Pietro Hiram Guzzi, Francesco Branda, Fabio Scarpa, Giancarlo Ceccarelli, Massimo Ciccozzi, Federico Manuel Giorgi, Pierangelo Veltri (2026). Integrated Downstream Analysis and Epidemiological Modelling of Hantavirus Infection: From Host Transcriptomics to Transmission Dynamics . Pathogens.

Pietro Hiram Guzzi, Francesco Branda, Fabio Scarpa, Giancarlo Ceccarelli, Massimo Ciccozzi, Federico Manuel Giorgi, Pierangelo Veltri (2026). Integrated Downstream Analysis and Epidemiological Modelling of Hantavirus Infection: From Host Transcriptomics to Transmission Dynamics . Pathogens.

Dunja Lukic, Pietro Hiram Guzzi, Federico Manuel Giorgi (2026). Integrated Evolutionary and Multi-Omic Analysis of STAT Family Activation Across Solid Tumors . Genes.

Dunja Lukic, Pietro Hiram Guzzi, Federico Manuel Giorgi (2026). Integrated Evolutionary and Multi-Omic Analysis of STAT Family Activation Across Solid Tumors . Genes.

Annamaria Defilippo, Kimberly Glass, Federico M Giorgi, Tamer Kahveci, Pierangelo Veltri, Pietro Hiram Guzzi (2025). Differential causal networks highlight sex-based differences in human tissues . Briefings in Bioinformatics.

Simona Paglia, Patrizia Morciano, Dario de Biase, Federico Manuel Giorgi, Annalisa Pession, Daniela Grifoni (2025). Transcriptome-Wide Analysis of Brain Cancer Initiated by Polarity Disruption in Drosophila Type II Neuroblasts . International Journal of Molecular Sciences.

Simona Paglia, Patrizia Morciano, Dario de Biase, Federico Manuel Giorgi, Annalisa Pession, Daniela Grifoni (2025). Transcriptome-Wide Analysis of Brain Cancer Initiated by Polarity Disruption in <i>Drosophila</i> Type II Neuroblasts . International Journal of Molecular Sciences.

Daniele Pozzobon, Arianna Bellezza, Federico M. Giorgi (2025). Pan-Cancer Upregulation of the FOXM1 Transcription Factor . Genes.

Pigini, P. and Giorgi, F. M. and Wee, K. B.(2025). Utargetome: A targetome prediction tool for modified U1-snRNAs to identify distal-target positions with improved selectivity . PLOS COMPUTATIONAL BIOLOGY. 21. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--20.

Barile, Simona Nicole and Magnifico, Maria Chiara and Poeta, Eleonora and Distelmaier, Felix and Viggiano, Luigi and Balboni, Nicola and Protti, Michele and Petralla, Sabrina and Pignataro, Antonella and Volpe, Giacomo and De Luise, Monica and Bonora, Massimo and Antonicelli, Marica and Babini, Giorgia and Massenzio, Francesca and Porcelli, Vito and Lama, Eleonora and Arrigoni, Roberto and Pisano, Isabella and Addabbo, Veronica and Campana, Anna and Begnozzi, Francesca and Anderson, Stewart A and Fiermonte, Giuseppe and Giorgi, Federico Manuel and Pinton, Paolo and Palmieri, Ferdinando and Gasparre, Giuseppe and Mercolini, Laura and Palmieri, Luigi and Wallace, Douglas C and Hentschel, Julia and Monti, Barbara and Lasorsa, Francesco Massimo(2025). Combined ketone body and glutamine supplementation restores aerobic energy production in AGC1-deficient neuronal progenitors . CELL DEATH & DISEASE. 17. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--17.

Pozzobon, D. and Bellezza, A. and Giorgi, F. M.(2025). Pan-Cancer Upregulation of the FOXM1 Transcription Factor . GENES. 16. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--16.

Defilippo, A. and Glass, K. and Giorgi, F. M. and Kahveci, T. and Veltri, P. and Guzzi, P. H.(2025). Differential causal networks highlight sex-based differences in human tissues . BRIEFINGS IN BIOINFORMATICS. 26. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--20.

Paglia, S. and Morciano, P. and De Biase, D. and Giorgi, F. M. and Pession, A. and Grifoni, D.(2025). Transcriptome-Wide Analysis of Brain Cancer Initiated by Polarity Disruption in Drosophila Type II Neuroblasts . INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 26. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--18.

Lomoio, U. and Carbonari, V. and Giorgi, F. M. and Ortuso, F. and Lio, P. and Veltri, P. and Guzzi, P. H.(2025). Integrative structural profiling and ligand optimisation across the transthyretin mutational landscape . NPJ SYSTEMS BIOLOGY AND APPLICATIONS. 11. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--16.

Coada, C. A. and Perrone, A. M. and Gorini, F. and De Leo, A. and De Biase, D. and Mantovani, G. and Di Costanzo, S. and Costantino, A. and Mezzapesa, F. and Giorgi, F. M. and Tallini, G. and Astolfi, A. and Strigari, L. and Angelini, S. and De Iaco, P. and Ravegnini, G.(2025). MiRNome alterations drive the malignant transformation of endometriosis into endometriosis-correlated ovarian cancer . SCIENTIFIC REPORTS. 15. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--12.

Ravegnini, Gloria and Coadă, Camelia Alexandra and Mantovani, Giulia and De Leo, Antonio and de Biase, Dario and Costantino, Alessia and Gorini, Francesca and Dondi, Giulia and Di Costanzo, Stella and Mezzapesa, Francesco and Giorgi, Federico Manuel and Tallini, Giovanni and Angelini, Sabrina and Astolfi, Annalisa and Strigari, Lidia and De Iaco, Pierandrea and Perrone, Anna Myriam(2025). MicroRNA profiling reveals potential biomarkers for the early transformation of endometriosis towards endometriosis-correlated ovarian cancer . TRANSLATIONAL ONCOLOGY. 55. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--8.

The miRNA–immune axis in bladder cancer: systematic evidence for a new era of immunotherapy precision @article{ 11585_1061031, author = {Dulf, D. V. and Ravegnini, G. and Giorgi, F. M. and Burnar, A. L. and Gorini, F. and De Leo, A. and Luţichievici, H. and Opriţa, C. L. and Todiruţ, C. N. and Ciuleanu, T. E. and Coadă, C. A.}, title = {The miRNA–immune axis in bladder cancer: systematic evidence for a new era of immunotherapy precision}, year = {2025}, journal = {FRONTIERS IN IMMUNOLOGY}, volume = {16}, keywords = {PD-L1; immune checkpoint inhibitor; immunotherapy; microRNA; personalized therapy; prognosis; tumor immune infiltration; urothelial carcinoma}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1639334/full}, doi = {10.3389/fimmu.2025.1639334}, pages = {1--15} } .

Daniele Pozzobon, Arianna Bellezza, Federico M. Giorgi (2025). Pan-Cancer Upregulation of the FOXM1 Transcription Factor . Genes.

Arpita Joshi, Federico Manuel Giorgi, Pietro Paolo Sanna (2024). Transcriptional Patterns in Stages of Alzheimer's Disease Are Cell-Type–Specific and Partially Converge with the Effects of Alcohol Use Disorder in Humans . eneuro.

Omri Avidan, Marina C M Martins, Regina Feil, Marc Lohse, Federico M Giorgi, Armin Schlereth, John E Lunn, Mark Stitt (2024). Direct and indirect responses of the Arabidopsis transcriptome to an induced increase in trehalose 6-phosphate . Plant Physiology.

Maria Stella de Biase, Florian Massip, Tzu-Ting Wei, Federico M. Giorgi, Rory Stark, Amanda Stone, Amy Gladwell, Martin O’Reilly, Daniel Sch&#252;tte, Ines de Santiago, et al. (2024). Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk . Genome Medicine.

De Biase, Maria Stella and Massip, Florian and Wei, Tzu-Ting and Giorgi, Federico M and Stark, Rory and Stone, Amanda and Gladwell, Amy and O'Reilly, Martin and Schütte, Daniel and De Santiago, Ines and Meyer, Kerstin B and Markowetz, Florian and Ponder, Bruce A J and Rintoul, Robert C and Schwarz, Roland F(2024). Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk . GENOME MEDICINE. 16. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--19.

Cabrelle, C. and Giorgi, F. M. and Mercatelli, D.(2024). Quantitative and qualitative detection of tRNAs, tRNA halves and tRFs in human cancer samples: Molecular grounds for biomarker development and clinical perspectives . GENE. 898. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--10.

Giorgi, F. M. and Pozzobon, D. and Di Meglio, A. and Mercatelli, D.(2024). Genomic and transcriptomic analysis of the recent Mpox outbreak . VACCINE. 42. (7). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1841--1849.

Avidan, O. and Martins, M. C. M. and Feil, R. and Lohse, M. and Giorgi, F. M. and Schlereth, A. and Lunn, J. E. and Stitt, M.(2024). Direct and indirect responses of the Arabidopsis transcriptome to an induced increase in trehalose 6-phosphate . PLANT PHYSIOLOGY. 196. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 409--431.

