Pubblicazioni di Paci Paola

2022

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: -

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

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: -

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-

2020

Conte F., Fiscon G., Licursi V., Bizzarri D., D'Anto T., Farina L., Paci P.

A paradigm shift in medicine: a comprehensive review of network-based approaches. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020: -

Belardinilli Francesca, Capalbo Carlo, Malapelle Umberto, Pisapia Pasquale, Raimondo Domenico, Milanetti Edoardo, Mahdavian Yasaman, Liccardi Carlotta, Paci Paola, Sibilio Pasquale, Pepe Francesco, Bonfiglio Caterina, Mezi Silvia, Magri Valentina, Coppa Anna, Nicolussi Arianna, Gradilone Angela, Petroni Marialaura, Di Giulio Stefano, Fabretti Francesca, Infante Paola, Coni Sonia, Canettieri Gianluca, Troncone Giancarlo, Giannini Giuseppe

Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer. FRONTIERS IN ONCOLOGY 2020: -

Gaglio Daniela, Bonanomi Marcella, Valtorta Silvia, Bharat Rohit, Ripamonti Marilena, Conte Federica, Fiscon Giulia, Righi Nicole, Napodano Elisabetta, Papa Federico, Raccagni Isabella, Parker Seth J., Cifola Ingrid, Camboni Tania, Paci Paola, Maria Colangelo Anna, Vanoni Marco, Metallo Christian M., Maria Moresco Rosa, Alberghina Lilia

Disruption of redox homeostasis for combinatorial drug eefficacy in K-Ras tumors as revealed by metabolic connectivity proling. CANCER & METABOLISM 2020: 1-15

Sias C., Guarrasi V., Minosse C., Lapa D., Nonno F. D., Capobianchi M. R., Garbuglia A. R., Del Porto P., Paci P.

Human Papillomavirus infections in cervical samples from HIV-positive women: evaluation of the presence of the nonavalent HPV genotypes and genetic diversity. FRONTIERS IN MICROBIOLOGY 2020: -

Paci Paola, Fiscon Giulia, Conte Federica, Licursi Valerio, Morrow Jarrett, Hersh Craig, Cho Michael, Castaldi Peter, Glass Kimberly, Silverman Edwin K., Farina Lorenzo

Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. SCIENTIFIC REPORTS 2020: -

Silverman E. K., Schmidt H. H. H. W., Anastasiadou E., Altucci L., Angelini M., Badimon L., Balligand J. -L., Benincasa G., Capasso G., Conte F., Di Costanzo A., Farina L., Fiscon G., Gatto L., Gentili M., Loscalzo J., Marchese C., Napoli C., Paci P., Petti M., Quackenbush J., Tieri P., Viggiano D., Vilahur G., Glass K., Baumbach J.

Molecular networks in Network Medicine: Development and applications. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020: -

Vernocchi P., Gili T., Conte F., Del Chierico F., Conta G., Miccheli A., Botticelli A., Paci P., Caldarelli G., Nuti M., Marchetti P., Putignani L.

Network analysis of gut microbiome and metabolome to discover microbiota-linked biomarkers in patients affected by non-small cell lung cancer. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 2020: 1-19

Panebianco Valeria, Pecoraro Martina, Fiscon Giulia, Paci Paola, Farina Lorenzo, Catalano Carlo

Prostate cancer screening research can benefit from network medicine: an emerging awareness. NPJ SYSTEMS BIOLOGY AND APPLICATIONS 2020: -

Maria Grimaldi Anna, Conte Federica, Pane Katia, Fiscon Giulia, Mirabelli Peppino, Baselice Simona, Giannatiempo Rosa, Messina Francesco, Franzese Monica, Salvatore Marco, Paci Paola, Mariarosaria Incoronato And

The new paradigm of Network Medicine to analyse breast cancer phenotypes. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 2020: -

2019

Capalbo Carlo, Belardinilli Francesca, Raimondo Domenico, Milanetti Edoardo, Malapelle Umberto, Pisapia Pasquale, Magri Valentina, Prete Alessandra, Pecorari Silvia, Colella Mariarosaria, Coppa Anna, Bonfiglio Caterina, Nicolussi Arianna, Valentini Virginia, Tessitore Alessandra, Cardinali Beatrice, Petroni Marialaura, Infante Paola, Santoni Matteo, Filetti Marco, Colicchia Valeria, Paci Paola, Mezi Silvia, Longo Flavia, Cortesi Enrico, Marchetti Paolo, Troncone Giancarlo, Bellavia Diana, Canettieri Gianluca, Giannini Giuseppe

A simplified genomic profiling approach predicts outcome in metastatic colorectal cancer. CANCERS 2019: -

Falcone Rosa, Conte Federica, Fiscon Giulia, Pecce Valeria, Sponziello Marialuisa, Durante Cosimo, Farina Lorenzo, Filetti Sebastiano, Paci Paola, Verrienti Antonella

BRAF V600E -mutant cancers display a variety of networks by SWIM analysis: prediction of vemurafenib clinical response. ENDOCRINE 2019: 406-413

Gabriele Magris, Gabriele Di Gaspero, Fabio Marroni, Sara Zenoni, Giovanni Battista Tornielli, Mirko Celii, Emanuele De Paoli, Mario Pezzotti, Federica Conte, PACI P, Michele Morgante

Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties. PLANT JOURNAL 2019: 895-909

Fiscon Giulia, Conte Federica, Farina Lorenzo, Pellegrini Marco, Russo Francesco, Paci Paola

Identification of Disease-miRNA networks across different cancer types using SWIM. MicroRNA Target Identication: Methods and Protocols 2019: 169-181

Mocavini Ivano, Pippa Simone, Licursi Valerio, Paci Paola, Trisciuoglio Daniela, Mannironi Cecilia, Presutti Carlo, Negri Rodolfo

JARID1B expression and its function in DNA damage repair are tightly regulated by miRNAs in breast cancer. CANCER SCIENCE 2019: 1232-1243

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

MIENTURNET: An interactive web tool for microRNA-target enrichment and network-based analysis. BMC BIOINFORMATICS 2019: 545-

Mahrou Vahabi, Claudio Pulito, Andrea Sacconi, Sara Donzelli, Marco D'Andrea, Valentina Manciocco, Raul Pellini, PACI P, Giuseppe Sanguineti, Lidia Strigari, Giuseppe Spriano, PaolaMuti , Pier Paolo Pandol, Sabrina Strano, Shahrokh Safarian , Federica Ganci, Giovanni Blandino

miR-96-5p targets PTEN expression affecting radio-chemosensitivity of HNSCC cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH 2019: -

Tieri Paolo, Farina Lorenzo, Petti Manuela, Astolfi Laura, Paci Paola, Castiglione Filippo

Network Inference and Reconstruction in Bioinformatics. Encyclopedia of Bioinformatics and Computational Biology 2019: 805-813

2018

Farina Lorenzo, Paci Paola

A feature-based integrated scoring scheme for cell cycle-regulated genes prioritization. JOURNAL OF THEORETICAL BIOLOGY 2018: 130-141

Fiscon G., Conte F., Licursi V., Nasi S., Paci P.

Computational identification of specific genes for glioblastoma stem-like cells identity. SCIENTIFIC REPORTS 2018: 1-10

Vernocchi P., Chierico F. D., Russo A., Majo F., Rossitto M., Valerio M., Casadei L., Storia A. L., De Filippis F., Rizzo C., Manetti C., Paci P., Ercolini D., Marini F., Fiscarelli E. V., Dallapiccola B., Lucidi V., Miccheli A., Putignani L.

Gut microbiota signatures in cystic fibrosis. Loss of host CFTR function drives the microbiota enterophenotype. PLOS ONE 2018: 1-23

Francesco Russo, Giulia Fiscon, Federica Conte, Milena Rizzo, Paci P, Marco Pellegrini

Interplay between long non-coding RNAs and microRNAs in cancer. Computational Cell Biology: Methods and Protocols 2018: 75-92

Guzzi R, Colombo T, Paci P

Inverse Problems in Systems Biology: A Critical Review. Systems Biology 2018: 69-94

Fiscon Giulia, Conte Federica, Farina Lorenzo, Paci Paola

Network-based approaches to explore complex biological systems towards network medicine. GENES 2018: -

Falcone R., Paci P., Verrienti A., Fiscon G., Sponziello M., Conte F., Pecce V., Rosignolo F., Grani G., Lamartina L., Ramundo V., Durante C., Farina L., Filetti S.

Prediction of response to vemurafenib in BRAF V600E mutant cancers based on a network approach. ANNALS OF ONCOLOGY 2018: viii667-viii668

Giulia Fiscon, Federica Conte, PACI P

SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines. BMC BIOINFORMATICS 2018: -

2017

Del Chierico Federica, Nobili Valerio, Vernocchi Pamela, Russo Alessandra, Stefanis Cristiano De, Gnani Daniela, Furlanello Cesare, Zandonà Alessandro, Paci Paola, Capuani Giorgio, Dallapiccola Bruno, Miccheli Alfredo, Alisi Anna, Putignani Lorenza

Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta-omics-based approach. HEPATOLOGY 2017: 451-464

Massonnet M, Fasoli M, Tornielli GB, Altieri M, Sandri M, Zuccolotto P, Paci P, Gardiman M, Zenoni S, and Pezzotti M

Ripening Transcriptomic Program in Red and White Grapevine Varieties Corre- lates with Berry Skin Anthocyanin Accumulation. PLANT PHYSIOLOGY 2017: 2376-2396

Conte Federica, Fiscon Giulia, Chiara Matteo, Colombo Teresa, Farina Lorenzo, Paci Paola

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer. PLOS ONE 2017: 1-22

Paci Paola, Colombo Teresa, Fiscon Giulia, Gurtner Aymone, Pavesi Giulio, Farina Lorenzo

SWIM: A computational tool to unveiling crucial nodes in complex biological networks. SCIENTIFIC REPORTS 2017: 44797-

Verduci Lorena, Ferraiuolo Maria, Sacconi Andrea, Ganci Federica, Vitale Jlenia, Colombo Teresa, Paci Paola, Strano Sabrina, Macino Giuseppe, Rajewsky Nikolaus, Blandino Giovanni

The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex. GENOME BIOLOGY 2017: 237-