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Paola Paci
Research Associate
Dipartimento di Ingegneria Informatica Automatica e Gestionale Antonio Ruberti - Universita' di Roma "La Sapienza"
Via Ariosto, 25
00185 Roma - Italia
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Research groups
Selected publications
- Amadio S, Federica Conte, Esposito G, Fiscon G, Paola Paci, Cinzia Volonté: Repurposing Histaminergic Drugs in Multiple Sclerosis, International Journal of Molecular Sciences, 23(11):6347, https://www.mdpi.com/1422-0067/23/11/6347, 2022
- Fiscon G, Federica Conte, Amadio S, Cinzia Volonté, Paola Paci: Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis, Neurotherapeutics, 2021
- Belardinilli F, Capalbo C, Malapelle U, Pisapia P, Raimondo D, Milanetti E, Yasaman M, Liccardi C, Paola Paci, Sibilio P, Pepe F, Bonfiglio C, Mezi S, Magri V, Coppa A, Nicolussi A, Gradilone A, Petroni M, Di Giulio S, Fabretti F, Infante P, Coni S, Canettieri G, Troncone G, Giannini G.: Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer, Frontiers in Oncology, 2020
- Federica Conte, Fiscon G, Licursi V, Bizzarri D, D'Anto' T, Farina L., Paola Paci: A paradigm shift in medicine: A comprehensive review of network-based approaches, BBA - Gene Regulatory Mechanisms, 1863, 2020
- Paola Paci, Fiscon G, Federica Conte, Licursi V, Morrow J, Hersh C, Cho M, Castaldi P, Glass K, Silverman EK, Farina L.: Integrated transcriptomic correlation network analysis identi fies COPD molecular determinants, Scientific Report, 10, 2020
- Panebianco V, Pecoraro M, Fiscon G, Paola Paci, Farina L., Catalano C: Prostate Cancer Screening Research Can Benefit from Network Medicine: An Emerging Awareness, npj Systems Biology and Applications, 2020
- Silverman EK, Schmid HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Federica Conte, Di Costanzo A, Farina L., Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paola Paci, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J: Molecular Networks in Network Medicine: Development and Applications, WIREs Systems Biology and Medicine, 2020
- Capalbo C, Belardinilli F, Raimondo D, Milanetti E, Malapelle U, Pisapia P, Magri V, Prete A, Pecorari S, Colella M, Coppa A, Bonfiglio C, Nicolussi A, Valentini V, Tessitore A, Cardinali B, Petroni M, Infante P, Santoni M, Filetti M, Colicchia V, Paola Paci, Mezi S, Longo F, Cortesi E, Marchetti P, Troncone G, Bellavia D, Canettieri G, Giannini G: A Simplified Genomic Profiling Approach Predicts Outcome in Metastatic Colorectal Cancer, Cancers, 11, 2019
- Falcone R, Federica Conte, Fiscon G, Pecce V, Sponziello M, Durante C, Farina L., Filetti S, Paola Paci, Verrienti A: BRAF(V600E)-mutant cancers display a variety of networks by SWIM analysis: prediction of vemurafenib clinical response, Endocrine, 64, 2019
- Fiscon G, Federica Conte, Farina L., Pellegrini M, Russo F, Paola Paci: Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM, Methods in Molecular Biology, 1970, Humana Press, New York, NY, 2019
- Licursi V, Federica Conte, Fiscon G, Paola Paci: MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis, BMC Bioinformatics, 20, 2019
- Magris G, Di Gaspero G, Marroni F, Zenoni S, Tornielli GB, Celii M, De Paoli E, Pezzotti M, Federica Conte, Paola Paci, Morgante M: Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties, The Plant Journal, 99, 2019
- Mocavini I, Pippa S, Licursi V, Paola Paci, Trisciuoglio D, Mannironi C, Presutti C, Negri R: JARID1B expression and its function in DNA damage repair are tightly regulated by miRNAs in breast cancer, Cancer Science, 110, 2019
- Vahabi m, Pulito C, Sacconi A, Donzelli S, D’Andrea M, Manciocco V, Pellini R, Paola Paci, Sanguineti G, Strigari L, Spriano G, Muti P, Pandolfi PP, Strano S, Safarian S, Ganci F, Blandino G: miR-96-5p targets PTEN expression affecting radio-chemosensitivity of HNSCC cells, Journal of Experimental & Clinical Cancer Research, 38, 2019
