1101/2021.11.20.469390 (2021) doi:10.1101/2021.11.20.469390. Cite Download
1.
Petralia, F. et al. BayesDeBulk: A Flexible Bayesian Algorithm for the Deconvolution of Bulk Tumor Data. http://biorxiv.org/lookup/doi/10.1101/2021.06.25.449763 (2021) doi:10.1101/2021.06.25.449763. Cite Download
1.
Mall, R. et al. Network-based identification of key master regulators associated with an immune-silent cancer phenotype. Briefings in Bioinformatics bbab168 (2021) http://doi.org/10.1093/bib/bbab168. Cite Download
1.
Paladino, A., D’Angelo, F., Noviello, T. M. R., Iavarone, A. & Ceccarelli, M. Structural Model for Recruitment of RIT1 to the LZTR1 E3 Ligase: Evidences from an Integrated Computational Approach. J. Chem. Inf. Model. acs.jcim.1c00296 (2021) http://doi.org/10.1021/acs.jcim.1c00296. Cite Download
1.
Caruso, F. P., Scala, G., Cerulo, L. & Ceccarelli, M. A review of COVID-19 biomarkers and drug targets: resources and tools. Briefings in Bioinformatics 22, 701–713 (2021). Cite Download
1.
Petrillo, F. et al. Dysregulation of Principal Cell miRNAs Facilitates Epigenetic Regulation of AQP2 and Results in Nephrogenic Diabetes Insipidus. J Am Soc Nephrol (2021) http://doi.org/10.1681/ASN.2020010031. Cite
1.
Di Munno, C. et al. Adaptive Thermogenesis Driving Catch-Up Fat Is Associated With Increased Muscle Type 3 and Decreased Hepatic Type 1 Iodothyronine Deiodinase Activities: A Functional and Proteomic Study. Front. Endocrinol. 12, 631176 (2021). Cite
1.
De Marco, C. et al. Genome-wide analysis of copy number alterations led to the characterisation of PDCD10 as oncogene in ovarian cancer. Translational Oncology 14, 101013 (2021). Cite Download
1.
Turan, T. et al. A balance score between immune stimulatory and suppressive microenvironments identifies mediators of tumour immunity and predicts pan-cancer survival. Br J Cancer 124, 760–769 (2021). Cite Download
1.
Sayaman, R. W. et al. Germline genetic contribution to the immune landscape of cancer. Immunity 54, 367-386.e8 (2021). Cite Download
1.
Garofano, L. et al. Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities. Nat Cancer (2021) http://doi.org/10.1038/s43018-020-00159-4. Cite Download
1.
Maio, M. et al. A vision of immuno-oncology: the Siena think tank of the Italian network for tumor biotherapy (NIBIT) foundation. J Exp Clin Cancer Res 40, 240 (2021). Cite Download
1.
Wang, L.-B. et al. Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell (2021) http://doi.org/10.1016/j.ccell.2021.01.006. Cite Download
1.
Remo, A. et al. Wnt (canonical and non canonical) pathways in Breast carcinoma with extensive vascular invasion and Inflammatory Breast Carcinoma. Pathology-Research and Practice 153347 (2021). Cite Download
1.
Pagano, M. et al. Mi-RNA-888-5p Is Involved in S-Adenosylmethionine Antitumor Effects in Laryngeal Squamous Cancer Cells. Cancers 12, 3665 (2020). Cite Download
1.
Blomquist, M. R. et al. Temporospatial genomic profiling in glioblastoma identifies commonly altered core pathways underlying tumor progression. Neurooncol Adv 2, vdaa078 (2020). Cite Download
1.
Noviello, T. M. R., Ceccarelli, F., Ceccarelli, M. & Cerulo, L. Deep learning predicts short non-coding RNA functions from only raw sequence data. PLoS Comput Biol 16, e1008415 (2020). Cite Download
1.
de Falco, A. et al. Adaptive One-Class gaussian processes allow accurate prioritization of oncology drug targets. Bioinformatics btaa968 (2020) http://doi.org/10.1093/bioinformatics/btaa968. Cite Download
1.
Caruso, F. P., Scala, Giovanni, Cerulo, L. & Ceccarelli, M. A review of COVID-19 biomarkers and drug targets: resources and tools. Briefings in Bioinformatics (2020) http://doi.org/10.1093/bib/bbaa328. Cite Download
1.
Caruso, F. P. et al. A map of tumor–host interactions in glioma at single-cell resolution. GigaScience 9, giaa109 (2020). Cite Download
1.
Noviello, T. M. R., Ceccarelli, M. & Cerulo, L. Deep learning predicts non-coding RNA functions from only raw sequence data. http://biorxiv.org/lookup/doi/10.1101/2020.05.27.118778 (2020) doi:10.1101/2020.05.27.118778. Cite Download
1.
