Works by Liò, Pietro

Results: 81

Investigating the Relationship Between Genome Structure, Composition, and Ecology in Prokaryotes.

Published in:

Molecular Biology & Evolution, 2002, v. 19, n. 6, p. 789, doi. 10.1093/oxfordjournals.molbev.a004136

By:

Liò, Pietro

Publication type:

Article

COSMONET: An R Package for Survival Analysis Using Screening-Network Methods.

Published in:

Mathematics (2227-7390), 2021, v. 9, n. 24, p. 3262, doi. 10.3390/math9243262

By:

Iuliano, Antonella;
Occhipinti, Annalisa;
Angelini, Claudia;
De Feis, Italia;
Liò, Pietro

Publication type:

Article

SafetyMed: A Novel IoMT Intrusion Detection System Using CNN-LSTM Hybridization.

Published in:

Electronics (2079-9292), 2023, v. 12, n. 17, p. 3541, doi. 10.3390/electronics12173541

By:

Faruqui, Nuruzzaman;
Yousuf, Mohammad Abu;
Whaiduzzaman, Md;
Azad, AKM;
Alyami, Salem A.;
Liò, Pietro;
Kabir, Muhammad Ashad;
Moni, Mohammad Ali

Publication type:

Article

Deep Learning Enables Fast and Accurate Imputation of Gene Expression.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.624128

By:

Viñas, Ramon;
Azevedo, Tiago;
Gamazon, Eric R.;
Liò, Pietro

Publication type:

Article

Physio-Environmental Sensing and Live Modeling.

Published in:

Journal of Medical Internet Research, 2013, v. 15, n. 1, p. 14, doi. 10.2196/ijmr.2092

By:

Castiglione, Filippo;
Diaz, Vanessa;
Gaggioli, Andrea;
Liò, Pietro;
Mazzà, Claudia;
Merelli, Emanuela;
Meskers, Carel G. M.;
Pappalardo, Francesco;
von Ammon, Rainer

Publication type:

Article

Latest advances in parallel, distributed, and network‐based processing.

Published in:

Concurrency & Computation: Practice & Experience, 2020, v. 32, n. 10, p. 1, doi. 10.1002/cpe.5683

By:

Merelli, Ivan;
Liò, Pietro;
Kotenko, Igor;
D'Agostino, Daniele

Publication type:

Article

Learning and actioning general principles of cancer cell drug sensitivity.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-56827-5

By:

Carli, Francesco;
Di Chiaro, Pierluigi;
Morelli, Mariangela;
Arora, Chakit;
Bisceglia, Luisa;
De Oliveira Rosa, Natalia;
Cortesi, Alice;
Franceschi, Sara;
Lessi, Francesca;
Di Stefano, Anna Luisa;
Santonocito, Orazio Santo;
Pasqualetti, Francesco;
Aretini, Paolo;
Miglionico, Pasquale;
Diaferia, Giuseppe R.;
Giannotti, Fosca;
Liò, Pietro;
Duran-Frigola, Miquel;
Mazzanti, Chiara Maria;
Natoli, Gioacchino

Publication type:

Article

The Evolution of Histidine Biosynthesis in Archaea: Insights into the his Genes Structure and Organization in LUCA.

Published in:

Journal of Molecular Evolution, 2009, v. 69, n. 5, p. 512, doi. 10.1007/s00239-009-9286-6

By:

Fondi, Marco;
Emiliani, Giovanni;
Liò, Pietro;
Gribaldo, Simonetta;
Fani, Renato

Publication type:

Article

Antarctic Fish Mitochondrial Genomes Lack ND6 Gene.

Published in:

Journal of Molecular Evolution, 2007, v. 65, n. 5, p. 519, doi. 10.1007/s00239-007-9030-z

By:

Papetti, Chiara;
Liò, Pietro;
Rüber, Lukas;
Patarnello, Tomaso;
Zardoya, Rafael

Publication type:

Article

The Origin and Evolution of Operons: The Piecewise Building of the Proteobacterial Histidine Operon.

Published in:

Journal of Molecular Evolution, 2005, v. 60, n. 3, p. 378, doi. 10.1007/s00239-004-0198-1

By:

Fani, Renato;
Brilli, Matteo;
Liò, Pietro

Publication type:

Article

Modeling Mitochondrial Protein Evolution Using Structural Information.

Published in:

Journal of Molecular Evolution, 2002, v. 54, n. 4, p. 519, doi. 10.1007/s00239001-0052-7

By:

Liò, Pietro;
Goldman, Nick

Publication type:

Article

Molecular Evolution of Nitrogen Fixation: The Evolutionary History of the nifD, nifK, nifE, and nifN Genes.

