Pubblicazioni di Paci Paola

2024

Sibilio P., Conte F., Huang Y., Castaldi P. J., Hersh C. P., Demeo D. L., Silverman E. K., Paci P.

Correlation-based network integration of lung RNA sequencing and DNA methylation data in chronic obstructive pulmonary disease. HELIYON 2024: -

2023

Vitiello M., Mercatanti A., Podda M. S., Baldanzi C., Prantera A., Sarti S., Rizzo M., Salvetti A., Conte F., Fiscon G., Paci P., Poliseno L.

A Network of MicroRNAs and mRNAs Involved in Melanosome Maturation and Trafficking Defines the Lower Response of Pigmentable Melanoma Cells to Targeted Therapy. CANCERS 2023: -

Fiscon G., Conte F., Paci P.

A network-based algorithm for identifying drug repurposing opportunities for complex diseases. Convegno Nazionale di Bioingegneria 2023: -

Brunetti M., Paci P., Fiscon G.

A network-based bioinformatic analysis for identifying potential repurposable active molecules in different types of human cancers. Proceedings - 2023 2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023 2023: 3626-3631

Sibilio Pasquale, DI GIULIO Stefano, Funari Alessio, Paci Paola, Veschi Veronica, Giannini Giuseppe

A single-cell transcriptomic analysis of Neuroblastomas revealed a selective cGAS-STING pathway suppression in malignant cells. PROCEEDINGS IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2023: -

Conte F., Fiscon G., Paci P.

Bioinformatics analyses to identify molecular gene signatures associated with breast cancer phenotypes. Convegno Nazionale di Bioingegneria 2023: -

Fiscon G., Funari A., Paci P.

Circular RNA mediated gene regulation in human breast cancer: A bioinformatics analysis. PLOS ONE 2023: -

Vernocchi P., Marangelo C., Guerrera S., Del Chierico F., Guarrasi V., Gardini S., Conte F., Paci P., Ianiro G., Gasbarrini A., Vicari S., Putignani L.

Gut microbiota functional profiling in autism spectrum disorders: bacterial VOCs and related metabolic pathways acting as disease biomarkers and predictors. FRONTIERS IN MICROBIOLOGY 2023: 1287350-

Zulian V., Fiscon G., Paci P., Garbuglia A. R.

Hepatitis B Virus and microRNAs: A Bioinformatics Approach. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 2023: -

Catanzaro Giuseppina, Conte Federica, Trocchianesi Sofia, Splendiani Elena, Bimonte Viviana Maria, Mocini Edoardo, Filardi Tiziana, Po Agnese, Besharat Zein Mersini, Gentile Maria Cristina, Paci Paola, Morano Susanna, Migliaccio Silvia, Ferretti Elisabetta

Network analysis identifies circulating miR-155 as predictive biomarker of type 2 diabetes mellitus development in obese patients: a pilot study. SCIENTIFIC REPORTS 2023: 19496-

Funari A., Paci P., Conte F.

Network-based analysis to uncover drug-induced adverse side-effects. Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023 2023: 3632-3637

Zulian V., Garbuglia A. R., Fiscon G., Paci P.

Overview of bioinformatic tools to study viral infections. Proceedings - 2023 2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023 2023: 3669-3675

Pecoraro Martina, Catanzaro Giuseppina, Conte Federica, Besharat ZEIN MERSINI, Messina Emanuele, Laschena Ludovica, Trocchianesi Sofia, Splendiani Elena, Sciarra Alessandro, Catalano Carlo, Paci Paola, Ferretti Elisabetta, Panebianco Valeria

Prospective validation study of a novel integrated pathway based on clinical features, MRI biomarkers and microRNAs for early detection of prostate cancer. EUROPEAN UROLOGY ONCOLOGY 2023: -

Paci P.

The long story of SWIM methodology: from grapevine to personalised medicine. Proceedings of the 8th National Congress of Bioengineering, GNB 2023 2023: -

2022

Fiscon Giulia, Conte Federica, Farina Lorenzo, Paci Paola

A Comparison of Network-Based Methods for Drug Repurposing along with an Application to Human Complex Diseases. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 2022: 1-15

Petroni Marialaura, Fabretti Francesca, DI GIULIO Stefano, NICOLIS DI ROBILANT Vittoria, LA MONICA Veronica, Moretti Marta, Belardinilli Francesca, Bufalieri Francesca, Coppa Anna, Paci Paola, Corsi Alessandro, DE SMAELE Enrico, Coni Sonia, Canettieri Gianluca, DI MARCOTULLIO Lucia, Zhao‐qi Wang, Giannini Giuseppe

A gene dosage‐dependent effect unveils NBS1 as both a haploinsufficient tumour suppressor and an essential gene for SHH‐medulloblastoma. NEUROPATHOLOGY & APPLIED NEUROBIOLOGY 2022: -

Conte F., Sibilio P., Fiscon G., Paci P.

