Role
Dr D’Andrea is a Lecturer in Bioinformatics at the School of Science and Technology.
He is equally responsible for research and teaching in interdisciplinary fields of bioinformatics, genomics and computational biology.
Career overview
Dr D’Andrea holds a Master's degree from the Federico II University of Naples in Computer Science and a Ph.D. degree from the Sapienza University of Rome in Bioinformatics, obtained within the Ph.D. program in Biology and Molecular Medicine. Additionally, he has five years of experience working as a Research Associate at Imperial College and three years as a Senior Research Associate at the MRC Centre for Neuropsychiatric Genetics and Genomics in Cardiff University. During his tenure, Daniel collaborated with Takeda Pharmaceutical Company Limited to identify potential molecular targets for therapeutic intervention in schizophrenia and other psychiatric disorders using high-throughput data analysis on complex biological data.
Research areas
Daniel's background is multidisciplinary, encompassing strong programming and data analysis skills, along with training in statistics, data science, and molecular biology. He has a keen interest in applying bioinformatic approaches to biomedical problems and possesses extensive experience with cutting-edge techniques such as bulk/single-cell high-throughput next-generation sequencing, multiomics data analysis and integration, translational medicine, and targeted therapies.
His research interests focus on three main areas: (1) identifying mechanistic insights through data analysis and interpretation of omics data to understand the mechanisms of complex biological systems and relevant changes affecting complex diseases, (2) translating integrative genomics and transcriptomics analyses on high-throughput data for therapeutic discovery to identify potential targets impacting diseases, and (3) designing and applying innovative computational/statistical algorithms to enhance the analysis of high-throughput experiments on heterogeneous and complex biological data.
Sponsors and collaborators
- Dr. D. Capece (L'Aquila University), to progress the target validation of CES1 for improving the treatment of aggressive colorectal carcinoma.
- Dr. P. Nistico’ (Regina Elena National Institute in Rome), to investigate the role of hMENA as a key regulator of tumour cell-cancer associated fibroblasts.
- Dr. A. Pocklington (Cardiff University), to identify potential molecular targets for therapeutic intervention in schizophrenia and other psychiatric disorders.
- Dr. E. Shin (Keele University), to investigate the role of genetic risk factors common to several neurodevelopmental disorders in cortical interneuron development and function.
- Prof. G. Franzoso (Imperial College London), to give the bioinformatic support for the clinical trial progression of a new drug for Multiple Myeloma and Diffuse Large B-Cell Lymphoma.
- Dr. M. Fedorova (University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden), to identify main lipid (sub)classes undergoing depot/phenotype specific remodelling.
- Dr. Antonysunil at Nottingham Trent University, to investigate the relationships between secreted micro-RNAs from adipose in low B12 and lipid accumulation in hepatocytes.
- Dr. J. Rosati (IRCCS-Mendel Institute in Rome), to study the role of RAI1 gene in lipid metabolism and autophagy in patients affected by Smith-Magenis syndrome.
- Prof Checquolo at Sapienza University of Rome, to investigate new potential biomarkers predictive of PT-response in high grade serous ovarian cancer patients.
- Prof. F. Zazzeroni (L'Aquila University), to investigate the clinical effects of the axis NF-кB/GLI1 in Prostate cancer.
- Prof M. Tripodi (Sapienza University of Rome) to investigate the impact of RNA-binding proteins on cell-to-cell communication in epithelial-to-mesenchymial transition.
Publications
- M. Hatziapostolou, M. Koutsioumpa, A. Zaitoun, C.Polytarchou, M. Edderkaoui, S. Mahurkar-Joshi, J. Vadakekolathu, D. D’Andrea, et al., Promoter methylation leads to Hepatocyte Nuclear Factor 4A loss and pancreatic cancer aggressiveness. in Press on Gastro Hep Advances
- F. Di Modugno, A. Di Carlo, S. Spada, B. Palermo, D. D’Andrea, et al., and P Nistic`o. Tumoral and stromal hMENA isoforms impact tertiary lymphoid structure localization in lung cancer and predict immunocheckpoint blockade response in cancer patients. eBiomedicine, 101, 2024
- P. Trono, A. Tocci, B. Palermo, D. D’Andrea, et al., and P. Nistic`o. hMENA isoforms regulate cancer intrinsic type I IFN signaling and extrinsic mechanisms of resistance to immune checkpoint blockade in NSCLC. Journal for ImmunoTherapy of Cancer, 11(e006913), 2023
- B. Palermo, O. Franzese, D. D’Andrea, et al., and P. Nistic`o. hCD28-PD1 coexpression: dual impact on CD8+ T cells in peripheral blood and tumor tissue, and its significance in nsclc patients survival and ICB response. Journal of Experimental and Clinical Cancer Research, 42(1):287, 2023
- E. Turco, A. Giovenale, L. Sireno, D. D’Andrea, et al., and J. Rosati. Retinoic acid induced 1 gene haploinsufficiency alters lipid metabolism and causes autophagy defects in Smith-Magenis syndrome. Cell Death Dis, 13(11):981, 2022.
- D. Vecchiotti, D. Verzella, D. D’Andrea, et al., and F. Zazzeroni. Elevated NFkB/SHh/GLI1 signature denotes a worse prognosis and represent a novel potential therapeutic target in advanced prostate cancer. Cells, 11(13):2118, 2022.