Published in:

Journal of Molecular Evolution, 2000, v. 51, n. 1, p. 1, doi. 10.1007/s002390010061

By:

Fani, Renato;
Gallo, Romina;
Liò, Pietro

Publication type:

Article

Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1320, doi. 10.1093/bioinformatics/btab830

By:

Scherer, Paul;
Trębacz, Maja;
Simidjievski, Nikola;
Viñas, Ramon;
Shams, Zohreh;
Terre, Helena Andres;
Jamnik, Mateja;
Liò, Pietro

Publication type:

Article

CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1277, doi. 10.1093/bioinformatics/btab804

By:

Buterez, David;
Bica, Ioana;
Tariq, Ifrah;
Andrés-Terré, Helena;
Liò, Pietro

Publication type:

Article

Adversarial generation of gene expression data.

Published in:

Bioinformatics, 2022, v. 38, n. 3, p. 730, doi. 10.1093/bioinformatics/btab035

By:

Viñas, Ramon;
Andrés-Terré, Helena;
Liò, Pietro;
Bryson, Kevin

Publication type:

Article

EpiChIP: gene-by-gene quantification of epigenetic modification levels.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 5, p. e27, doi. 10.1093/nar/gkq1226

By:

Hebenstreit, Daniel;
Gu, Muxin;
Haider, Syed;
Turner, Daniel J.;
Liò, Pietro;
Teichmann, Sarah A.

Publication type:

Article

ChronoMID—Cross-modal neural networks for 3-D temporal medical imaging data.

Published in:

PLoS ONE, 2020, v. 15, n. 2, p. 1, doi. 10.1371/journal.pone.0228962

By:

Rakowski, Alexander G.;
Veličković, Petar;
Dall'Ara, Enrico;
Liò, Pietro

Publication type:

Article

Modeling breast cancer progression to bone: how driver mutation order and metabolism matter.

Published in:

BMC Medical Genomics, 2019, v. 12, n. 6, p. N.PAG, doi. 10.1186/s12920-019-0541-4

By:

Ascolani, Gianluca;
Liò, Pietro

Publication type:

Article

Diabetes and Obesity in Down Syndrome Across the Lifespan: A Retrospective Cohort Study Using U.K. Electronic Health Records.

Published in:

Diabetes Care, 2022, v. 45, n. 12, p. 2892, doi. 10.2337/dc22-0482

By:

Aslam, Aisha A.;
Baksh, R. Asaad;
Pape, Sarah E.;
Strydom, Andre;
Gulliford, Martin C.;
Chan, Li F.;
HeraultYannStrydomAndreChanLiPotierMarie-ClaudeBeckersJohannesLiòPietroDierssenMara;
Herault, Yann;
Chan, Li;
Potier, Marie-Claude;
Beckers, Johannes;
Liò, Pietro;
Dierssen, Mara;
GO-DS21 Consortium

Publication type:

Article

Identification of DNA regulatory motifs using Bayesian variable selection.

Published in:

Bioinformatics, 2004, v. 20, n. 16, p. 2553, doi. 10.1093/bioinformatics/bth282

By:

Mahlet G. Tadesse;
Marina Vannucci;
Pietro Liò

Publication type:

Article

Wavelets in bioinformatics and computational biology: state of art and perspectives.

Published in:

Bioinformatics, 2003, v. 19, n. 1, p. 2, doi. 10.1093/bioinformatics/19.1.2

By:

Liò, Pietro

Publication type:

Article

Finding pathogenicity islands and gene transfer events in genome data.

Published in:

Bioinformatics, 2000, v. 16, n. 10, p. 932, doi. 10.1093/bioinformatics/16.10.932

By:

Liò, Pietro;
Vannucci, Marina

Publication type:

Article

PASSML: combining evolutionary inference and protein secondary structure prediction.

Published in:

Bioinformatics, 1998, v. 14, n. 8, p. 726, doi. 10.1093/bioinformatics/14.8.726

By:

Liò, Pietro;
Goldman, Nick;
Thorne, Jeffrey L;
Jones, David T

Publication type:

Article

Evidence in cortical folding patterns for prenatal predispositions to hallucinations in schizophrenia.

Published in:

Translational Psychiatry, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41398-020-01075-y

By:

Rollins, Colleen P. E.;
Garrison, Jane R.;
Arribas, Maite;
Seyedsalehi, Aida;
Li, Zhi;
Chan, Raymond C. K.;
Yang, Junwei;
Wang, Duo;
Liò, Pietro;
Yan, Chao;
Yi, Zheng-hui;
Cachia, Arnaud;
Upthegrove, Rachel;
Deakin, Bill;
Simons, Jon S.;
Murray, Graham K.;
Suckling, John

Publication type:

Article

Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacterium P seudoalteromonas haloplanktis TAC125.