Transcriptional Patterns in Stages of Alzheimer’s Disease Are Cell-Type–Specific and Partially Converge with the Effects of Alcohol Use Disorder in Humans @article{ 11585_1048126, author = {Joshi, A. and Giorgi, F. M. and Sanna, P. P.}, title = {Transcriptional Patterns in Stages of Alzheimer’s Disease Are Cell-Type–Specific and Partially Converge with the Effects of Alcohol Use Disorder in Humans}, year = {2024}, journal = {ENEURO}, volume = {11}, keywords = {Alzheimer's disease; alcohol use disorder; differential gene expression; gene networks; master regulator analysis; snRNA-seq}, url = {https://www.eneuro.org/content/11/10/ENEURO.0118-24.2024}, doi = {10.1523/ENEURO.0118-24.2024}, pages = {1--21}, number = {10} } .

Ament, S. A. and Campbell, R. R. and Lobo, M. K. and Receveur, J. P. and Agrawal, K. and Borjabad, A. and Byrareddy, S. N. and Chang, L. and Clarke, D. and Emani, P. and Gabuzda, D. and Gaulton, K. J. and Giglio, M. and Giorgi, F. M. and Gok, B. and Guda, C. and Hadas, E. and Herb, B. R. and Hu, W. and Huttner, A. and Ishmam, M. R. and Jacobs, M. M. and Kelschenbach, J. and Kim, D. -W. and Lee, C. and Liu, S. and Liu, X. and Madras, B. K. and Mahurkar, A. A. and Mash, D. C. and Mukamel, E. A. and Niu, M. and O'Connor, R. M. and Pagan, C. M. and Pang, A. P. S. and Pillai, P. and Repunte-Canonigo, V. and Ruzicka, W. B. and Stanley, J. and Tickle, T. and Tsai, S. -Y. A. and Wang, A. and Wills, L. and Wilson, A. M. and Wright, S. N. and Xu, S. and Yang, J. and Zand, M. and Zhang, L. and Zhang, J. and Akbarian, S. and Buch, S. and Cheng, C. S. and Corley, M. J. and Fox, H. S. and Gerstein, M. and Gummuluru, S. and Heiman, M. and Ho, Y. -C. and Kellis, M. and Kenny, P. J. and Kluger, Y. and Milner, T. A. and Moore, D. J. and Morgello, S. and Ndhlovu, L. C. and Rana, T. M. and Sanna, P. P. and Satterlee, J. S. and Sestan, N. and Spector, S. A. and Spudich, S. and Tilgner, H. U. and Volsky, D. J. and White, O. R. and Williams, D. W. and Zeng, H.(2024). The single-cell opioid responses in the context of HIV (SCORCH) consortium . MOLECULAR PSYCHIATRY. 29. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3950--3961.

Murray, J. E. and Valli, E. and Milazzo, G. and Mayoh, C. and Gifford, A. J. and Fletcher, J. I. and Xue, C. and Jayatilleke, N. and Salehzadeh, F. and Gamble, L. D. and Rouaen, J. R. C. and Carter, D. R. and Forgham, H. and Sekyere, E. O. and Keating, J. and Eden, G. and Allan, S. and Alfred, S. and Kusuma, F. K. and Clark, A. and Webber, H. and Russell, A. J. and de Weck, A. and Kile, B. T. and Santulli, M. and De Rosa, P. and Fleuren, E. D. G. and Gao, W. and Wilkinson-White, L. and Low, J. K. K. and Mackay, J. P. and Marshall, G. M. and Hilton, D. J. and Giorgi, F. M. and Koster, J. and Perini, G. and Haber, M. and Norris, M. D.(2024). The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis . NATURE COMMUNICATIONS. 15. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--21.

Balboni, Nicola and Babini, Giorgia and Poeta, Eleonora and Protti, Michele and Mercolini, Laura and Maria Chiara Magnifico, and Simona Nicole Barile, and Massenzio, Francesca and Pignataro, Antonella and Federico, M Giorgi and Francesco Massimo Lasorsa, and Monti, Barbara(2024). Transcriptional and metabolic effects of aspartate-glutamate carrier isoform 1 (AGC1) downregulation in mouse oligodendrocyte precursor cells (OPCs) . CELLULAR AND MOLECULAR BIOLOGY LETTERS. 29. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 44--73.

Defilippo, Annamaria and Giorgi, Federico Manuel and Veltri, Pierangelo and Guzzi, Pietro Hiram(2024). Understanding complex systems through differential causal networks . SCIENTIFIC REPORTS. 14. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--14.

Zhao, Weiye and Rose, Susanna F and Blake, Ryan and Godicelj, Aňze and Cullen, Amy E and Stenning, Jack and Beevors, Lucy and Gehrung, Marcel and Kumar, Sanjeev and Kishore, Kamal and Sawle, Ashley and Eldridge, Matthew and Giorgi, Federico M and Bridge, Katherine S and Markowetz, Florian and Holding, Andrew N(2024). ZMIZ1 enhances ERα-dependent expression of E2F2 in breast cancer . JOURNAL OF MOLECULAR ENDOCRINOLOGY. 40. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--65.

Livia Beccacece, Filippo Costa, Jennifer Paola Pascali, Federico Manuel Giorgi (2023). Cross-Species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances . Toxics.

Livia Beccacece, Filippo Costa, Jennifer Paola Pascali, Federico Manuel Giorgi (2023). Cross-Species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances . Toxics.

Daria Messelodi, Silvia Strocchi, Salvatore Nicola Bertuccio, Pascale Baden, Valentina Indio, Federico M. Giorgi, Alberto Taddia, Salvatore Serravalle, Sabrina Valente, Alessio di Fonzo, et al. (2023). Neuronopathic Gaucher disease models reveal defects in cell growth promoted by Hippo pathway activation . Communications Biology.

Poursani, E. M. and Mercatelli, D. and Raninga, P. and Bell, J. L. and Saletta, F. and Kohane, F. V. and Neumann, D. P. and Zheng, Y. and Rouaen, J. R. C. and Jue, T. R. and Michniewicz, F. T. and Schadel, P. and Kasiou, E. and Tsoli, M. and Cirillo, G. and Waters, S. and Shai-Hee, T. and Cazzoli, R. and Brettle, M. and Slapetova, I. and Kasherman, M. and Whan, R. and Souza-Fonseca-Guimaraes, F. and Vahdat, L. and Ziegler, D. and Lock, J. G. and Giorgi, F. M. and Khanna, K. K. and Vittorio, O.(2023). Copper chelation suppresses epithelial-mesenchymal transition by inhibition of canonical and non-canonical TGF-β signaling pathways in cancer . CELL & BIOSCIENCE. 13. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 132--150.

Bassi, M. and Vannucci, J. and Giorgi, F. M. and Souza, R. V. and Ferrante, F. and Bianco, M. and Mottola, E. and De Giacomo, T. and Diso, D. and Poggi, C. and Venuta, F. and Anile, M.(2023). Lung cancer surgery in octogenarians: a meta-analysis of predictors for postoperative complications . SHANGHAI CHEST. 7. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--9.

A History of Repeated Alcohol Intoxication Promotes Cognitive Impairment and Gene Expression Signatures of Disease Progression in the 3xTg Mouse Model of Alzheimer’s Disease @article{ 11585_935695, author = {Sanna, P. P. and Cabrelle, C. and Kawamura, T. and Mercatelli, D. and O'connor, N. and Roberts, A. J. and Repunte-Canonigo, V. and Giorgi, F. M.}, title = {A History of Repeated Alcohol Intoxication Promotes Cognitive Impairment and Gene Expression Signatures of Disease Progression in the 3xTg Mouse Model of Alzheimer’s Disease}, year = {2023}, journal = {ENEURO}, volume = {10}, keywords = {Alzheimer's disease AD; alcohol; neuroinflammation; single-cell; transcriptomics.}, url = {https://www.eneuro.org/content/10/7/ENEURO.0456-22.2023.long}, doi = {10.1523/ENEURO.0456-22.2023}, pages = {456--471}, number = {7} } .

Protti, Michele and Cirrincione, Marco and Palano, Sarah and Poeta, Eleonora and Babini, Giorgia and Maria Chiara Magnifico, and Simona Nicole Barile, and Balboni, Nicola and Massenzio, Francesca and Mahdavijalal, Mohammadreza and Giorgi, Federico M. and Mandrioli, Roberto and Lasorsa, Francesco M. and Monti, Barbara and Mercolini, Laura(2023). Targeted quantitative metabolic profiling of brain-derived cell cultures by semi-automated MEPS and LC-MS/MS . JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS. 236. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 115757--115767.

Messelodi, Daria and Strocchi, Silvia and Bertuccio, Salvatore Nicola and Baden, Pascale and Indio, Valentina and Giorgi, Federico M and Taddia, Alberto and Serravalle, Salvatore and Valente, Sabrina and di Fonzo, Alessio and Frattini, Emanuele and Bernardoni, Roberto and Pession, Annalisa and Grifoni, Daniela and Deleidi, Michela and Astolfi, Annalisa and Pession, Andrea(2023). Neuronopathic Gaucher disease models reveal defects in cell growth promoted by Hippo pathway activation . COMMUNICATIONS BIOLOGY. 6. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--13.

Beccacece, Livia and Costa, Filippo and Pascali, Jennifer Paola and Giorgi, Federico Manuel(2023). Cross-Species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances . TOXICS. 11. (7). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 567--588.

Single-Cell Sequencing Identifies Master Regulators Affected by Panobinostat in Neuroblastoma Cells <head> <META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent"> </head> . Genes.