- B. Sanders, D. D’Andrea, MO. Collins, E. Rees, et al., AJ. Pocklington, and E. Shin. Transcriptional programs regulating neuronal differentiation are disrupted in dlg2 knockout human embryonic stem cells and enriched for schizophrenia and related disorders risk variants. Nature Communication, 13(27), 2022.
- M. Watanabe, R. Risi, MA. Tafuri, V. Silvestri, D. D’Andrea, et al., and L. Gnessi. Bone density and genomic analysis unfold cold adaptation mechanisms of extinct inhabitants of tierra del fuego. Scientific Reports, 2021.
- D. Capece*, D. D’Andrea*, and et al. Enhanced triacylglycerol catabolism by carboxylesterase 1 promotes aggressive colorectal carcinoma. Journal of Clinical Investigation, 2021.
- R. Melchionna, S. Spada, F. Di Modugno, D. D’Andrea, and et al. The actin modulator hMENA regulates GAS 6- AXL axis and pro-tumor cancer/stromal cell cooperation. EMBO reports, 2020.
- L. Tornatore*, D. Capece*, D. D’Andrea*, and et al. Preclinical toxicology and safety pharmacology of the first-in-class GADD45β/MMK7 inhibitor and clinical candidate, DTP3. Toxicology Reports, 2019.
- L. Tornatore*, D. Capece*, D. D’Andrea*, and et al. Clinical proof of concept for a safe and effective NF-κB-targeting strategy in multiple myeloma. British Journal of Haematology, 2019.
- D. Capece, D. D’Andrea, and et al. Turning an old GADDget into a troublemaker. Cell Death and Differentiation, 2018.
- Z.M. Besharat, L. Abballe, F. Cicconardi, A. Bhutkar, L. Grassi, L. Le Pera, M. Moretti, M. Chinappi, D. D’Andrea, and et al.. Foxm1 controls a pro-stemness microRNA network in neural stem cells. Scientific Reports, 2018.
- J. Bennett, D. Capece, F. Begalli, D. Verzella, D. D’Andrea, L. Tornatore, and G. Franzoso. NF-κB in the crosshairs: Rethinking an old riddle. International Journal of Biochemistry and Cell Biology, 2018.
- D. Verzella, J. Bennett, M. Fischietti, A.K. Thotakura, C. Recordati, F. Pasqualini, D. Capece, D. Vecchiotti, D. D’Andrea, and et al. GADD45β loss ablates innate immunosuppression in cancer. Cancer Research, 2018.
- F. Begalli, J. Bennett, D. Capece, D. Verzella, D. D’Andrea, L. Tornatore, and G. Franzoso. Unlocking the NF-κB Conundrum: Embracing complexity to achieve specificity. Biomedicines, 2017.
- F. Guerrieri, L. Belloni, D. D’Andrea, and et al. Genome-wide identification of direct HBx genomic targets. BMC Genomics, 2017.
- Y. Jiang, T.R. Oron, W. T. Clark, A. R. Bankapur, D. D’Andrea, and et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome biology, 2016.
- B. Monastyrskyy, D. D’Andrea, K. Fidelis, A. Tramontano, and A. Kryshtafovych. New encouraging developments in contact prediction: Assessment of the CASP11 results. Proteins: Structure, Function and Bioinformatics, 2015.
- B. Fazi, A. Felsani, L. Grassi, A. Moles, D. D’Andrea, et al.. The transcriptome and miRNome profiling of glioblastoma tissues and peritumoral regions highlights molecular pathways shared by tumors and surrounding areas and reveals differences between short-term and long-term survivors. Oncotarget, 2015.
- M. Ballarino, V. Cazzella, D. D’Andrea, and et al. Novel long noncoding RNAs (lncRNAs) in myogenesis: a miR-31 overlapping lncRNA transcript controls myoblast differentiation. Molecular and cellular biology, 2015.
- M. Domina, V. Lanza Cariccio, S. Benfatto, D. D’Aliberti, M. Venza, E. Borgogni, F. Castellino, C. Biondo, D. D’Andrea, et al.. Rapid Profiling of the Antigen Regions Recognized by Serum Antibodies Using Massively Parallel Sequencing of Antigen-Specific Libraries. PloS one, 2014.
- L. Tornatore, A. Sandomenico, D. Raimondo, C. Low, A. Rocci, C. Tralau-Stewart, D. Capece, D. D’Andrea, and et al. Cancer-Selective Targeting of the NF-κB Survival Pathway with GADD45β/MKK7 Inhibitors. Cancer Cell, 2014.
- B. Monastyrskyy*, D. D’Andrea*, and et al. Evaluation of residue-residue contact prediction in CASP10. Proteins, 2014.
- D. D’Andrea, L. Grassi, M. Mazzapioda, and A. Tramontano. FIDEA: a server for the functional interpretation of differential expression analysis. Nucleic acids research, 2013.
- A. Nardone, S. Corvigno, A. Brescia, D. D’Andrea, G. Limite, and B. M. Veneziani. Long-term cultures of stem/progenitor cells from lobular and ductal breast carcinomas under non-adherent conditions. Cytotechnology, 2011.
- R. Amato, M. Pinelli, D. D’Andrea, et al.. A novel approach to simulate gene-environment interactions in complex diseases. BMC bioinformatics, 2010.