Published in:

Environmental Microbiology, 2015, v. 17, n. 3, p. 751, doi. 10.1111/1462-2920.12513

By:

Fondi, Marco;
Maida, Isabel;
Perrin, Elena;
Mellera, Alessandra;
Mocali, Stefano;
Parrilli, Ermenegilda;
Tutino, Maria Luisa;
Liò, Pietro;
Fani, Renato

Publication type:

Article

The Operon as a Conundrum of Gene Dynamics and Biochemical Constraints: What We Have Learned from Histidine Biosynthesis.

Published in:

Genes, 2023, v. 14, n. 4, p. 949, doi. 10.3390/genes14040949

By:

Del Duca, Sara;
Semenzato, Giulia;
Esposito, Antonia;
Liò, Pietro;
Fani, Renato

Publication type:

Article

GenHap: a novel computational method based on genetic algorithms for haplotype assembly.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 4, p. 1, doi. 10.1186/s12859-019-2691-y

By:

Tangherloni, Andrea;
Spolaor, Simone;
Rundo, Leonardo;
Nobile, Marco S.;
Cazzaniga, Paolo;
Mauri, Giancarlo;
Liò, Pietro;
Merelli, Ivan;
Besozzi, Daniela

Publication type:

Article

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 15, p. 123, doi. 10.1186/s12859-018-2422-9

By:

Mancini, Alessio;
Eyassu, Filmon;
Conway, Maxwell;
Occhipinti, Annalisa;
Liò, Pietro;
Angione, Claudio;
Pucciarelli, Sandra

Publication type:

Article

Cell graph neural networks enable the precise prediction of patient survival in gastric cancer.

Published in:

NPJ Precision Oncology, 2022, v. 6, n. 1, p. 1, doi. 10.1038/s41698-022-00285-5

By:

Wang, Yanan;
Wang, Yu Guang;
Hu, Changyuan;
Li, Ming;
Fan, Yanan;
Otter, Nina;
Sam, Ikuan;
Gou, Hongquan;
Hu, Yiqun;
Kwok, Terry;
Zalcberg, John;
Boussioutas, Alex;
Daly, Roger J.;
Montúfar, Guido;
Liò, Pietro;
Xu, Dakang;
Webb, Geoffrey I.;
Song, Jiangning

Publication type:

Article

Pathogenetic profiling of COVID-19 and SARS-like viruses.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 2, p. 1175, doi. 10.1093/bib/bbaa173

By:

Nain, Zulkar;
Rana, Humayan Kabir;
Liò, Pietro;
Islam, Sheikh Mohammed Shariful;
Summers, Matthew A;
Moni, Mohammad Ali

Publication type:

Article

Bioinformatics methodologies for coeliac disease and its comorbidities.

Published in:

Briefings in Bioinformatics, 2020, v. 21, n. 1, p. 355, doi. 10.1093/bib/bby109

By:

Prete, Eugenio Del;
Facchiano, Angelo;
Liò, Pietro

Publication type:

Article

Opportunities for community awareness platforms in personal genomics and bioinformatics education.

Published in:

Briefings in Bioinformatics, 2017, v. 18, n. 6, p. 1082, doi. 10.1093/bib/bbw078

By:

Bianchi, Lucia;
Liò, Pietro

Publication type:

Article

Systems medicine of inflammaging.

Published in:

Briefings in Bioinformatics, 2016, v. 17, n. 3, p. 527, doi. 10.1093/bib/bbv062

By:

Castellani, Gastone C.;
Menichetti, Giulia;
Garagnani, Paolo;
Bacalini, Maria Giulia;
Pirazzini, Chiara;
Franceschi, Claudio;
Collino, Sebastiano;
Sala, Claudia;
Remondini, Daniel;
Giampieri, Enrico;
Mosca, Ettore;
Bersanelli, Matteo;
Vitali, Silvia;
do Valle, Italo Faria;
Liò, Pietro;
Milanesi, Luciano

Publication type:

Article

Vision graph U-Net: Geometric learning enhanced encoder for medical image segmentation and restoration.

Published in:

Inverse Problems & Imaging, 2024, v. 18, n. 3, p. 1, doi. 10.3934/ipi.2023049

By:

Jiang, Yuanhong;
Ding, Qiaoqiao;
Wang, Yu Guang;
Liò, Pietro;
Zhang, Xiaoqun

Publication type:

Article

Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea.

Published in:

BMC Evolutionary Biology, 2007, v. 7, p. S8, doi. 10.1186/1471-2148-7-S2-S8

By:

Carapelli, Antonio;
Liò, Pietro;
Nardi, Francesco;
Van der Wath, Elizabeth;
Frati, Francesco

Publication type:

Article

STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow.