Giorgio Milazzo, Giovanni Perini, Federico M. Giorgi (2022). Single-Cell Sequencing Identifies Master Regulators Affected by Panobinostat in Neuroblastoma Cells . Genes.

Francesco Ortuso, Daniele Mercatelli, Pietro Hiram Guzzi, Federico Manuel Giorgi (2022). Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex . Journal of Biomolecular Structure and Dynamics.

Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data <head> <META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent"> </head> . Briefings in Bioinformatics.

Federico M. Giorgi, Carmine Ceraolo, Daniele Mercatelli (2022). The R Language: An Engine for Bioinformatics and Data Science . Life.

Federico M. Giorgi, Carmine Ceraolo, Daniele Mercatelli (2022). The R Language: An Engine for Bioinformatics and Data Science . Life.

Maria Vittoria Cavicchioli, Mariangela Santorsola, Nicola Balboni, Daniele Mercatelli, Federico Manuel Giorgi(2022). Prediction of Metabolic Profiles from Transcriptomics Data in Human Cancer Cell Lines . International Journal of Molecular Sciences. 23. (7). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3867. {MDPI} {AG}

Maria Vittoria Cavicchioli, Mariangela Santorsola, Nicola Balboni, Daniele Mercatelli, Federico Manuel Giorgi (2022). Prediction of Metabolic Profiles from Transcriptomics Data in Human Cancer Cell Lines . International Journal of Molecular Sciences.

Yu Fu, Irene Lorrai, Barry Zorman, Daniele Mercatelli, Chase Shankula, Jorge Marquez Gaytan, Celine Lefebvre, Giordano de Guglielmo, Hyunjae Ryan Kim, Pavel Sumazin, et al. (2022). Escalated (Dependent) Oxycodone Self-Administration Is Associated with Cognitive Impairment and Transcriptional Evidence of Neurodegeneration in Human Immunodeficiency Virus (HIV) Transgenic Rats . Viruses.

Carmack, S. A. and Vendruscolo, J. C. M. and Adrienne McGinn, M. and Miranda-Barrientos, J. and Repunte-Canonigo, V. and Bosse, G. D. and Mercatelli, D. and Giorgi, F. M. and Fu, Y. and Hinrich, A. J. and Jodelka, F. M. and Ling, K. and Messing, R. O. and Peterson, R. T. and Rigo, F. and Edwards, S. and Sanna, P. P. and Morales, M. and Hastings, M. L. and Koob, G. F. and Vendruscolo, L. F.(2022). Corticosteroid sensitization drives opioid addiction . MOLECULAR PSYCHIATRY. 27. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2492--2501.

Fu, Y. and Lorrai, I. and Zorman, B. and Mercatelli, D. and Shankula, C. and Gaytan, J. M. and Lefebvre, C. and de Guglielmo, G. and Kim, H. R. and Sumazin, P. and Giorgi, F. M. and Repunte-Canonigo, V. and Sanna, P. P.(2022). Escalated (Dependent) Oxycodone Self-Administration Is Associated with Cognitive Impairment and Transcriptional Evidence of Neurodegeneration in Human Immunodeficiency Virus (HIV) Transgenic Rats . VIRUSES. 14. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--19.

Cavicchioli, M. V. and Santorsola, M. and Balboni, N. and Mercatelli, D. and Giorgi, F. M.(2022). Prediction of Metabolic Profiles from Transcriptomics Data in Human Cancer Cell Lines . INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 23. (7). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--17.

Giorgi, Federico M and Ceraolo, Carmine and Mercatelli, Daniele(2022). The R Language: An Engine for Bioinformatics and Data Science . LIFE. 12. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--25.

Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data @article{ 11585_893865, author = {Mercatelli, Daniele and Cabrelle, Chiara and Veltri, Pierangelo and Giorgi, Federico M and Guzzi, Pietro H}, title = {Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data}, year = {2022}, journal = {BRIEFINGS IN BIOINFORMATICS}, volume = {23}, abstract = {Cell surface proteins have been used as diagnostic and prognostic markers in cancer research and as targets for the development of anticancer agents. Many of these proteins lie at the top of signaling cascades regulating cell responses and gene expression, therefore acting as ‘signaling hubs’. It has been previously demonstrated that the integrated network analysis on transcriptomic data is able to infer cell surface protein activity in breast cancer. Such an approach has been implemented in a publicly available method called ‘SURFACER’. SURFACER implements a network-based analysis of transcriptomic data focusing on the overall activity of curated surface proteins, with the final aim to identify those proteins driving major phenotypic changes at a network level, named surface signaling hubs. Here, we show the ability of SURFACER to discover relevant knowledge within and across cancer datasets. We also show how different cancers can be stratified in surface-activity-specific groups. Our strategy may identify cancer-wide markers to design targeted therapies and biomarker-based diagnostic approaches.}, keywords = {bioinformatics, biomarkers, surfaceome, transcriptomics, biological networks}, url = {https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbac400/6695270}, doi = {10.1093/bib/bbac400}, pages = {1--11}, number = {5} } .

Milazzo, G. and Perini, G. and Giorgi, F. M.(2022). Single-Cell Sequencing Identifies Master Regulators Affected by Panobinostat in Neuroblastoma Cells . GENES. 13. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2240--2254.

Ortuso, F and Mercatelli, D and Guzzi, PH and Giorgi, FM(2022). Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex . JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. 40. (14). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 6545--6555.

Daniele Mercatelli, Francesco Formaggio, Marco Caprini, Andrew Holding, Federico&#160;M. Giorgi (2021). Detection of subtype-specific breast cancer surface protein biomarkers via a novel transcriptomics approach . Bioscience Reports.

Simone Di Giacomo, Daniele Mercatelli, Amir Rakhimov, Federico M. Giorgi(2021). Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Spike mutation T478K . Journal of Medical Virology. 93. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 5638--5643. Wiley

Gonzalo Lopez, Laura E Egolf, Federico M Giorgi, Sharon J Diskin, Adam A Margolin, Peter Robinson(2021). svpluscnv: analysis and visualization of complex structural variation data . Bioinformatics. 37. (13). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1912--1914. Oxford University Press ({OUP})

Francesco Castagna, Rachna Kataria, Shivank Madan, Syed Zain Ali, Karim Diab, Christopher Leyton, Angelos Arfaras-Melainis, Paul Kim, Federico M. Giorgi, Sasa Vukelic, et al. (2021). A History of Heart Failure Is an Independent Risk Factor for Death in Patients Admitted with Coronavirus 19 Disease . Journal of Cardiovascular Development and Disease.

Francesco Castagna, Rachna Kataria, Shivank Madan, Syed Zain Ali, Karim Diab, Christopher Leyton, Angelos Arfaras-Melainis, Paul Kim, Federico M. Giorgi, Sasa Vukelic, et al. (2021). A History of Heart Failure Is an Independent Risk Factor for Death in Patients Admitted with Coronavirus 19 Disease . Journal of Cardiovascular Development and Disease.

(2021). The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow . Methods and protocols.

Daniele Mercatelli, Nicola Balboni, Francesca De Giorgio, Emanuela Aleo, Caterina Garone, Federico Manuel Giorgi(2021). The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow . Methods and Protocols. 4. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 28. {MDPI} {AG}

Daniele Mercatelli, Nicola Balboni, Francesca De Giorgio, Emanuela Aleo, Caterina Garone, Federico Manuel Giorgi (2021). The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow . Methods and Protocols.

Daniele Mercatelli, Luca Triboli, Eleonora Fornasari, Forest Ray, Federico M. Giorgi (2021). Coronapp: A web application to annotate and monitor SARS‐CoV‐2 mutations . Journal of Medical Virology.

Laura D. Gamble, Stefania Purgato, Michelle J. Henderson, Simone Di Giacomo, Amanda J. Russell, Paolo Pigini, Jayne Murray, Emanuele Valli, Giorgio Milazzo, Federico M. Giorgi, et al. (2021). A G316A Polymorphism in the Ornithine Decarboxylase Gene Promoter Modulates MYCN-Driven Childhood Neuroblastoma . Cancers.

Laura D. Gamble, Stefania Purgato, Michelle J. Henderson, Simone Di Giacomo, Amanda J. Russell, Paolo Pigini, Jayne Murray, Emanuele Valli, Giorgio Milazzo, Federico M. Giorgi, et al. (2021). A G316A Polymorphism in the Ornithine Decarboxylase Gene Promoter Modulates MYCN-Driven Childhood Neuroblastoma . Cancers.

Anahid Ehteda, Sandy Simon, Laura Franshaw, Federico M. Giorgi, Jie Liu, Swapna Joshi, Jourdin R.C. Rouaen, Chi Nam Ignatius Pang, Ruby Pandher, Chelsea Mayoh, et al. (2021). Dual targeting of the epigenome via FACT complex and histone deacetylase is a potent treatment strategy for DIPG . Cell Reports.

Joshua Broyde, David R. Simpson, Diana Murray, Evan O. Paull, Brennan W. Chu, Somnath Tagore, Sunny J. Jones, Aaron T. Griffin, Federico M. Giorgi, Alexander Lachmann, et al.(2021). Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses . Nature Biotechnology. 39. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 215--224. Springer Science and Business Media {LLC}

Daniele Mercatelli, Nicola Balboni, Alessandro Palma, Emanuela Aleo, Pietro Paolo Sanna, Giovanni Perini, Federico Manuel Giorgi(2021). Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines . Biomolecules. 11. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 177. {MDPI} {AG}

Broyde, J. and Simpson, D. R. and Murray, D. and Paull, E. O. and Chu, B. W. and Tagore, S. and Jones, S. J. and Griffin, A. T. and Giorgi, F. M. and Lachmann, A. and Jackson, P. and Sweet-Cordero, E. A. and Honig, B. and Califano, A.(2021). Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses . NATURE BIOTECHNOLOGY. 39. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 215--224.

