Publications

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

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

Roelands, J. et al. Oncogenic states dictate the prognostic and predictive connotations of intratumoral immune response. J Immunother Cancer 8, (2020). Cite Download

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

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

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

Dezső, Z. & Ceccarelli, M. Machine learning prediction of oncology drug targets based on protein and network properties. BMC Bioinformatics 21, 104 (2020). Cite Download

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

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

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

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

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

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

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

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

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

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

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

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

Silva, T. C. et al. TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data. F1000Research 7, 439 (2018). Cite Download

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

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

Mall, R. et al. RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes. Nucleic Acids Research (2018) http://doi.org/10.1093/nar/gky015. Cite Download

Frattini, V. et al. A metabolic function of FGFR3-TACC3 gene fusions in cancer. Nature 553, 222–227 (2018). Cite Download

Yuan, J. et al. Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Genome Medicine 10, (2018). Cite Download

Rosenberg, S. et al. A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas. Nature Communications 9, (2018). Cite Download

Pascarella, A. et al. DNAJC17 is localized in nuclear speckles and interacts with splicing machinery components. Scientific Reports 8, (2018). Cite Download

Angelova, M. et al. Evolution of Metastases in Space and Time under Immune Selection. Cell (2018) http://doi.org/10.1016/j.cell.2018.09.018. Cite

De Marco, C. et al. Specific gene expression signatures induced by the multiple oncogenic alterations that occur within the PTEN/PI3K/AKT pathway in lung cancer. PLOS ONE 12, e0178865 (2017). Cite

Silva, T. C. et al. TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data. (2017) http://doi.org/10.1101/147496. Cite Download

Mall, R. et al. Differential Community Detection in Paired Biological Networks. (2017) http://doi.org/10.1101/147538. Cite

Roelands, J. et al. A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification. F1000Research 6, 296 (2017). Cite Download

Pancione, M. et al. Emerging insight into MAPK inhibitors and immunotherapy in colorectal cancer. Curr. Med. Chem. (2017) http://doi.org/10.2174/0929867324666170227114356. Cite

Hendrickx, W. et al. Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis. OncoImmunology e1253654 (2017) http://doi.org/10.1080/2162402X.2016.1253654. Cite

Ventola, G. M. M. et al. Identification of long non-coding transcripts with feature selection: a comparative study. BMC Bioinformatics 18, (2017). Cite Download

Mall, R., Cerulo, L., Bensmail, H., Iavarone, A. & Ceccarelli, M. Detection of statistically significant network changes in complex biological networks. BMC Systems Biology 11, (2017). Cite

Mall, R. et al. RGBM: Regularized Gradient Boosting Machines For The Identification of Transcriptional Regulators Of Discrete Glioma Subtypes. bioRxiv (2017) http://doi.org/10.1101/132670. Cite

Porreca, I. et al. Pesticide toxicogenomics across scales: in vitro transcriptome predicts mechanisms and outcomes of exposure in vivo. Scientific Reports 6, 38131 (2016). Cite

Agnihotri, S. et al. The genomic landscape of schwannoma. Nat. Genet. 48, 1339–1348 (2016). Cite

Petrizzo, A. et al. Identification and Validation of HCC-specific Gene Transcriptional Signature for Tumor Antigen Discovery. Sci Rep 6, 29258 (2016). Cite

Silva, T. C. et al. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages. F1000Research 5, 1542 (2016). Cite

Colaprico, A. et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 44, e71 (2016). Cite

Bedognetti, D., Hendrickx, W., Ceccarelli, M., Miller, L. D. & Seliger, B. Disentangling the relationship between tumor genetic programs and immune responsiveness. Curr. Opin. Immunol. 39, 150–158 (2016). Cite

Ciccarelli, M. et al. The possible role of chromosome X variability in hypertensive familiarity. J Hum Hypertens (2016) http://doi.org/10.1038/jhh.2016.9. Cite

Ceccarelli, M. et al. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell 164, 550–563 (2016). Cite

Tagliaferri, D. et al. Retinoic Acid Specifically Enhances Embryonic Stem Cell Metastate Marked by Zscan4. PLoS ONE 11, e0147683 (2016). Cite

Porreca, I. et al. ‘Stockpile’ of Slight Transcriptomic Changes Determines the Indirect Genotoxicity of Low-Dose BPA in Thyroid Cells. PLoS ONE 11, e0151618 (2016). Cite

Malanga, D. et al. The Akt1/IL-6/STAT3 pathway regulates growth of lung tumor initiating cells. Oncotarget (2015) http://doi.org/10.18632/oncotarget.5626. Cite

Anjum, S., Morganella, S., D’Angelo, F., Iavarone, A. & Ceccarelli, M. VEGAWES: variational segmentation on whole exome sequencing for copy number detection. BMC Bioinformatics 16, 315 (2015). Cite

Giordano, G. et al. Cancer-related CD15/FUT4 overexpression decreases benefit to agents targeting EGFR or VEGF acting as a novel RAF-MEK-ERK kinase downstream regulator in metastatic colorectal cancer. J. Exp. Clin. Cancer Res. 34, 108 (2015). Cite