Roelands, J. et al. Oncogenic states dictate the prognostic and predictive connotations of intratumoral immune response. J Immunother Cancer 8, (2020). Cite Download
1.
Sayaman, R. W. et al. Germline genetic contribution to the immune landscape of cancer. http://biorxiv.org/lookup/doi/10.1101/2020.01.30.926527 (2020) doi:10.1101/2020.01.30.926527. Cite Download
1.
Tagliaferri, D. et al. Retinoic Acid Induces Embryonic Stem Cells (ESCs) Transition to 2 Cell-Like State Through a Coordinated Expression of Dux and Duxbl1. Front. Cell Dev. Biol. 7, 385 (2020). Cite Download
1.
Alexander, J. et al. Multimodal single‐cell analysis reveals distinct radioresistant stem‐like and progenitor cell populations in murine glioma. Glia 68, 2486–2502 (2020). Cite Download
1.
Sa, J. K. et al. Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma. Genome Biol 21, 216 (2020). Cite Download
1.
Dezső, Z. & Ceccarelli, M. Machine learning prediction of oncology drug targets based on protein and network properties. BMC Bioinformatics 21, 104 (2020). Cite Download
1.
Mauriello, A. et al. High Somatic Mutation and Neoantigen Burden Do Not Correlate with Decreased Progression-Free Survival in HCC Patients not Undergoing Immunotherapy. Cancers (Basel) 11, (2019). Cite Download
1.
Caruso, F. P. et al. A MAP of tumor-host interactions in glioma at single cell resolution. http://biorxiv.org/lookup/doi/10.1101/827758 (2019) doi:10.1101/827758. Cite Download
1.
Di Iorio, B. R. et al. Treatment of metabolic acidosis with sodium bicarbonate delays progression of chronic kidney disease: the UBI Study. J. Nephrol. (2019) http://doi.org/10.1007/s40620-019-00656-5. Cite Download
1.
Guerriero, I. et al. Exploring the Molecular Crosstalk between Pancreatic Bud and Mesenchyme in Embryogenesis: Novel Signals Involved. Int J Mol Sci 20, (2019). Cite Download
1.
Bedognetti, D. et al. Toward a comprehensive view of cancer immune responsiveness: a synopsis from the SITC workshop. J Immunother Cancer 7, 131 (2019). Cite Download
1.
Roelands, J. et al. Genomic landscape of tumor-host interactions with differential prognostic and predictive connotations. http://biorxiv.org/lookup/doi/10.1101/546069 (2019) doi:10.1101/546069. Cite Download
1.
Silvestri, E. et al. 3,5-Diiodo-L-Thyronine Exerts Metabolically Favorable Effects on Visceral Adipose Tissue of Rats Receiving a High-Fat Diet. Nutrients 11, 278 (2019). Cite Download
1.
Zhang, J. et al. The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival. Communications Biology 2, (2019). Cite Download
1.
Giordano, G. et al. JAK/Stat5-mediated subtype-specific lymphocyte antigen 6 complex, locus G6D (LY6G6D) expression drives mismatch repair proficient colorectal cancer. Journal of Experimental & Clinical Cancer Research 38, (2019). Cite Download
1.
Monaco, G. et al. RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types. Cell Reports 26, 1627-1640.e7 (2019). Cite Download
1.
D’Angelo, F. et al. The molecular landscape of glioma in patients with Neurofibromatosis 1. Nat Med 25, 176–187 (2019). Cite Download
1.
Bertucci, F. et al. The immunologic constant of rejection classification refines the prognostic value of conventional prognostic signatures in breast cancer. British Journal of Cancer (2018) http://doi.org/10.1038/s41416-018-0309-1. Cite Download
1.
Ferreira, L. A. M. et al. Circulating microRNAs expression profile in newly diagnosed and imatinib treated chronic phase – chronic myeloid leukemia. Leukemia & Lymphoma 1–7 (2018) http://doi.org/10.1080/10428194.2018.1499905. Cite
1.
Silva, T. C. et al. TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data. F1000Research 7, 439 (2018). Cite Download
1.
Mall, R., Ullah, E., Kunji, K., Ceccarelli, M. & Bensmail, H. An unsupervised disease module identification technique in biological networks using novel quality metric based on connectivity, conductance and modularity. F1000Research 7, 378 (2018). Cite Download
1.
Silvestri, E. et al. 3,5-Diiodo-L-Thyronine Affects Structural and Metabolic Features of Skeletal Muscle Mitochondria in High-Fat-Diet Fed Rats Producing a Co-adaptation to the Glycolytic Fiber Phenotype. Frontiers in Physiology 9, (2018). Cite