Mercatelli, D. and Triboli, L. and Fornasari, E. and Ray, F. and Giorgi, F. M.(2021). Coronapp: A web application to annotate and monitor SARS-CoV-2 mutations . JOURNAL OF MEDICAL VIROLOGY. 93. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3238--3245.

Ehteda, A. and Simon, S. and Franshaw, L. and Giorgi, F. M. and Liu, J. and Joshi, S. and Rouaen, J. R. C. and Pang, C. N. I. and Pandher, R. and Mayoh, C. and Tang, Y. and Khan, A. and Ung, C. and Tolhurst, O. and Kankean, A. and Hayden, E. and Lehmann, R. and Shen, S. and Gopalakrishnan, A. and Trebilcock, P. and Gurova, K. and Gudkov, A. V. and Norris, M. D. and Haber, M. and Vittorio, O. and Tsoli, M. and Ziegler, D. S.(2021). Dual targeting of the epigenome via FACT complex and histone deacetylase is a potent treatment strategy for DIPG . CELL REPORTS. 35. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--22.

Mercatelli, D. and Balboni, N. and De Giorgio, F. and Aleo, E. and Garone, C. and Giorgi, F. M.(2021). The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow . METHODS AND PROTOCOLS. 4. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--16.

Lopez, G. and Egolf, L. E. and Giorgi, F. M. and Diskin, S. J. and Margolin, A. A.(2021). Svpluscnv: Analysis and visualization of complex structural variation data . BIOINFORMATICS. 37. (13). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1912--1914.

Di Giacomo, S. and Mercatelli, D. and Rakhimov, A. and Giorgi, F. M.(2021). Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K . JOURNAL OF MEDICAL VIROLOGY. 93. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 5638--5643.

Mercatelli, Daniele and Formaggio, Francesco and Caprini, Marco and Holding, Andrew and Giorgi, Federico M(2021). Detection of subtype-specific breast cancer surface protein biomarkers via a novel transcriptomics approach . BIOSCIENCE REPORTS. 41. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--15.

Mercatelli, D. and Balboni, N. and Palma, A. and Aleo, E. and Sanna, P. P. and Perini, G. and Giorgi, F. M.(2021). Single-cell gene network analysis and transcriptional landscape of MYCN-amplified neuroblastoma cell lines . BIOMOLECULES. 11. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--18.

Mercatelli, D. and Pedace, E. and Veltri, P. and Giorgi, F. M. and Guzzi, P. H.(2021). Exploiting the molecular basis of age and gender differences in outcomes of SARS-CoV-2 infections . COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 19. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 4092--4101.

Mercatelli, Daniele and Holding, Andrew N and Giorgi, Federico M(2021). Web tools to fight pandemics: the COVID-19 experience . BRIEFINGS IN BIOINFORMATICS. 22. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 690--700.

Copper: An Intracellular Achilles’ Heel Allowing the Targeting of Epigenetics, Kinase Pathways, and Cell Metabolism in Cancer Therapeutics @article{ 11585_831844, author = {Michniewicz, F. and Saletta, F. and Rouaen, J. R. C. and Hewavisenti, R. V. and Mercatelli, D. and Cirillo, G. and Giorgi, F. M. and Trahair, T. and Ziegler, D. and Vittorio, O.}, title = {Copper: An Intracellular Achilles’ Heel Allowing the Targeting of Epigenetics, Kinase Pathways, and Cell Metabolism in Cancer Therapeutics}, year = {2021}, journal = {CHEMMEDCHEM}, volume = {16}, keywords = {Cancer; Copper; Epigenetics; Metabolism; RTK}, doi = {10.1002/cmdc.202100172}, pages = {2315--2329}, number = {15} } .

Paull, Evan O and Aytes, Alvaro and Jones, Sunny J and Subramaniam, Prem S and Giorgi, Federico M and Douglass, Eugene F and Tagore, Somnath and Chu, Brennan and Vasciaveo, Alessandro and Zheng, Siyuan and Verhaak, Roel and Abate-Shen, Cory and Alvarez, Mariano J and Califano, Andrea(2021). A modular master regulator landscape controls cancer transcriptional identity . CELL. 184. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 334--351.

Evan O. Paull, Alvaro Aytes, Sunny J. Jones, Prem S. Subramaniam, Federico M. Giorgi, Eugene F. Douglass, Somnath Tagore, Brennan Chu, Alessandro Vasciaveo, Siyuan Zheng, et al. (2021). A modular master regulator landscape controls cancer transcriptional identity . Cell.

Daniele Mercatelli, Nicola Balboni, Alessandro Palma, Emanuela Aleo, Pietro Paolo Sanna, Giovanni Perini, Federico Manuel Giorgi (2021). Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines . Biomolecules.

Erika Gardini, Federico M Giorgi, Sergio Decherchi, Andrea Cavalli, Jonathan Wren(2020). Spathial: an R package for the evolutionary analysis of biological data . Bioinformatics. Oxford University Press ({OUP})

Liem T. Bui, Vinay Shukla, Federico M. Giorgi, Alice Trivellini, Pierdomenico Perata, Francesco Licausi, Beatrice Giuntoli (2020). Differential submergence tolerance between juvenile and adult Arabidopsis plants involves the ANAC017 transcription factor . The Plant Journal.

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al.(2020). Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion . Cancer Research. 80. (19). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 4129--4144. American Association for Cancer Research ({AACR})

Daniele Mercatelli, Massimo Bortolotti, Federico M. Giorgi(2020). Transcriptional network inference and master regulator analysis of the response to ribosome-inactivating proteins in leukemia cells . Toxicology. 441. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 152531. Elsevier {BV}

Daniele Mercatelli, Gonzalo Lopez-Garcia, Federico M Giorgi, Lenore Cowen(2020). corto: a lightweight R package for gene network inference and master regulator analysis . Bioinformatics. Oxford University Press ({OUP})

Giorgio Milazzo, Daniele Mercatelli, Giulia Di Muzio, Luca Triboli, Piergiuseppe De Rosa, Giovanni Perini, Federico M. Giorgi (2020). Histone Deacetylases (HDACs): Evolution, Specificity, Role in Transcriptional Complexes, and Pharmacological Actionability . Genes.

Giorgio Milazzo, Daniele Mercatelli, Giulia Di Muzio, Luca Triboli, Piergiuseppe De Rosa, Giovanni Perini, Federico M. Giorgi (2020). Histone Deacetylases (HDACs): Evolution, Specificity, Role in Transcriptional Complexes, and Pharmacological Actionability . Genes.

Carmine Ceraolo, Federico M. Giorgi (2020). Genomic variance of the 2019‐nCoV coronavirus . Journal of Medical Virology.

Pietro H. Guzzi, Daniele Mercatelli, Carmine Ceraolo, Federico M. Giorgi(2020). Master Regulator Analysis of the SARS-CoV-2/Human Interactome . Journal of Clinical Medicine. 9. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 982. {MDPI} {AG}

Pietro H. Guzzi, Daniele Mercatelli, Carmine Ceraolo, Federico M. Giorgi (2020). Master Regulator Analysis of the SARS-CoV-2/Human Interactome . Journal of Clinical Medicine.

Tamar Paz-Elizur, Yael Leitner-Dagan, Kerstin B Meyer, Barak Markus, Federico M Giorgi, Martin O’Reilly, Hyunjin Kim, Yentl Evgy, Ronen Fluss, Laurence S Freedman, et al.(2020). DNA Repair Biomarker for Lung Cancer Risk and its Correlation With Airway Cells Gene Expression . JNCI Cancer Spectrum. 4. (1). Oxford University Press ({OUP})

Ceraolo, Carmine and Giorgi, Federico M(2020). Genomic variance of the 2019-nCoV coronavirus . JOURNAL OF MEDICAL VIROLOGY. 92. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 522--528.

Mercatelli, D., Giorgi, F. M.(2020). Geographic and Genomic Distribution of SARS-CoV-2 Mutations . FRONTIERS IN MICROBIOLOGY. 11. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1800--1812.

Paz-Elizur, Tamar and Leitner-Dagan, Yael and Meyer, Kerstin B and Markus, Barak and Giorgi, Federico M and O'Reilly, Martin and Kim, Hyunjin and Evgy, Yentl and Fluss, Ronen and Freedman, Laurence S and Rintoul, Robert C and Ponder, Bruce and Livneh, Zvi(2020). DNA Repair Biomarker for Lung Cancer Risk and its Correlation With Airway Cells Gene Expression . JNCI CANCER SPECTRUM. 4. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--10.

Galicia, J. C. and Guzzi, P. H. and Giorgi, F. M. and Khan, A. A.(2020). Predicting the response of the dental pulp to SARS-CoV2 infection: a transcriptome-wide effect cross-analysis . GENES AND IMMUNITY. 21. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 360--363.

Giorgi, F. M.(2020). Gene network reverse engineering: The Next Generation . BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS. 1863. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--2.

