Pubblicazioni di Farina Lorenzo

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: -

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: -

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

Petti M., Farina L., Francone F., Lucidi S., Macali Amalia, Palagi L., De Santis M.

Moses: A new approach to integrate interactome topology and functional features for disease gene prediction. GENES 2021: 1-16

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: -

Farina Lorenzo

Network as a language for precision medicine. ANNALI DELL'ISTITUTO SUPERIORE DI SANITÀ 2021: 331-344

Colonnese Stefania, Petti Manuela, Farina Lorenzo, Scarano Gaetano, Cuomo Francesca

Protein-protein Interaction prediction via graph signal processing. IEEE ACCESS 2021: 1-12

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: -

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

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: -

Petti Manuela, Bizzarri Daniele, Verrienti Antonella, Falcone Rosa, Farina Lorenzo

Connectivity significance for disease gene prioritization in an expanding universe. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020: 2155-2161

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: -

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: -

2019

Gentili M., Martini L., Petti M., Farina L., Becchetti L.

Biological Random Walks: Integrating heterogeneous data in disease gene prioritization. 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2019 2019: 1-8

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

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

Angelini M., Blasilli G., Farina L., Lenti S., Santucci G.

NEMESIS (NEtwork MEdicine analySIS): Towards visual exploration of network medicine data. VISIGRAPP 2019 - Proceedings of the 14th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications 2019: 322-329

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

Falcone R., Strigari L., Farina L., Marchetti P.

Response to: comment on “Impact of tumor site on the prognosis of small bowel adenocarcinoma”. TUMORI 2019: 532-532

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 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

2017

Cacace Filippo, Farina Lorenzo, Setola Roberto, Germani Alfredo

Preface. Positive Systems Theory and Applications (POSTA 2016) Rome, Italy, September 14-16, 2016 2017: v-vi

Benvenuti L., Farina L.

Revisiting the linear recursions with nonnegative coefficients problem. LINEAR ALGEBRA AND ITS APPLICATIONS 2017: 191-194

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-

Guarascio F., Farina L.

Topological analysis of migration flows (the case of political refugees). INTERNATIONAL JOURNAL OF COMPUTATIONAL ECONOMICS AND ECONOMETRICS 2017: 359-380

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: -

2015

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

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

Belli Kullan Jayakumar, Lopes Paim Pinto Daniela, Bertolini Edoardo, Fasoli Marianna, Zenoni Sara, Tornielli Giovanni Battista, Pezzotti Mario, Meyers Blake C., Farina Lorenzo, Pè Mario Enrico, Mica Erica

miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing. BMC GENOMICS 2015: -

Colombo Teresa, Farina Lorenzo, Macino Giuseppe, Paci Paola

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

2014

DE SANTIS Marianna, F. Rinaldi, E. Falcone, Lucidi Stefano, G. Piaggio, A. Gurtner, Farina Lorenzo

Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes. BIOINFORMATICS 2014: 228-233

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: -

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

2013

Silvia Dal Santo, Giovanni Tornielli, Sara Zenoni, Marianna Fasoli, Farina Lorenzo, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti

The plasticity of the grapevine berry transcriptome. GENOME BIOLOGY 2013: r54-

2012

F. Cacace, Farina Lorenzo, A. Germani, C. Manes

Internally Positive Representation of a Class of Continuous Time Systems. IEEE TRANSACTIONS ON AUTOMATIC CONTROL 2012: 3158-3163

Cacace Filippo, PACI PAOLA, Cusimano Valerio, Germani Alfredo, FARINA Lorenzo

Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay. PLOS COMPUTATIONAL BIOLOGY 2012: -

M. Fasoli, S. Dal Santo, S. Zenoni, G. B. Tornielli, Farina Lorenzo, A. Zamboni, A. Porceddu, L. Venturini, M. Bicego, V. Murino, A. Ferrarini, M. Delledonne, M. Pezzotti

The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program. PLANT CELL 2012: 3489-3505

S. Camiolo, Farina Lorenzo, A. Porceddu

The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana. GENETICS 2012: 641-+

2011

Gabriele Romagnoli, Enrico Cundari, Negri Rodolfo, Marco Crescenzi, Farina Lorenzo, Alessandro Giuliani, Bianchi Michele Maria

Synchronous protein cycling in batch cultures of the yeast Saccharomyces cerevisiae at log growth phase. EXPERIMENTAL CELL RESEARCH 2011: 2958-2968

2010

Cacace Filippo, Farina Lorenzo, Germani Alfredo, Manes Costanzo

A method for internally positive realization of continuous time systems. Proceedings of the IEEE Conference on Decision and Control 2010: 4978-4983

Cacace Filippo, Farina Lorenzo, Germani Alfredo, Palumbo Pasquale

Discrete-time models for gene transcriptional regulation networks. Proceedings of the IEEE Conference on Decision and Control 2010: 7618-7623

Farina Lorenzo

Discussion on: "Representation of a Class of MIMO Systems via Internally Positive Realization. EUROPEAN JOURNAL OF CONTROL 2010: 305-306

P. Palumbo, G. Mavelli, Farina Lorenzo, Alfredo Germani

Identification of regulatory network motifs from gene expression data. JOURNAL OF MATHEMATICAL MODELLING AND ALGORITHMS 2010: 233-245

Pasquale Palumbo, Gabriella Mavelli, Farina Lorenzo, Lilia Alberghina

Networks and circuits in cell regulation. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2010: 881-886

2009

MARIA CONCETTA Palumbo, Farina Lorenzo, Colosimo Alfredo, L. Farina

Metabolic Networks. Handbook on Biological Networks 2009: 159-195

Nicola Soranzo, Mattia Zampieri, Farina Lorenzo, Claudio Altafini

mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle. BMC SYSTEMS BIOLOGY 2009: 18-15

Benvenuti Luca, DE SANTIS Alberto, Farina Lorenzo

Sistemi dinamici. Modellistica, analisi e controllo. Sistemi dinamici. Modellistica, analisi e controllo 2009: -