A Transcriptome- and Interactome-Based Analysis Identifies Repurposable Drugs for Human Breast Cancer Subtypes. SYMMETRY 2022: 2230-

Conte F., Paci P.

Alzheimer’s disease: insights from a network medicine perspective. SCIENTIFIC REPORTS 2022: -

Sibilio P., Belardinilli F., Licursi V., Paci P., Giannini G.

An integrative in-silico analysis discloses a novel molecular subset of colorectal cancer possibly eligible for immune checkpoint immunotherapy. BIOLOGY DIRECT 2022: 10-

Paci P., Fiscon G., Conte F., Wang R. -S., Handy D. E., Farina L., Loscalzo J.

Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects. NPJ SYSTEMS BIOLOGY AND APPLICATIONS 2022: 12-

Cipollari S., Guarrasi V., Pecoraro M., Bicchetti M., Messina E., Farina L., Paci P., Catalano C., Panebianco V.

Convolutional neural networks for automated classification of prostate multiparametric magnetic resonance imaging based on image quality. JOURNAL OF MAGNETIC RESONANCE IMAGING 2022: -

Vernocchi P., Ristori M. V., Guerrera S., Guarrasi V., Conte F., Russo A., Lupi E., Albitar-Nehme S., Gardini S., Paci P., Ianiro G., Vicari S., Gasbarrini A., Putignani L.

Gut Microbiota Ecology and Inferred Functions in Children With ASD Compared to Neurotypical Subjects. FRONTIERS IN MICROBIOLOGY 2022: -

Tiberti S., Catozzi C., Croci O., Ballerini M., Cagnina D., Soriani C., Scirgolea C., Gong Z., He J., Macandog A. D., Nabinejad A., Nava Lauson C. B., Quinte' A., Bertalot G., Petz W. L., Ravenda S. P., Licursi V., Paci P., Rasponi M., Rotta L., Fazio N., Ren G., Fumagalli-Romario U., Schaefer M. H., Campaner S., Lugli E., Nezi L., Manzo T.

GZMKhigh CD8+ T effector memory cells are associated with CD15high neutrophil abundance in non-metastatic colorectal tumors and predict poor clinical outcome. NATURE COMMUNICATIONS 2022: -

Fiscon Giulia, Sibilio Pasquale, Funari Alessio, Conte Federica, Paci Paola

Identification of Potential Repurposable Drugs in Alzheimer’s Disease Exploiting a Bioinformatics Analysis. JOURNAL OF PERSONALIZED MEDICINE 2022: -

Conte F., Sibilio P., Grimaldi A. M., Salvatore M., Paci P., Incoronato M.

In silico recognition of a prognostic signature in basal-like breast cancer patients. PLOS ONE 2022: e0264024-

Angiulli F., Colombo T., Fassetti F., Furfaro A., Paci P.

Mining sponge phenomena in RNA expression data. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2022: 2150022-

Tumino N., Besi F., Martini S., Di Pace A. L., Munari E., Quatrini L., Pelosi A., Fiore P. F., Fiscon G., Paci P., Scordamaglia F., Covesnon M. G., Bogina G., Mingari M. C., Moretta L., Vacca P.

Polymorphonuclear Myeloid-Derived Suppressor Cells Are Abundant in Peripheral Blood of Cancer Patients and Suppress Natural Killer Cell Anti-Tumor Activity. FRONTIERS IN IMMUNOLOGY 2022: 1-12

Amadio Susanna, Conte Federica, Esposito Giorgia, Fiscon Giulia, Paci Paola, Volonté Cinzia

Repurposing Histaminergic Drugs in Multiple Sclerosis. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 2022: 1-16

Paci P., Fiscon G.

SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks. BMC BIOINFORMATICS 2022: 1-13

Conte F., Papa F., Paci P., Farina L.

StaRTrEK:in silico estimation of RNA half-lives from genome-wide time-course experiments without transcriptional inhibition. BMC BIOINFORMATICS 2022: 190-

Paci P., Fiscon G.