Mercatelli, D. and Scalambra, L. and Triboli, L. and Ray, F. and Giorgi, F. M.(2020). Gene regulatory network inference resources: A practical overview . BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS. 1863. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 194430--194450.

Guzzi, Pietro H and Mercatelli, Daniele and Ceraolo, Carmine and Giorgi, Federico M(2020). Master Regulator Analysis of the SARS-CoV-2/Human Interactome . JOURNAL OF CLINICAL MEDICINE. 9. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 982--996.

Milazzo, G. and Mercatelli, D. and Di Muzio, G. and Triboli, L. and De Rosa, P. and Perini, G. and Giorgi, F. M.(2020). Histone deacetylases (HDACs): Evolution, specificity, role in transcriptional complexes, and pharmacological actionability . GENES. 11. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--49.

Mercatelli, D. and Lopez-Garcia, G. and Giorgi, F. M.(2020). Corto: A lightweight R package for gene network inference and master regulator analysis . BIOINFORMATICS. 36. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3916--3917.

Mercatelli, D. and Bortolotti, M. and Giorgi, F. M.(2020). Transcriptional network inference and master regulator analysis of the response to ribosome-inactivating proteins in leukemia cells . TOXICOLOGY. 441. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--9.

Voli, Florida and Valli, Emanuele and Lerra, Luigi and Kimpton, Kathleen and Saletta, Federica and Giorgi, Federico M and Mercatelli, Daniele and Rouaen, Jourdin R C and Shen, Sylvie and Murray, Jayne E and Ahmed-Cox, Aria and Cirillo, Giuseppe and Mayoh, Chelsea and Beavis, Paul A and Haber, Michelle and Trapani, Joseph A and Kavallaris, Maria and Vittorio, Orazio(2020). Intra-tumoral copper modulates PD-L1 expression and influences tumor immune evasion . CANCER RESEARCH. 80. (19). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 4129--4144.

Gardini, Erika and Giorgi, Federico M and Decherchi, Sergio and Cavalli, Andrea(2020). Spathial: an R package for the evolutionary analysis of biological data . BIOINFORMATICS. 36. (17). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 4664-4667--4667.

Bui, L. T. and Shukla, V. and Giorgi, F. M. and Trivellini, A. and Perata, P. and Licausi, F. and Giuntoli, B.(2020). Differential submergence tolerance between juvenile and adult Arabidopsis plants involves the ANAC017 transcription factor . PLANT JOURNAL. 104. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 979--994.

Mercatelli, Daniele, Bortolotti, Massimo, Giorgi, Federico M., Mercatelli, Daniele, Bortolotti, Massimo, Giorgi, Federico M. (2020). Transcriptional network inference and master regulator analysis of the response to ribosome-inactivating proteins in leukemia cells . Toxicology.

Guzzi, Pietro H, Mercatelli, Daniele, Ceraolo, Carmine, Giorgi, Federico M, Guzzi, Pietro H, Mercatelli, Daniele, Ceraolo, Carmine, Giorgi, Federico M (2020). Master Regulator Analysis of the SARS-CoV-2/Human Interactome . Journal of Clinical Medicine.

Ceraolo, Carmine, Giorgi, Federico M, Ceraolo, Carmine, Giorgi, Federico M (2020). Genomic variance of the 2019-nCoV coronavirus . Journal of Medical Virology.

Daniele Mercatelli, Federico Manuel Giorgi, Daniele Mercatelli, Federico Manuel Giorgi (2020). Geographic and Genomic Distribution of SARS-CoV-2 Mutations .

Mercatelli, Daniele, Mercatelli, Daniele, Scalambra, Laura, Scalambra, Laura, Triboli, Luca, Triboli, Luca, Ray, Forest, Ray, Forest, Giorgi, Federico M., Giorgi, Federico M., et al. (2020). Gene regulatory network inference resources: A practical overview . Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms.

Giorgi, Federico M., Giorgi, Federico M. (2020). Gene network reverse engineering: The Next Generation Preface . Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms.

Paz-Elizur, Tamar, Leitner-Dagan, Yael, Meyer, Kerstin B., Markus, Barak, Giorgi, Federico M., O&#39;Reilly, Martin, Kim, Hyunjin, Evgy, Yentl, Fluss, Ronen, Freedman, Laurence S., et al. (2020). DNA Repair Biomarker for Lung Cancer Risk and its Correlation With Airway Cells Gene Expression . JNCI Cancer Spectrum.

(2019). VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer .

Laura D. Gamble, Stefania Purgato, Jayne Murray, Lin Xiao, Denise M. T. Yu, Kimberley M. Hanssen, Federico M. Giorgi, Daniel R. Carter, Andrew J. Gifford, Emanuele Valli, et al.(2019). Inhibition of polyamine synthesis and uptake reduces tumor progression and prolongs survival in mouse models of neuroblastoma . Science Translational Medicine. 11. (477). American Association for the Advancement of Science ({AAAS})

Mercatelli, D. and Ray, F. and Giorgi, F. M.(2019). Pan-cancer and single-cell modelling of genomic alterations through gene expression . FRONTIERS IN GENETICS. 10. (JUN). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 671--683.

Gamble, Laura D. and Purgato, Stefania and Murray, Jayne and Xiao, Lin and Yu, Denise M. T. and Hanssen, Kimberley M. and Giorgi, Federico M. and Carter, Daniel R. and Gifford, Andrew J. and Valli, Emanuele and Milazzo, Giorgio and Kamili, Alvin and Mayoh, Chelsea and Liu, Bing and Eden, Georgina and Sarraf, Sara and Allan, Sophie and Simone Di Giacomo, and Flemming, Claudia L. and Russell, Amanda J. and Cheung, Belamy B. and Oberthuer, Andre and London, Wendy B. and Fischer, Matthias and Trahair, Toby N. and Fletcher, Jamie I. and Marshall, Glenn M. and Ziegler, David S. and Hogarty, Michael D. and Burns, Mark R. and Perini, Giovanni and Norris, Murray D. and and Michelle Haber(2019). Inhibition of polyamine synthesis and uptake reduces tumor progression and prolongs survival in mouse models of neuroblastoma . SCIENCE TRANSLATIONAL MEDICINE. 11. (477). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--12.

Holding, Andrew N. and Giorgi, Federico M. and Donnelly, Amanda and Cullen, Amy E. and Nagarajan, Sankari and Selth, Luke A. and Markowetz, Florian(2019). VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer . GENOME BIOLOGY. 20. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--16.

Holding, A.N., Giorgi, F.M., Donnelly, A., Cullen, A.E., Nagarajan, S., Selth, L.A., Markowetz, F., Holding, A.N., Giorgi, F.M., Donnelly, A., et al.(2019). VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer . Genome Biology. 20. (1).

Livneh, Z., Paz-Elizur, T., Leitner-Dagan, Y., Meyer, K., Markus, B. Barak, Giorgi, F., O&#39;Reilly, M., Kim, H., Evgy, Y., Rintoul, R. C., et al. (2019). Potential DNA Repair Biomarker for Response to Immunotherapy of Lung Cancer Patients . Journal of Thoracic Oncology.

Paz-Elizur, T., Leitner-Dagan, Y., Meyer, K., Markus, B., Giorgi, F., O&#39;Reilly, M., Kim, H., Evgy, Y., Fluss, R., Freedman, L., et al. (2019). Utilizing DNA Repair Activity Biomarkers for Lung Cancer Risk Assessment and Early Detection . Journal of Thoracic Oncology.

Milazzo, G., Ciaccio, R., Di Giacomo, S., Lombardi, S., De Rosa, P., Parisi, N., Giorgi, F., Perini, G., Milazzo, G., Ciaccio, R., et al. (2019). Role of ABCC3 Drug Transporter in Neuroblastoma Cell Invasion . Pediatric Blood and Cancer.

Milazzo, G., Mercatelli, D., Perini, G., Giorgi, F., Milazzo, G., Mercatelli, D., Perini, G., Giorgi, F. (2019). Unveiling Early Differentiation Induced by Histone Deacetylase Inhibitors in Neuroblastoma Cell Lines: A Single-Cell Transcriptomics Approach . Pediatric Blood and Cancer.

Holding, A.N., Giorgi, F.M., Donnelly, A., Cullen, A.E., Nagarajan, S., Selth, L.A., Markowetz, F., Holding, A.N., Giorgi, F.M., Donnelly, A., et al.(2019). Correction to: VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer (Genome Biol (2019) 20:91 DOI: 10.1186/s13059-019-1698-z) . Genome Biology. 20. (1).

Di Giacomo, S., Sollazzo, M., Paglia, S., Milazzo, G., Giorgi, F. M., Ciaccio, R., Pession, A., Perini, G., Grifoni, D., Di Giacomo, S., et al. (2019). P53 Modulates MYC-Mediated Cell Competition in Cancer Backgrounds . Pediatric Blood and Cancer.

Mercatelli, D., Ray, F., Giorgi, F.M., Mercatelli, D., Ray, F., Giorgi, F.M.(2019). Pan-cancer and single-cell modelling of genomic alterations through gene expression . Frontiers in Genetics. 10. (JUN).

Gamble, L.D., Purgato, S., Murray, J., Xiao, L., Yu, D.M.T., Hanssen, K.M., Giorgi, F.M., Carter, D.R., Gifford, A.J., Valli, E., et al.(2019). Inhibition of polyamine synthesis and uptake reduces tumor progression and prolongs survival in mouse models of neuroblastoma . Science Translational Medicine. 11. (477).

