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Daniel D'Andrea

Lecturer

School of Science & Technology

Staff Group(s)
Bioscience

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 hold a Master degree from the Federico II, University of Naples in Computer Science and a Ph.D. degree from the Sapienza University of Rome in Bioinformatics. Furthermore, he has been working for 5 years as Research Associate at Imperial College and for 3 years as Senior Research Associate at Cardiff University.  
At Imperial College London his principal roles as cancer bioinformatician were 1) to identify new targets for clarifying and validating the role of NF-κB gene on metabolic adaptation in colon cancer through analysis of heterogeneous metabolic and transcriptomic high-throughput datasets; 2) to develop new bioinformatic strategies aimed at supporting the clinical trial progression of the first-in-class inhibitor, DTP3, for haematological malignancies.
At Cardiff University, he worked in collaboration with Takeda Pharmaceutical Company Limited to identify potential molecular targets for therapeutic intervention in schizophrenia and other psychiatric disorders.
During Ph.D. Dr D’Andrea focused on the application and integration of high-throughput experiments to different biomedical systems and the development of tools for improving/solving critical steps of the analyses derived by system complexity.

Research areas

Dr D’Andrea has a strong interest in the application of bioinformatic approaches to biomedical problems, by using a wide range of cutting edge techniques, such as bulk/single-cell high-throughput next-generation sequencing, analysis and integration of multiomics data, translational medicine and targeted therapies.
His research interests are focused on:

1) identification of mechanistic insights through data analysis, integration and interpretation of ’omics data, to understand the mechanisms of complex biological systems and relevant changes affecting complex diseases;

2) translation of integrative genomics and transcriptomics analyses on high-throughput data for therapeutic discovery, to identify potential targets impacting the diseases;

3) design and application of innovative computational/statistical algorithms to improve the analysis of a high-throughput experiment 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. 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. 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

- 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.