- Farina L., Paola Paci: A feature-based integrated scoring scheme for cell cycle-regulated genes prioritization, Journal of Theoretical Biology, 459, 2018
- Fiscon G, Federica Conte, Farina L., Paola Paci: Network-based approaches to explore complex biological systems towards network medicine, Genes, 2018
- Fiscon G, Federica Conte, Licursi V, Sergio Nasi, Paola Paci: Computational identification of specific genes for glioblastoma stem-like cells identity, Scientific Report, 8, 2018
- Fiscon G, Federica Conte, Paola Paci: SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines, BMC Bioinformatics, 19, 2018
- Guzzi R., Colombo T, Paola Paci: Inverse Problems in Systems Biology: A Critical Review, in: Systems Biology, Bizzarri M ed., Methods in Molecular Biology, 1702, Humana Press, New York, NY, 69-94, 2018
- Russo F, Fiscon G, Federica Conte, Rizzo M, Paola Paci, Pellegrini M: Interplay between long non-coding RNAs and microRNAs in cancer, in: Computational Cell Biology: Methods and Protocols, von Stechow L, Santos Delgado A eds., Methods in Molecular Biology, 1819, Humana Press, New York, NY, 75-92, 2018
- Tieri P, Farina L., Petti M, Astolfi L, Paola Paci, Castiglione F.: Network inference and reconstruction in Bioinformatics, in: Encyclopedia of Bioinformatics and Computational Biology, Gribskov M, Ranganathan S, Nakai K, Schnbach C eds., Reference Module in Life Sciences, 2, Elsevier, 805-813, 2018
- Vernocchi P, Del Chierico F, Russo A, Majo F, Rossitto M, Valerio M, Casadei L, La Storia A, De Filippis F, Rizzo C, Manetti C, Paola Paci, Ercolini D, Marini F, Fiscarelli EV, 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, 13, 2018
- Federica Conte, Fiscon G, Chiara M, Colombo T, Farina L., Paola Paci: Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer, Plos One 12, 2017
- Del Chierico F, Nobili V, Vernocchi P, Russo A, De Stefanis C, Gnani D, Paola Paci, Dallapiccola B, Alisi A, Putignani L: Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an inte- grated meta-omics based approach, Hepatology, 65, 2017
- Massonnet M., Fasoli M, Tornielli GB, Altieri M, Sandri M, Zuccolotto P, Paola Paci, Gardiman M, Zenoni S, Pezzotti M: Ripening Transcriptomic Program in Red and White Grapevine Varieties Correlates with Berry Skin Anthocyanin Accumulation, Plant Physiology, 174, 2017
- Paola Paci, Colombo T, Fiscon G, Gurtner A, Pavesi G, Farina L.: SWIM: a computational tool to unveiling crucial nodes in complex biological networks, Scientific Report, 7, 2017
- Verducci L, Ferraiuolo M, Sacconi A, Ganci F, Vitale J, Colombo T, Paola Paci, Strano S, Macino G, Rajewsky N, Blandino G: 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, 18, 2017
- Dal Santo S, Palliotti A, Zenoni S, Tornielli GB, Fasoli M, Paola Paci, Tombesi S, Frioni T, Silvestroni O, Bellincontro A, d'Onofrio C, Matarese F, Gatti M, Poni S, Pezzotti M: Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars, BMC Genomics, 2016
- Fiscon G, Iannello G, Paola Paci: A perspective on the algorithms predicting and evaluating the RNA secondary structure, Journal of Genetics and Genome Research, 3, 2016
- Garbuglia A, Visco-Comandini U, Lionetti R, Lapa D, Castiglione F, D’Offizi G, Taibi C, Montalbano M, Capobianchi MR, Paola Paci: Ultrasensitive HCV RNA quantification in antiviral triple therapy: new insight on viral clearance dynamics and treatment outcome predictors, Plos One, 11, 2016
- Gurtner A, Garibaldi F, Falcone E, Trisciuoglio D, Colombo T, Lisek K, Walerych D, Dal Sal G, Paola Paci, Bossi G, Piaggio G: Mutant p53 inhibits miRNA biogenesis by interfering with the Microprocessor com- plex, Oncogene - Nature, 35, 2016