Cesana, Marcella and Guo, Michael H. and Cacchiarelli, Davide and Wahlster, Lara and Barragan, Jessica and Doulatov, Sergei and Vo, Linda T. and Salvatori, Beatrice and Trapnell, Cole and Clement, Kendell and Cahan, Patrick and Tsanov, Kaloyan M. and Sousa, Patricia M. and Tazon-Vega, Barbara and Bolondi, Adriano and Giorgi, Federico M. and Califano, Andrea and Rinn, John L. and Meissner, Alexander and Hirschhorn, Joel N. and Daley, George Q.(2018). A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development . CELL STEM CELL. 22. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 575--588.

Cesana, M., Guo, M.H., Cacchiarelli, D., Wahlster, L., Barragan, J., Doulatov, S., Vo, L.T., Salvatori, B., Trapnell, C., Clement, K., et al.(2018). A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development . Cell Stem Cell. 22. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 575-588.e7.

Sibout, Richard and Proost, Sebastian and Hansen, Bjoern Oest and Vaid, Neha and Giorgi, Federico M. and Ho-Yue-Kuang, Severine and Legée, Frédéric and Cézart, Laurent and Bouchabké-Coussa, Oumaya and Soulhat, Camille and Provart, Nicholas and Pasha, Asher and Le Bris, Philippe and Roujol, David and Hofte, Herman and Jamet, Elisabeth and Lapierre, Catherine and Persson, Staffan and Mutwil, Marek(2017). Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon . NEW PHYTOLOGIST. 215. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1009--1025.

Giuntoli, Beatrice and Shukla, Vinay and Maggiorelli, Federica and Giorgi, Federico M. and Lombardi, Lara and Perata, Pierdomenico and Licausi, Francesco(2017). Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana . PLANT, CELL AND ENVIRONMENT. 40. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2333--2346.

Giuntoli, B., Shukla, V., Maggiorelli, F., Giorgi, F.M., Lombardi, L., Perata, P., Licausi, F., Giuntoli, B., Shukla, V., Maggiorelli, F., et al.(2017). Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana . Plant Cell and Environment. 40. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2333-2346.

Broyde, Joshua, Simpson, David, Murray, Diana, Lachmann, Alexander, Giorgi, Federico M., Honig, Barry, Sweet-Cordero, Alejandro E., Califano, Andrea, Broyde, Joshua, Simpson, David, et al. (2017). Computational detection of oncogene-centric pathway members . Cancer Research.

Sibout, R., Proost, S., Hansen, B.O., Vaid, N., Giorgi, F.M., Ho-Yue-Kuang, S., Leg&#233;e, F., C&#233;zart, L., Bouchabk&#233;-Coussa, O., Soulhat, C., et al.(2017). Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon . New Phytologist. 215. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1009-1025.

Alvarez, Mariano J. and Shen, Yao and Giorgi, Federico M and Lachmann, Alexander and Ding, B Belinda and Hilda Ye, B. and Califano, Andrea(2016). Functional characterization of somatic mutations in cancer using network-based inference of protein activity. NATURE GENETICS. 48. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 838--847.

Sepulveda, Jorge L. and Gutierrez-Pajares, Jorge L. and Luna, Aesis and Yao, Yuan and Tobias, John W. and Thomas, Steven and Woo, Yanghee and Giorgi, Federico and Komissarova, Elena V. and Califano, Andrea and Wang, Timothy C. and Sepulveda, Antonia R.(2016). High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing . MODERN PATHOLOGY. 29. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 182--193.

Lachmann, Alexander and Giorgi, Federico M. and Lopez, Gonzalo and Califano, Andrea(2016). ARACNe-AP: Gene network reverse engineering through adaptive partitioning inference of mutual information . BIOINFORMATICS. 32. (14). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2233--2235.

Lachmann, Alexander and Giorgi, Federico M. and Alvarez, Mariano J. and Califano, Andrea(2016). Detection and removal of spatial bias in multiwell assays . BIOINFORMATICS. 32. (13). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1959--1965.

Adamopoulou, E., Bobbio, E., De Philippis, M., Giorgi, F., Adamopoulou, E., Bobbio, E., De Philippis, M., Giorgi, F.(2016). Wage rigidities and business cycle fluctuations: A linked employer-employee analysis . IZA Journal of Labor Policy. 5. (1).

Giorgi, Federico, Maurer, H. Carlo, He, Jing, Alvarez, Mariano J., Holmstrom, Sam, Califano, Andrea, Olive, Kenneth P., Maurer, H. Carlo, He, Jing, Alvarez, Mariano J., et al. (2016). Reconstructing compartment-specific regulatory programs in pancreatic cancer . Cancer Research.

Alvarez, M.J., Shen, Y., Giorgi, F.M., Lachmann, A., Ding, B.B., Hilda Ye, B., Califano, A., Alvarez, M.J., Shen, Y., Giorgi, F.M., et al.(2016). Functional characterization of somatic mutations in cancer using network-based inference of protein activity . Nature Genetics. 48. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 838-847.

Giorgi, Federico M., Lopez, Gonzalo, Woo, Jung H., Bisikirska, Brygida, Califano, Andrea, Bansal, Mukesh, Giorgi, Federico M., Lopez, Gonzalo, Woo, Jung H., Bisikirska, Brygida, et al. (2016). Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information (vol 9, e109569, 2014) . Plos One.

Lachmann, A., Giorgi, F.M., Lopez, G., Califano, A., Lachmann, A., Giorgi, F.M., Lopez, G., Califano, A.(2016). ARACNe-AP: Gene network reverse engineering through adaptive partitioning inference of mutual information . Bioinformatics. 32. (14). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2233-2235.

Lachmann, A., Giorgi, F.M., Alvarez, M.J., Califano, A., Lachmann, A., Giorgi, F.M., Alvarez, M.J., Califano, A.(2016). Detection and removal of spatial bias in multiwell assays . Bioinformatics. 32. (13). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1959-1965.

Sepulveda, J.L., Gutierrez-Pajares, J.L., Luna, A., Yao, Y., Tobias, J.W., Thomas, S., Woo, Y., Giorgi, F., Komissarova, E.V., Califano, A., et al.(2016). High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing . Modern Pathology. 29. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 182-193.

Broyde, Joshua, Simpson, David, Wah, David A., Giorgi, Federico M., Petrey, Donald, Alvarez, Mariano J., Silkov, Antonina, Lachmann, Alexander, Hill, David E., Vidal, Marc, et al. (2015). Systems and structural biology approaches to elucidate new effectors in KRAS mutant tumors . Cancer Research.

Giorgi, Federico M. and Lopez, Gonzalo and Woo, Jung H. and Bisikirska, Brygida and Califano, Andrea and Bansal, Mukesh(2014). Inferring protein modulation from gene expression data using conditional mutual information . PLOS ONE. 9. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 569--578.

Wah, David A., Giorgi, Federico M., Petrey, Donald, Alvarez, Mariano J., Silkov, Tonya, Broyde, Josh, Rieckhof, Gabrielle E., Honig, Barry, Califano, Andrea, Wah, David A., et al. (2014). A systems biology approach to elucidate novel drug targets in KRAS mutant tumors . Molecular Cancer Research.

Wah, David A., Giorgi, Federico M., Petrey, Donald, Alvarez, Mariano J., Silkov, Tonya, Broyde, Josh, Rieckhof, Gabrielle E., Honig, Barry, Califano, Andrea, Wah, David A., et al. (2014). A systems biology approach to elucidate novel drug targets in KRAS mutant tumors . Molecular Cancer Research.

Giorgi, F.M., Lopez, G., Woo, J.H., Bisikirska, B., Califano, A., Bansal, M., Giorgi, F.M., Lopez, G., Woo, J.H., Bisikirska, B., et al.(2014). Inferring protein modulation from gene expression data using conditional mutual information . PLoS ONE. 9. (10).

Hughes, J.M., Salvatori, B., Giorgi, F.M., Bozzoni, I., Fatica, A., Hughes, J.M., Salvatori, B., Giorgi, F.M., Bozzoni, I., Fatica, A.(2014). CEBPA-regulated lncRNAs, new players in the study of acute myeloid leukemia . Journal of Hematology and Oncology. 7. (1).

Tosetti, R., Tardelli, F., Tadiello, A., Zaffalon, V., Giorgi, F.M., Guidi, L., Trainotti, L., Bonghi, C., Tonutti, P., Tosetti, R., et al.(2014). Molecular and biochemical responses to wounding in mesocarp of ripe peach (Prunus persica L. Batsch) fruit . Postharvest Biology and Technology. 90. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 40-51.

Aad, G., Abbott, B., Abdallah, J., Abdel Khalek, S., Abdinov, O., Aben, R., Abi, B., Abolins, M., AbouZeid, O.S., Abramowicz, H., et al.(2014). Measurements of jet vetoes and azimuthal decorrelations in dijet events produced in pp collisions at √s = 7 TeV using the ATLAS detector . European Physical Journal C. 74. (11).

Aad, G., Abbott, B., Abdallah, J., Abdel Khalek, S., Abdinov, O., Aben, R., Abi, B., Abolins, M., AbouZeid, O.S., Abramowicz, H., et al.(2014). Measurement of distributions sensitive to the underlying event in inclusive Z-boson production in pp collisions at √s = 7 TeV with the ATLAS detector . European Physical Journal C. 74. (12).

