Publications by authors named "Paola Paci"

50Publications

Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer.

Int J Mol Sci 2020 Nov 19;21(22). Epub 2020 Nov 19.

Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms21228730DOI Listing
November 2020

Prostate cancer screening research can benefit from network medicine: an emerging awareness.

NPJ Syst Biol Appl 2020 05 7;6(1):13. Epub 2020 May 7.

Department of Radiological Sciences, Oncology and Pathology, Sapienza University/Policlinico Umberto I of Rome, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41540-020-0133-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206063PMC
May 2020

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis.

BMC Bioinformatics 2019 Nov 4;20(1):545. Epub 2019 Nov 4.

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, Rome, 00185, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-019-3105-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829817PMC
November 2019

A paradigm shift in medicine: A comprehensive review of network-based approaches.

Biochim Biophys Acta Gene Regul Mech 2020 06 2;1863(6):194416. Epub 2019 Aug 2.

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbagrm.2019.194416DOI Listing
June 2020

Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties.

Plant J 2019 09 7;99(5):895-909. Epub 2019 Jun 7.

Department of Agricultural Food, Environmental and Animal Sciences, University of Udine, Udine, I-33100, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.14370DOI Listing
September 2019

Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM.

Methods Mol Biol 2019 ;1970:169-181

Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-9207-2_10DOI Listing
September 2019

BRAF-mutant cancers display a variety of networks by SWIM analysis: prediction of vemurafenib clinical response.

Endocrine 2019 05 8;64(2):406-413. Epub 2019 Mar 8.

Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12020-019-01890-4DOI Listing
May 2019

JARID1B expression and its function in DNA damage repair are tightly regulated by miRNAs in breast cancer.

Cancer Sci 2019 Apr 18;110(4):1232-1243. Epub 2019 Mar 18.

Department of Biology and Biotechnology "C. Darwin,", "Sapienza" - University of Rome, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/cas.13925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447846PMC
April 2019

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

BMC Bioinformatics 2018 Nov 30;19(Suppl 15):436. Epub 2018 Nov 30.

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, Rome, 00185, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-018-2421-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266956PMC
November 2018

Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer.

Methods Mol Biol 2018 ;1819:75-92

Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, Italy.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/978-1-4939-8618-7_4
Publisher Site
http://dx.doi.org/10.1007/978-1-4939-8618-7_4DOI Listing
March 2019

A feature-based integrated scoring scheme for cell cycle-regulated genes prioritization.

J Theor Biol 2018 12 24;459:130-141. Epub 2018 Sep 24.

Institute for Systems Analysis and Computer Science "A. Ruberti", National Research Council, Rome, Italy; SysBio Centre for Systems Biology, Rome, Italy. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00225193183046
Publisher Site
http://dx.doi.org/10.1016/j.jtbi.2018.09.025DOI Listing
December 2018

Network-Based Approaches to Explore Complex Biological Systems towards Network Medicine.

Genes (Basel) 2018 Aug 31;9(9). Epub 2018 Aug 31.

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, via dei Taurini 19, 00185 Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes9090437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162385PMC
August 2018

Publisher Correction: Computational identification of specific genes for glioblastoma stem-like cells identity.

Sci Rep 2018 Jul 9;8(1):10593. Epub 2018 Jul 9.

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-28287-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037759PMC
July 2018

Computational identification of specific genes for glioblastoma stem-like cells identity.

Sci Rep 2018 05 17;8(1):7769. Epub 2018 May 17.

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-26081-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5958093PMC
May 2018

Inverse Problems in Systems Biology: A Critical Review.

Methods Mol Biol 2018 ;1702:69-94

Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, 00185 Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-7456-6_6DOI Listing
July 2018

SWIM: a computational tool to unveiling crucial nodes in complex biological networks.

Sci Rep 2017 03 20;7:44797. Epub 2017 Mar 20.

Department of Computer, Control and Management Engineering, "Sapienza" University, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep44797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357943PMC
March 2017

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer.

PLoS One 2017 10;12(2):e0171661. Epub 2017 Feb 10.

Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171661PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302781PMC
August 2017

Are Proteins Just Coiled Cords? Local and Global Analysis of Contact Maps Reveals the Backbone-Dependent Nature of Proteins.

Curr Protein Pept Sci 2016 ;17(1):26-9

Environment and Health Department, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Roma, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2174/138920371701151130203441DOI Listing
September 2016

PVT1: a rising star among oncogenic long noncoding RNAs.

Biomed Res Int 2015 26;2015:304208. Epub 2015 Mar 26.

Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Via dei Taurini 19, 00185 Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1155/2015/304208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391155PMC
February 2016

Kinetics effects and modeling of mRNA turnover.

Wiley Interdiscip Rev RNA 2015 May-Jun;6(3):327-36. Epub 2015 Mar 1.

Institute for Computing Applications "Mauro Picone", National Research Council, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/wrna.1277DOI Listing
January 2016

GIANT: a cytoscape plugin for modular networks.

PLoS One 2014 2;9(9):e105001. Epub 2014 Oct 2.

Environment and Health Department, Istituto Superiore di Sanità, Roma, Italy.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105001PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183485PMC
June 2015

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

BMC Syst Biol 2014 Jul 17;8:83. Epub 2014 Jul 17.

Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Viale Manzoni 30, 00185 Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1752-0509-8-83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113672PMC
July 2014

Modules identification in protein structures: the topological and geometrical solutions.

J Chem Inf Model 2014 Jan 13;54(1):159-68. Epub 2013 Dec 13.

Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University , K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci400218vDOI Listing
January 2014

Identifying correlations between chromosomal proximity of genes and distance of their products in protein-protein interaction networks of yeast.

PLoS One 2013 6;8(3):e57707. Epub 2013 Mar 6.

Institute for System Analysis and Computer Science Antonio Ruberti, National Research Council of Italy, Rome, Italy.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057707PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590303PMC
September 2013

Shedding light on protein-ligand binding by graph theory: the topological nature of allostery.

Biophys Chem 2012 May 12;165-166:21-9. Epub 2012 Mar 12.

Faculty of Engineering, Università CAMPUS BioMedico, Via A. del Portillo, 21, 00128 Roma, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bpc.2012.03.001DOI Listing
May 2012

Proteins as sponges: a statistical journey along protein structure organization principles.

J Chem Inf Model 2012 Feb 19;52(2):474-82. Epub 2012 Jan 19.

Università Campus Biomedico, via Alvaro del Portillo 21, 00128 Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ci2005127DOI Listing
February 2012

Criticality of timing for anti-HIV therapy initiation.

PLoS One 2010 Dec 23;5(12):e15294. Epub 2010 Dec 23.

Institute for Computing Applications Mauro Picone, National Research Council of Italy, Rome, Italy.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015294PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009726PMC
December 2010

Modeling lymphocyte homing and encounters in lymph nodes.

BMC Bioinformatics 2009 Nov 25;10:387. Epub 2009 Nov 25.

Istituto per le Applicazioni del Calcolo M, Picone, Consiglio Nazionale delle Ricerche (CNR), c/o IASI-CNR, V,le Manzoni 30, 00185 - Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-10-387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790470PMC
November 2009

Immune control of HIV-1 infection after therapy interruption: immediate versus deferred antiretroviral therapy.

BMC Infect Dis 2009 Oct 19;9:172. Epub 2009 Oct 19.

Institute for Computing Applications Mauro Picone, National Research Council, Rome, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2334-9-172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771028PMC
October 2009