- Daniele Santoni, Paola Paci, Di Paola L, 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, 17:26-29, 2016
- Colombo T, Farina L., Macino G., Paola Paci: PVT1: A rising star among oncogenic long noncoding RNAs, BioMed Research International, http://www.scopus.com/inward/record.url?eid=2-s2.0-84926673517&partnerID=q2rCbXpz, 2015
- Del Chierico F, Vernocchi P, Petrucca A, Paola Paci, Fuentes S, Pratic G, Capuani G, Masotti A, Reddel S, Russo A, Vallone C, Salvatori G, Buffone E, Signore F, Rigon G, Dotta A, Miccheli A, de Vos WM, Dallapiccola B, Putignani L: Gut microbiota phylogenetic and metabolic tracking during perinatal age, Plos One, 10, 2015
- Fiscon G, Paola Paci, Colombo T, Iannello G: A new procedure to analyze RNA non-branching structures, Current bioinformatics 10, 2015
- Fiscon G, Paola Paci, Iannello G: MONSTER v1.1: a tool to extract and search for RNA non-branching structures., BMC Genomics 16, 2015
- Garbuglia A.R., Lionetti R., Lapa D., Taibi C., Visco-Comandini U., Montalbano M., D'Offizi G., Castiglione F., Capobianchi M.R., Paola Paci: 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 69, 68-73, 2015
- Palumbo MC, Farina L., Paola Paci: Kinetic effects and modelling of mRNA turnover, Wiley interdisciplinary reviews. RNA 6, 327-336, 2015
- Paola Bertolazzi, Bock M.E., Guerra C., Paola Paci, Daniele Santoni: On the integration of protein-protein interaction networks with gene expression and 3D structural data: What can be gained?, European Physical Journal Plus, 129(6), 2014
- Cumbo F, Paola Paci, Daniele Santoni, Giuliani A, Di Paola L: GIANT: a Cytoscape plugin for modular networks, Plos One, 9(10): e105001, 2014
- Fiscon G, Paola Paci, Colombo T, Iannello G: MONSTER v1.0: a novel procedure to extract and search for RNA non-branching structures, 2014
- Paola Paci, Colombo T, Farina L.: Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer, BMC Systems Biology, 2014
- Paola Paci, Colombo T, Farina L.: Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer., BMC Systems Biology, 2014
- Palumbo MC, Zenoni S., Fasoli M., Massonnet M., Farina L., Castiglione F, Pezzotti M., Paola Paci: 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, The Plant Cell, 2014
- Tasdighian S, Di Paola L, De Ruvo M, Paola Paci, Daniele Santoni, Pasquale Palumbo, Mei G, Di Venere A, Giuliani A: Modules identification in protein structures: the topological and geometrical solutions, Journal of Chemical Information and Modeling, 54(1): 159-168, 2014
- Paola Bertolazzi, Bock M.E., Guerra C., Paola Paci, Daniele Santoni: On the integration of protein-protein interaction networks with gene expression and 3d structural data: what can be gained?, IASI-CNR, R. 13-07, 2013
- Di Paola L, De Ruvo M, Paola Paci, Daniele Santoni, Giuliani A: Proteins Contact Networks: an emerging paradigm in chemistry, Chemical Reviews 113(3), 1598-1613, 2013
- Fiscon G, Paola Paci, Colombo T, Iannello G: Development of an algorithm to identify RNA secondary structures., Poster - FEBS Workshop. Translating the epigenomes into function: a next-generation challenge for human disease. October 13-16, Capri, Italy, 2013
- Fiscon G, Paola Paci, Colombo T, Iannello G: Structural Analysis of Long Non-coding RNAs, IASI-CNR, R. 13-21, 12/2013
- Daniele Santoni, Castiglione F, Paola Paci: Identifying Correlations between Chromosomal Proximity of Genes and Distance of their Products in Protein-Protein Interaction Networks of Yeast, Plos One, 8(3):e57707, 2013
- Arrigo N, Paola Paci, Di Paola L, Daniele Santoni, De Ruvo M, Giuliani A, Castiglione F: Characterizing Protein Shape by a Volume Distribution Asymmetry Index, The Open Bioinformatics Journal 6(1), 20-27, 2012