Aad, G., Abbott, B., Abdallah, J., Abdel Khalek, S., Abdinov, O., Aben, R., Abi, B., Abolins, M., AbouZeid, O.S., Abramowicz, H., et al.(2014). Measurement of the muon reconstruction performance of the ATLAS detector using 2011 and 2012 LHC proton–proton collision data . European Physical Journal C. 74. (11).

Del Fabbro, Cristian and Scalabrin, Simone and Morgante, Michele and Giorgi, Federico M.(2013). An extensive evaluation of read trimming effects on illumina NGS data analysis . PLOS ONE. 8. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1932--1943.

Giorgi, Federico M. and Del Fabbro, Cristian and Licausi, Francesco(2013). Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana . BIOINFORMATICS. 29. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 717--724.

Lee, Yang P. and Giorgi, Federico M. and Lohse, Marc and Kvederaviciute, Kotryna and Klages, Sven and Usadel, Björn and Meskiene, Irute and Reinhardt, Richard and Hincha, Dirk K.(2013). Transcriptome sequencing and microarray design for functional genomics in the extremophile arabidopsis relative thellungiella salsuginea (eutrema salsugineum) . BMC GENOMICS. 14. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--19.

Lee, Y.P., Giorgi, F.M., Lohse, M., Kvederaviciute, K., Klages, S., Usadel, B., Meskiene, I., Reinhardt, R., Hincha, D.K., Lee, Y.P., et al.(2013). Transcriptome sequencing and microarray design for functional genomics in the extremophile arabidopsis relative thellungiella salsuginea (eutrema salsugineum) . BMC Genomics. 14. (1).

Giorgi, F.M., Del Fabbro, C., Licausi, F., Giorgi, F.M., Del Fabbro, C., Licausi, F.(2013). Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana . Bioinformatics. 29. (6). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 717-724.

Li, J.-W., Bolser, D., Manske, M., Giorgi, F.M., Vyahhi, N., Usadel, B., Clavijo, B.J., Chan, T.-F., Wong, N., Zerbino, D., et al.(2013). The NGS wikibook: A dynamic collaborative online training effort with long-termsustainability . Briefings in Bioinformatics. 14. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 548-555.

Del Fabbro, C., Scalabrin, S., Morgante, M., Giorgi, F.M., Del Fabbro, C., Scalabrin, S., Morgante, M., Giorgi, F.M.(2013). An extensive evaluation of read trimming effects on illumina NGS data analysis . PLoS ONE. 8. (12).

Santaniello, A., Giorgi, F. M., Di Tommaso, D., Di Tommaso, G., Piaggesi, A., Perata, P., Santaniello, A., Giorgi, F. M., Di Tommaso, D., Di Tommaso, G., et al. (2013). Genomic Approaches to Unveil the Physiological Pathways Activated in Arabidopsis Treated with Plant-Derived Raw Extracts . Acta Horticulturae.

Santaniello, A. and Giorgi, F. M. and Tommaso, D. Di and Tommaso, G. Di and Piaggesi, A. and Perata, P.(2012). Genomic approaches to unveil the physiological pathways activated in Arabidopsis treated with plant-derived raw extracts . ACTA HORTICULTURAE. 1009. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 161--174.

Paparelli, Eleonora and Gonzali, Silvia and Parlanti, Sandro and Novi, Giacomo and Giorgi, Federico M. and Licausi, Francesco and Kosmacz, Monika and Feil, Regina and Lunn, John E. and Brust, Henrike and van Dongen, Joost T. and Steup, Martin and Perata, Pierdomenico(2012). Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in arabidopsis . PLANT PHYSIOLOGY. 160. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1237--1250.

Vasilevski, A., Giorgi, F.M., Bertinetti, L., Usadel, B., Vasilevski, A., Giorgi, F.M., Bertinetti, L., Usadel, B.(2012). LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: A model case for detection of novel mucilage and pectin metabolism genes . Molecular BioSystems. 8. (10). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2566-2574.

Paparelli, E., Gonzali, S., Parlanti, S., Novi, G., Giorgi, F.M., Licausi, F., Kosmacz, M., Feil, R., Lunn, J.E., Brust, H., et al.(2012). Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in arabidopsis . Plant Physiology. 160. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1237-1250.

Licausi, Francesco and Kosmacz, Monika and Weits, Daan A. and Giuntoli, Beatrice and Giorgi, Federico M. and Voesenek, Laurentius A. C. J. and Perata, Pierdomenico and Van Dongen, Joost T.(2011). Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization . NATURE. 479. (7373). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 419--422.

Mutwil, Marek and Klie, Sebastian and Tohge, Takayuki and Giorgi, Federico M. and Wilkins, Olivia and Campbell, Malcolm M. and Fernie, Alisdair R. and Usadel, Björn and Nikoloski, Zoran and Persson, Staffan(2011). PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species . PLANT CELL. 23. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 895--910.

Ryngajllo, Malgorzata and Childs, Liam and Lohse, Marc and Giorgi, Federico M. and Lude, Anja and Selbig, Joachim and Usadel, Björn(2011). SLocX: Predicting subcellular localization of Arabidopsis proteins leveraging gene expression data . FRONTIERS IN PLANT SCIENCE. 2. (SEP). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 96--106.

Ryngajllo, M., Childs, L., Lohse, M., Giorgi, F.M., Lude, A., Selbig, J., Usadel, B., Ryngajllo, M., Childs, L., Lohse, M., et al.(2011). SLocX: Predicting subcellular localization of Arabidopsis proteins leveraging gene expression data . Frontiers in Plant Science. 2. (SEP).

Mutwil, M., Klie, S., Tohge, T., Giorgi, F.M., Wilkins, O., Campbell, M.M., Fernie, A.R., Usadel, B., Nikoloski, Z., Persson, S., et al.(2011). PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species . Plant Cell. 23. (3). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 895-910.

Licausi, F., Giorgi, F.M., Schm&#228;lzlin, E., Usadel, B., Perata, P., Van Dongen, J.T., Geigenberger, P., Licausi, F., Giorgi, F.M., Schm&#228;lzlin, E., et al.(2011). HRE-type genes are regulated by growth-related changes in internal oxygen concentrations during the normal development of potato (solanum tuberosum) tubers . Plant and Cell Physiology. 52. (11). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1957-1972.

Licausi, F., Kosmacz, M., Weits, D.A., Giuntoli, B., Giorgi, F.M., Voesenek, L.A.C.J., Perata, P., Van Dongen, J.T., Licausi, F., Kosmacz, M., et al.(2011). Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization . Nature. 479. (7373). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 419-422.

Giorgi, Federico M. and Bolger, Anthony M. and Lohse, Marc and Usadel, Bjoern(2010). Algorithm-driven Artifacts in median polish summarization of Microarray data . BMC BIOINFORMATICS. 11. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--12.

Licausi, Francesco and Giorgi, Federico M. and Zenoni, Sara and Osti, Fabio and Pezzotti, Mario and Perata, Pierdomenico(2010). Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera . BMC GENOMICS. 11. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1--15.

Lohse, Marc and Nunes-Nesi, Adriano and Kruger, Peter and Nagel, Axel and Hannemann, Jan and Giorgi, Federico M. and Childs, Liam and Osorio, Sonia and Walther, Dirk and Selbig, Joachim and Sreenivasulu, Nese and Stitt, Mark and Fernie, Alisdair R. and Usadel, Bjorn(2010). Robin: An intuitive wizard application for R-based expression microarray quality assessment and analysis . PLANT PHYSIOLOGY. 153. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 642--651.

&#199;ivril, F., Wehenkel, A., Giorgi, F.M., Santaguida, S., Di Fonzo, A., Grigorean, G., Ciccarelli, F.D., Musacchio, A., &#199;ivril, F., Wehenkel, A., et al.(2010). Structural analysis of the RZZ complex reveals common ancestry with multisubunit vesicle tethering machinery . Structure. 18. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 616-626.

Lohse, M., Nunes-Nesi, A., Kruger, P., Nagel, A., Hannemann, J., Giorgi, F.M., Childs, L., Osorio, S., Walther, D., Selbig, J., et al.(2010). Robin: An intuitive wizard application for R-based expression microarray quality assessment and analysis . Plant Physiology. 153. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 642-651.

Licausi, F., Giorgi, F.M., Zenoni, S., Osti, F., Pezzotti, M., Perata, P., Licausi, F., Giorgi, F.M., Zenoni, S., Osti, F., et al.(2010). Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera . BMC Genomics. 11. (1).

Giorgi, F.M., Bolger, A.M., Lohse, M., Usadel, B., Giorgi, F.M., Bolger, A.M., Lohse, M., Usadel, B.(2010). Algorithm-driven Artifacts in median polish summarization of Microarray data . BMC Bioinformatics. 11.

Mutwil, Marek and Ruprecht, Colin and Giorgi, Federico M. and Bringmann, Martin and Usadel, Björn and Persson, Staffan(2009). Transcriptional wiring of cell wall-related genes in Arabidopsis . MOLECULAR PLANT. 2. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1015--1024.