SWIMmeR: An R-based software to unveiling crucial nodes in complex biological networks. BIOINFORMATICS 2022: 586-588

2021

Conte F., Fiscon G., Sibilio P., Licursi V., Paci P.

An Overview of the computational models dealing with the regulatory ceRNA mechanism and ceRNA deregulation in cancer. Methods in Molecular Biology 2021: 149-164

Fiscon G., Salvadore F., Guarrasi V., Garbuglia A. R., Paci P.

Assessing the impact of data-driven limitations on tracing and forecasting the outbreak dynamics of COVID-19. COMPUTERS IN BIOLOGY AND MEDICINE 2021: 104657-

Sarno F., Benincasa G., List M., Barabasi A. -L., Baumbach J., Ciardiello F., Filetti S., Glass K., Loscalzo J., Marchese C., Maron B. A., Paci P., Parini P., Petrillo E., Silverman E. K., Verrienti A., Altucci L., Napoli C.

Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside. CLINICAL EPIGENETICS 2021: 66-103

Fiscon G., Conte F., Amadio S., Volonte C., Paci P.

Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. NEUROTHERAPEUTICS 2021: -

Paci P., Fiscon G., Conte F., Wang R. -S., Farina L., Loscalzo J.

Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery. NPJ SYSTEMS BIOLOGY AND APPLICATIONS 2021: -

Fiscon G., Pegoraro S., Conte F., Manfioletti G., Paci P.

Gene network analysis using SWIM reveals interplay between the transcription factor-encoding genes HMGA1, FOXM1, and MYBL2 in triple-negative breast cancer. FEBS LETTERS 2021: 1569-1586

Sibilio Pasquale, Bini Simone, Fiscon Giulia, Sponziello Marialuisa, Conte Federica, Pecce Valeria, Durante Cosimo, Paci Paola, Falcone Rosa, Norata Giuseppe Danilo, Farina Lorenzo, Verrienti Antonella

In silico drug repurposing in COVID-19. A network-based analysis. BIOMÉDECINE & PHARMACOTHÉRAPIE 2021: 1-10

Salvadore F., Fiscon G., Paci P.

Integro-differential approach for modeling the COVID-19 dynamics - Impact of confinement measures in Italy. COMPUTERS IN BIOLOGY AND MEDICINE 2021: 105013-

Panebianco Valeria, Paci Paola, Pecoraro Martina, Conte Federica, Carnicelli Giorgia, Besharat Zein Mersini, Catanzaro Giuseppina, Splendiani Elena, Sciarra Alessandro, Farina Lorenzo, Catalano Carlo, Ferretti Elisabetta

Network analysis integrating microRNA expression profiling with MRI biomarkers and clinical data for prostate cancer early detection: a proof of concept study. BIOMEDICINES 2021: -

Tumino N., Weber G., Besi F., Del Bufalo F., Bertaina V., Paci P., Quatrini L., Antonucci L., Sinibaldi M., Quintarelli C., Maggi E., De Angelis B., Locatelli F., Moretta L., Vacca P., Caruana I.

Polymorphonuclear myeloid-derived suppressor cells impair the anti-tumor efficacy of gd2.car t-cells in patients with neuroblastoma. JOURNAL OF HEMATOLOGY & ONCOLOGY 2021: 1-7

Fiscon G., Conte F., Farina L., Paci P.

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19. PLOS COMPUTATIONAL BIOLOGY 2021: e1008686-

Fiscon G., Paci P.

SAveRUNNER: an R-based tool for drug repurposing. BMC BIOINFORMATICS 2021: -

Petti M., Verrienti A., Paci P., Farina L.

SEaCorAl: Identifying and contrasting the regulation-correlation bias in RNA-Seq paired expression data of patient groups. COMPUTERS IN BIOLOGY AND MEDICINE 2021: -

Pecce V., Verrienti A., Fiscon G., Sponziello M., Conte F., Abballe L., Durante C., Farina L., Filetti S., Paci P.

The role of FOSL1 in stem-like cell reprogramming processes. SCIENTIFIC REPORTS 2021: 1-11

Bonanomi M., Salmistraro N., Fiscon G., Conte F., Paci P., Bravata V., Forte G. I., Volpari T., Scorza M., Mastroianni F., D'errico S., Avolio E., Piccialli G., Colangelo A. M., Vanoni M., Gaglio D., Alberghina L.

Transcriptomics and metabolomics integration reveals redox-dependent metabolic rewiring in breast cancer cells. CANCERS 2021: 5058-