Pubblicazioni di Paci Paola

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-

2016

Fiscon G, Iannello G, Paci P

A perspective on the algorithms predicting and evaluating the RNA secondary structure. JOURNAL OF GENETICS AND GENOME RESEARCH 2016: -

Santoni D, Paci P, Di Paola L and Giuliani A

Are proteins just coiled cords? Local and Global analysis of Contact Maps reveals the backbone-dependent nature of proteins. CURRENT PROTEIN & PEPTIDE SCIENCE 2016: 26-29

Dal Santo S, Palliotti A, Zenoni S, Tornielli GB, Fasoli M, Paci P, Tombesi S, Frioni T, Silvestroni O, Bellincontro A, d'Onofrio C, Matarese F, Gatti M, Poni S and Pezzotti M

Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars. BMC GENOMICS 2016: -

Fiscon G, Conte F, Colombo T, Farina L, Paci P

Integrated network analysis for studying human lung squamous cell carcinoma. Proceeding of GNB2016 2016, section: Bioinformatica 2016: -

Cumbo F, Weitschek E, Paci P, Colombo T, Bertolazzi P and Felici G

IRIS-TCGA: An Information Retrieval And Integration System For Cancer Genomic Data. Proceeding of 13th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics 2016 (CIBB 2016) 2016: -

Gurtner A, Garibaldi F, Falcone E, Trisciuoglio D, Colombo T, Lisek K, Walerych D, Dal Sal G, Paci P, Bossi G, and Piaggio G

Mutant p53 inhibits miRNA biogenesis by interfering with the Microprocessor complex. ONCOGENE 2016: 3760-3770

Garbuglia AR, Visco-Comandini U, Lionetti R, Lapa D, Castiglione F, D’Offizi G, Taibi C, Montalbano M, Capobianchi MR, Paci P

Ultrasensitive HCV RNA quantification in antiviral triple therapy: new insight on viral clearance dynamics and treatment outcome predictors. PLOS ONE 2016: -

2015

Fiscon Giulia, P. Paci, T. Colombo, G. Iannello

A new procedure to analyze RNA non-branching structures. CURRENT BIOINFORMATICS 2015: 242-258

M. C. Palumbo, Farina Lorenzo, P. Paci

Kinetic effects and modeling of mRNA turnover. WILEY INTERDISCIPLINARY REVIEWS. RNA 2015: 327-336

Fiscon Giulia, P. Paci, G. Iannello

MONSTER v1.1: a tool to extract and search for RNA non-branching structures. BMC GENOMICS 2015: S1-

Del Chierico Federica, Vernocchi Pamela, Petrucca Andrea, Paci Paola, Fuentes Susana, Pratico' Giulia, Capuani Giorgio, Masotti Andrea, Reddel Sofia, Russo Alessandra, Vallone Cristina, Salvatori Guglielmo, Buffone Elsa, Signore Fabrizio, Rigon Giuliano, Dotta Andrea, Miccheli Alfredo, de Vos Willem M, Dallapiccola Bruno, Putignani Lorenza

Phylogenetic and metabolic tracking of gut microbiota during perinatal development.. PLOS ONE 2015: 1-26

Colombo Teresa, Farina Lorenzo, Macino Giuseppe, Paci Paola

PVT1: a rising star among oncogenic long non-coding RNAs. BIOMED RESEARCH INTERNATIONAL 2015: -

Garbuglia Anna Rosa, Lionetti Raffaella, Lapa Daniele, Taibi Chiara, Visco-Comandini Ubaldo, Montalbano Marzia, D'Offizi Gianpiero, Castiglione Filippo, Capobianchi Maria Rosaria, Paci P

The clinical significance of HCV core antigen detection during Telaprevir/Peg-Interferon/Ribavirin therapy in patients with HCV 1 genotype infection. JOURNAL OF CLINICAL VIROLOGY 2015: 68-73

2014

PACI PAOLA, Colombo Teresa, FARINA Lorenzo

Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. BMC SYSTEMS BIOLOGY 2014: -

Cumbo Fabio, Paci P, Santoni Daniele, Di Paola Luisa, Giuliani Alessandro

GIANT: A Cytoscape Plugin for Modular Networks. PLOS ONE 2014: -

Palumbo M. C., Zenoni S., Fasoli M., Massonet M., FARINA Lorenzo, Castiglione F., Pezzotti M., Paci P.

Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development. PLANT CELL 2014: 4617-4635

Tasdighian Setareh, Di Paola Luisa, De Ruvo Micol, Paci P, Santoni Daniele, Palumbo Pasquale, Mei Giampiero, Di Venere Almerinda, Giuliani Alessandro

Modules Identification in Protein Structures: The Topological and Geometrical Solutions. JOURNAL OF CHEMICAL INFORMATION AND MODELING 2014: 159-168

Fiscon Giulia, P. Paci, T. Colombo, G. Iannello

MONSTER v1.0: a novel procedure to extract and search for RNA non-branching structures. BITS annual meeting 2014 2014: 77-78

Bertolazzi Paola, Bock Mary Ellen, Guerra Concettina, Paci P, Santoni Daniele

On the integration of protein-protein interaction networks with gene expression and 3D structural data: What can be gained?. THE EUROPEAN PHYSICAL JOURNAL PLUS 2014: -

2013

Fiscon Giulia, P. Paci, T. Colombo, G. Iannello

Development of an algorithm to identify RNA secondary structures.. FEBS workshop on Translating Epigenomes into Function: a Next Generation Challenge for Human Disease- Abstract Book 2013: 71-71

Canitano N, Paci P, Ippoliti F

Emerging Role of the Fat Free Mass Preservation during Weight Loss Therapy through a Novel Advanced Bio-Impedance Device (BIA-ACC). JOURNAL OF OBESITY & WEIGHT LOSS THERAPY 2013: -

Santoni Daniele, Castiglione Filippo, Paci P

Identifying Correlations between Chromosomal Proximity of Genes and Distance of Their Products in Protein-Protein Interaction Networks of Yeast. PLOS ONE 2013: -

Di Paola L., De Ruvo M., Paci P, Santoni D., Giuliani A.

Protein Contact Networks: An Emerging Paradigm in Chemistry. CHEMICAL REVIEWS 2013: 1598-1613

Giuliani A, Di Paola L, Paci P, De Ruvo M, Arcangeli C, Santoni D and Celino M

Proteins as Netwoks: Usefulness of Graph Theory in Protein Science. Advances in Protein and Peptide Sciences 2013: 307-317

Fiscon Giulia, P. Paci, T. Colombo, G. Iannello

STRUCTURAL ANALYSIS OF LONG NON-CODING RNAs. 2013: -