Usadel, Björn and Obayashi, Takeshi and Mutwil, Marek and Giorgi, Federico M. and Bassel, George W. and Tanimoto, Mimi and Chow, Amanda and Steinhauser, Dirk and Persson, Staffan and Provart, Nicholas J.(2009). Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats . PLANT, CELL AND ENVIRONMENT. 32. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1633--1651.

Mutwil, M., Ruprecht, C., Giorgi, F.M., Bringmann, M., Usadel, B., Persson, S., Mutwil, M., Ruprecht, C., Giorgi, F.M., Bringmann, M., et al.(2009). Transcriptional wiring of cell wall-related genes in Arabidopsis . Molecular Plant. 2. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1015-1024.

Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F.M., Bassel, G.W., Tanimoto, M., Chow, A., Steinhauser, D., Persson, S., Provart, N.J., et al.(2009). Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats . Plant, Cell and Environment. 32. (12). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1633-1651.

Rambaldi, Davide and Giorgi, Federico M. and Capuani, Fabrizio and Ciliberto, Andrea and Ciccarelli, Francesca D.(2008). Low duplicability and network fragility of cancer genes . TRENDS IN GENETICS. 24. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 427--430.

Rambaldi, D., Giorgi, F.M., Capuani, F., Ciliberto, A., Ciccarelli, F.D., Rambaldi, D., Giorgi, F.M., Capuani, F., Ciliberto, A., Ciccarelli, F.D.(2008). Low duplicability and network fragility of cancer genes . Trends in Genetics. 24. (9). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 427-430.

Pietro Hiram Guzzi, Francesco Branda, Fabio Scarpa, Giancarlo Ceccarelli, Massimo Ciccozzi, Federico Manuel Giorgi, Pierangelo Veltri (2026). Integrated Downstream Analysis and Epidemiological Modelling of Hantavirus Infection: From Host Transcriptomics to Transmission Dynamics .

Irene Lorrai, Riccardo Maccioni, Itzamar Torres, Roberta Puliga, Jorge Marquez-Gaytan, Federico M. Giorgi, Vez Repunte-Canonigo, Pietro Paolo Sanna (2025). Gene network inference and master regulator analysis identifies the estrogen-related receptor gamma (ERRγ) as a therapeutic target for alcohol use disorder (AUD) .

Omri Avidan, Marina C. M. Martins, Regina Feil, Marc Lohse, Federico M. Giorgi, Armin Schlereth, John E. Lunn, Mark Stitt (2023). Direct and indirect responses of the Arabidopsis transcriptome to an induced increase in trehalose 6-phosphate .

Livia Beccacece, Filippo Costa, Jennifer Paola Pascali, Federico Manuel Giorgi (2023). Cross-species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances (PFAS) .

Livia Beccacece, Filippo Costa, Jennifer Paola Pascali, Federico Manuel Giorgi (2023). Cross-species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances (PFAS) .

Livia Beccacece, Filippo Costa, Jennifer Paola Pascali, Federico Manuel Giorgi (2023). Cross-species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances (PFAS) .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S3 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S3 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S4 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S5 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S5 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S6 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S6 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S7 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S7 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S4 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Master Regulator Analysis from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Data from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Data from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S1 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S1 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S2 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Figure S2 from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Florida Voli, Emanuele Valli, Luigi Lerra, Kathleen Kimpton, Federica Saletta, Federico M. Giorgi, Daniele Mercatelli, Jourdin R.C. Rouaen, Sylvie Shen, Jayne E. Murray, et al. (2023). Master Regulator Analysis from Intratumoral Copper Modulates PD-L1 Expression and Influences Tumor Immune Evasion .

Federico M. Giorgi, Daniele Pozzobon, Antonio Di Meglio, Daniele Mercatelli(2022). Genomic analysis of the recent monkeypox outbreak . Cold Spring Harbor Laboratory

Maria Stella de Biase, Florian Massip, Tzu-Ting Wei, Federico M. Giorgi, Rory Stark, Amanda Stone, Amy Gladwell, MarJn O’Reilly, Daniel Sch&#252;tte, Ines de Santiago, et al. (2021). Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk .

Simone Di Giacomo, Daniele Mercatelli, Amir Rakhimov, Federico M. Giorgi (2021). Preliminary report on SARS-CoV-2 Spike mutation T478K .

Francesco Ortuso, Daniele Mercatelli, Pietro Hiram Guzzi, Federico Manuel Giorgi (2020). Structural Genetics of circulating variants affecting the SARS-CoV-2 Spike / human ACE2 complex .

Daniele Mercatelli, Luca Triboli, Eleonora Fornasari, Forest Ray, Federico M. Giorgi (2020). coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations .

Pietro Hiram Guzzi, Daniele Mercatelli, Carmine Ceraolo, Federico M. Giorgi (2020). Master Regulator Analysis of the SARS-CoV-2/Human interactome .

Daniele Mercatelli, Gonzalo Lopez-Garcia, Federico M. Giorgi (2020). corto: a lightweight R package for Gene Network Inference and Master Regulator Analysis .

Carmine Ceraolo, Federico M. Giorgi (2020). Genomic variance of the 2019-nCoV coronavirus .

Metabolic supplementations and epigenetic alterations in in vitro AGC1 deficiency models @conference{ 11585_960053, author = {Babini, Giorgia and Poeta, Eleonora and Massenzio, Francesca and Federico Manuel Giorgi, and Mercolini, Laura and Lasorsa, Massimo and Monti, Barbara}, title = {Metabolic supplementations and epigenetic alterations in in vitro AGC1 deficiency models}, year = {2024}, booktitle = {Conference Report The Sixth Brainstorming Research Assembly for Young Neuroscientists (BraYn), Naples, Italy, 27–29 September 2023}, keywords = {Demyelinating disease, AGC1-deficiency, oligodendrocyte progenitor cells (OPCs), metabolic supplementation, epigenetic alterations}, doi = {10.3390/neurolint16010011}, pages = {186--188}, number = {1} } .

MIlazzo, Giorgio and Mercatelli, Daniele and Perini, Giovanni and Giorgi, Federico M.(2019). Unveiling Early Differentiation Induced by Histone Deacetylase Inhibitors in Neuroblastoma Cell Lines: A Single-Cell Transcriptomics Approach . 66324--325

Daniele Mercatelli, Elisabetta Pedace, Federico M. Giorgi, Pietro Hiram Guzzi(2021). Exploiting Molecular Basis of Age and Gender Differences in Outcomes of SARS-CoV-2 Infections . Cold Spring Harbor Laboratory

Pietro Hiram Guzzi, Elisabetta Pedace, Federico Manuel Giorgi (2020). Intersection between ageing-related Genes and SARS-CoV-2 Interactome: Is it higher than expected? .

Pietro Hiram Guzzi, Elisabetta Pedace, Federico Manuel Giorgi (2020). Intersection between ageing-related Genes and SARS-CoV-2 Interactome: Is it higher than expected? .

Daniele Mercatelli, Federico Manuel Giorgi(2020). Geographic and Genomic Distribution of SARS-CoV-2 Mutations . {MDPI} {AG}

Federico Manuel Giorgi(2020). Guest Editor of Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms . BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS.

Anže Godicelj, Ryan Blake, Federico M Giorgi, Marcel Gehrung, Sanjeev Kumar, Amy E Cullen, Kamal Kishore, Ashley Sawle, Matthew Eldridge, Florian Markowetz, et al.(2019). ZMIZ1 — A novel Estrogen Receptor co-activator that enhances the growth of ER+ breast cancer . Cold Spring Harbor Laboratory

Evan O. Paull, Alvaro Aytes, Prem Subramaniam, Federico M. Giorgi, Eugene F. Douglass, Brennan Chu, Sunny J. Jones, Siyuan Zheng, Roel Verhaak, Cory Abate-Shen, et al.(2019). A Modular Master Regulator Landscape Determines the Impact of Genetic Alterations on the Transcriptional Identity of Cancer Cells . Cold Spring Harbor Laboratory

Daniele Mercatelli, Forest Ray, Federico M. Giorgi(2018). Pan-Cancer and Single-Cell modelling of genomic alterations through gene expression . Cold Spring Harbor Laboratory

Andrew N. Holding, Federico M. Giorgi, Amanda Donnelly, Amy E. Cullen, Sankari Nagarajan, Luke A Selth, Florian Markowetz(2018). Network analysis of ChIP-seq data by VULCAN identifies GRHL2 as a key co-regulator of ERa in luminal breast cancer . Cold Spring Harbor Laboratory

Giorgi, F(2012). Expression-based reverse engineering of plant transcriptional networks . 1--140LAP LAMBERT Academic Publishing

Santaniello, A., Giorgi, F.M., Tommaso, D.D., Tommaso, G.D., Piaggesi, A., Perata, P., Santaniello, A., Giorgi, F.M., Tommaso, D.D., Tommaso, G.D., et al.(2012). Genomic approaches to unveil the physiological pathways activated in Arabidopsis treated with plant-derived raw extracts . Acta Horticulturae. 1009. Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 161-174.

Cross-species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances (PFAS) .

Cross-species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances (PFAS) .

Cross-species Transcriptomics Analysis Highlights Conserved Molecular Responses to Per- and Polyfluoroalkyl Substances (PFAS) .

Integrated Downstream Analysis and Epidemiological Modelling of Hantavirus Infection: From Host Transcriptomics to Transmission Dynamics .

Geographic and Genomic Distribution of SARS-CoV-2 Mutations .