- De Ruvo M, Giuliani A, Paola Paci, Daniele Santoni, Di Paola L: Shedding light on protein-ligand binding by graph theory: the topological nature of allostery, Biophysical Chemistry 165-166, 21-29, 2012
- Di Paola L, Paola Paci, Daniele Santoni, De Ruvo M, Giuliani A: Proteins as sponges: a statistical journey along protein structure organization principles, Journal of Chemical Information and Modeling 52(2), 474-482, 2012
- Giuliani A, Di Paola L, Paola Paci, De Ruvo M, Arcangeli C, Daniele Santoni, Celino M: Chapter - Updating and revising "Proteins as Networks: Usefulness of Graph Theory in Protein Science", Advances in Protein and Peptide Science, 2012
- Paola Paci, Cacace F., Valerio Cusimano, Germani A., Farina L.: Stochastic modeling of expression kinetics identifies messenger half-lives and reveals sequential waves of co-ordinated transcription and decay, PLoS Computational Biology, 2012
- Paola Paci, Di Paola L, Daniele Santoni, De Ruvo M, Giuliani A: Structural and Functional Analysis of Hemoglobin and Serum Albumin through Protein Long-range Interaction Networks, current proteomics 9(3), 160-166, 2012
- Paola Paci, Martini F., Bernaschi M., D'Offizi G., Castiglione F: Timely HAART initiation may pave the way for a better viral control, BMC Infectious Diseases 11:56, 2011
- Castiglione F, Paola Paci: Criticality of timing for anti-HIV therapy initiation, Plos One, 5(12):e15294, 2010
- Baldazzi V, Paola Paci, Bernaschi M., Castiglione F.: Modeling lymphocyte homing and encounters in lymph nodes, BMC Bioinformatics, 10:387, 2009
- Paola Paci, Carello R, Bernaschi M., D'Offizi G., Castiglione F.: Immune control of HIV-1 infection after therapy interruption: Immediate versus deferred antiretroviral therapy, BMC Infectious Diseases, 9:172, 2009
- Pappalardo F, Halling-Brown MD, Rapin N, Zhang P, Alemani D., Emerson A, Paola Paci, Duroux P, Pennisi M, Palladini A, Miotto O, Churchill D, Rossi E, Shepherd A.J., Moss F, Castiglione F., Bernaschi M., Lefranc M, Brunak S, Motta S, Lollini P, Basford KE, Brusic V: ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization, Briefings in Bioinformatics 10(3), 330-340, 2009
- Paola Paci, Castiglione F., Bernaschi M., Baldazzi V: A discrete/continuous model of anti-HIV response and therapy, IEEE Computer Society, Digital library Proceedins UKSIM, 2008
- Paola Paci, Capone M, Cappelluti E, Ciuchi S, Grimaldi C: Isotope Effects in the Hubbard-Holstein model within dynamical mean-field theory, Physical Review B, 74:205108, 2006
- Cappelluti E, Paola Paci, Grimaldi C, Pietronero L: Relevance of multiband Jahn-Teller effects on the electron-phonon interaction in A3C60, Physical Review B, 72:054521, 2005
- Paola Paci, Capone M, Cappelluti E, Ciuchi S, Grimaldi C, Pietronero L: Polaronic and nonadiabatic phase diagram from anomalous isotope effects, Physical Review Letters, 94:036406, 2005
- Paola Paci, Cappelluti E, Grimaldi C, Pietronero L, Strassler S.: Nonadiabatic high-Tc superconductivity in hole-doped fullerens, Physical Review B, 69:024507, 2004
- Paola Paci, Cappelluti E, Grimaldi C, Pietronero L, Strassler S.: Unconventional Pairing in Fullerides by Nonadiabatic Channels, Physica C 408-410, 240-241, 2004
- Paola Paci: Nonadiabatic superconductivity: from theory to materials, Scientifica Acta, XVII (1), 2002
- Paola Paci, Cappelluti E, Grimaldi C, Pietronero L: Nonadiabatic superconductivity and vertex corrections in uncorrelated systems, Physical Review B, 65:012512, 2002
- Paola Paci, Cappelluti E, Grimaldi C, Pietronero L: s- and d-wave symmetries in nonadiabatic theory of superconductivity, International Journal of Modern Physics B, 2982-2987, 2000
- Paola Paci, Grimaldi C, Pietronero L: d-wave nonadiabatic superconductivity, European Physical Journal B, 235-243, 2000
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