Published in:

BMC Bioinformatics, 2018, v. 19, p. 127, doi. 10.1186/s12859-018-2174-6

By:

Saggese, Igor;
Bona, Elisa;
Conway, Max;
Favero, Francesco;
Ladetto, Marco;
Liò, Pietro;
Manzini, Giovanni;
Mignone, Flavio

Publication type:

Article

Bottleneck Genes and Community Structure in the Cell Cycle Network of S. pombe.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 6, p. e103, doi. 10.1371/journal.pcbi.0030103

By:

Caretta-Cartozo, Cécile;
De Los Rios, Paolo;
Piazza, Francesco;
Liò, Pietro

Publication type:

Article

Quantum deep learning in neuroinformatics: a systematic review.

Published in:

2025

By:

Orka, Nabil Anan;
Awal, Md. Abdul;
Liò, Pietro;
Pogrebna, Ganna;
Ross, Allen G.;
Moni, Mohammad Ali

Publication type:

Literature Review

Parapred: antibody paratope prediction using convolutional and recurrent neural networks.

Published in:

Bioinformatics, 2018, v. 34, n. 17, p. 2944, doi. 10.1093/bioinformatics/bty305

By:

Liberis, Edgar;
Veličković, Petar;
Sormanni, Pietro;
Vendruscolo, Michele;
Liò, Pietro

Publication type:

Article

Muxstep: an open-source C++ multiplex HMM library for making inferences on multiple data types.

Published in:

Bioinformatics, 2016, v. 32, n. 16, p. 2562, doi. 10.1093/bioinformatics/btw196

By:

Veličković, Petar;
Liò, Pietro

Publication type:

Article

CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks.

Published in:

Bioinformatics, 2015, v. 31, n. 6, p. 969, doi. 10.1093/bioinformatics/btu731

By:

Moni, Mohammad Ali;
Haoming Xu;
Liò, Pietro

Publication type:

Article

Modelling local and general quantum mechanical properties with attention-based pooling.

Published in:

Communications Chemistry, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42004-023-01045-7

By:

Buterez, David;
Janet, Jon Paul;
Kiddle, Steven J.;
Oglic, Dino;
Liò, Pietro

Publication type:

Article

A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity.

Published in:

Cell Discovery, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41421-024-00728-2

By:

Zhou, Bingxin;
Zheng, Lirong;
Wu, Banghao;
Yi, Kai;
Zhong, Bozitao;
Tan, Yang;
Liu, Qian;
Liò, Pietro;
Hong, Liang

Publication type:

Article

Statistical bioinformatic methods in microbial genome analysis.

Published in:

BioEssays, 2003, v. 25, n. 3, p. 266, doi. 10.1002/bies.10231

By:

Liò, Pietro

Publication type:

Article

NuChart-II: The road to a fast and scalable tool for Hi-C data analysis.

Published in:

International Journal of High Performance Computing Applications, 2017, v. 31, n. 3, p. 196, doi. 10.1177/1094342016668567

By:

Tordini, Fabio;
Drocco, Maurizio;
Misale, Claudia;
Milanesi, Luciano;
Liò, Pietro;
Merelli, Ivan;
Torquati, Massimo;
Aldinucci, Marco

Publication type:

Article

Short and long-term genome stability analysis of prokaryotic genomes.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-309

By:

Brilli, Matteo;
Liò, Pietro;
Lacroix, Vincent;
Sagot, Marie-France

Publication type:

Article

Quantifying the propagation of distress and mental disorders in social networks.

Published in:

Scientific Reports, 2018, p. 1, doi. 10.1038/s41598-018-23260-2

By:

Scatà, Marialisa;
Stefano, Alessandro Di;
Corte, Aurelio La;
Liò, Pietro

Publication type:

Article

How to integrate wet lab and bioinformatics procedures for wine DNA admixture analysis and compositional profiling: Case studies and perspectives.

Published in:

PLoS ONE, 2019, v. 14, n. 2, p. 1, doi. 10.1371/journal.pone.0211962

By:

Vignani, Rita;
Liò, Pietro;
Scali, Monica

Publication type:

Article

Computational framework for the prediction of transcription factor binding sites by multiple data integration.

Published in:

BMC Neuroscience, 2006, v. 7, p. S8, doi. 10.1186/1471-2202-7-S1-S8

By:

Ambesi-Impiombato, Alberto;
Bansal, Mukesh;
Liò, Pietro;
Di Bernardo, Diego

Publication type:

Article

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies.

Published in:

BMC Bioinformatics, 2014, v. 15, p. 1, doi. 10.1186/1471-2105-15-333

By:

Moni, Mohammad Ali;
Liò, Pietro

Publication type:

Article