Publications by authors named "Pietro Lio"

100Publications

Dynamic survival prediction in intensive care units from heterogeneous time series without the need for variable selection or curation.

Sci Rep 2020 12 17;10(1):22129. Epub 2020 Dec 17.

Division of Anaesthesia, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK.

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December 2020

Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks.

Bioinformatics 2020 Nov 13. Epub 2020 Nov 13.

NeuRoNe Lab, DISA-MIS, University of Salerno, Via Giovanni Paolo II 132, Fisciano, Italy.

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November 2020

A machine learning model to identify early stage symptoms of SARS-Cov-2 infected patients.

Expert Syst Appl 2020 Dec 20;160:113661. Epub 2020 Jun 20.

The Garvan Institute of Medical Research, Healthy Ageing Theme, Darlinghurst, NSW, Australia.

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December 2020

Unsupervised generative and graph representation learning for modelling cell differentiation.

Sci Rep 2020 06 17;10(1):9790. Epub 2020 Jun 17.

Department of Computer Science and Technology, University of Cambridge, Cambridge, CB3 0FD, United Kingdom.

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June 2020

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

PLoS One 2020 21;15(2):e0228962. Epub 2020 Feb 21.

Computer Laboratory, University of Cambridge, Cambridge, Cambs, England, United Kingdom.

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May 2020

Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression.

Sci Rep 2020 02 17;10(1):2795. Epub 2020 Feb 17.

Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.

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February 2020

Variational Autoencoders for Cancer Data Integration: Design Principles and Computational Practice.

Front Genet 2019 11;10:1205. Epub 2019 Dec 11.

Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom.

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December 2019

XFlow: Cross-Modal Deep Neural Networks for Audiovisual Classification.

IEEE Trans Neural Netw Learn Syst 2020 Sep 8;31(9):3711-3720. Epub 2019 Nov 8.

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September 2020

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

BMC Med Genomics 2019 07 25;12(Suppl 6):106. Epub 2019 Jul 25.

Department of Computer Science and Technology, Computer Laboratory, University of Cambridge, William Gates Building, 15 JJ Thomson Avenue, Cambridge, CB3 0FD, UK.

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July 2019

Genetic effects of welding fumes on the development of respiratory system diseases.

Comput Biol Med 2019 05 8;108:142-149. Epub 2019 Apr 8.

Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia. Electronic address:

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May 2019

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

BMC Bioinformatics 2019 Apr 18;20(Suppl 4):172. Epub 2019 Apr 18.

Department of Informatics, Systems and Communication (DISCo), University of Milano-Bicocca, Viale Sarca 336, U14 Building, Milan, 20126, Italy.

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April 2019

Predicting factors for survival of breast cancer patients using machine learning techniques.

BMC Med Inform Decis Mak 2019 03 22;19(1):48. Epub 2019 Mar 22.

Data Science and Bioinformatics Laboratory, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.

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March 2019

Social dynamics modeling of chrono-nutrition.

PLoS Comput Biol 2019 01 30;15(1):e1006714. Epub 2019 Jan 30.

Computer Laboratory, University of Cambridge, Cambridge, United Kingdom.

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January 2019

A parameter-efficient deep learning approach to predict conversion from mild cognitive impairment to Alzheimer's disease.

Neuroimage 2019 04 14;189:276-287. Epub 2019 Jan 14.

Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Via Cracovia, 00133, Roma, RM, Italy; A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, USA. Electronic address:

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April 2019

Genetic effects of welding fumes on the progression of neurodegenerative diseases.

Neurotoxicology 2019 03 17;71:93-101. Epub 2018 Dec 17.

Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Biomedical Science, Faculty of Medicine and Health, The University of Sydney, Australia. Electronic address:

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March 2019

Multi-omic analysis of signalling factors in inflammatory comorbidities.

BMC Bioinformatics 2018 Nov 30;19(Suppl 15):439. Epub 2018 Nov 30.

Computer Laboratory, University of Cambridge, Cambridge, UK.

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November 2018

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

BMC Bioinformatics 2018 Nov 30;19(Suppl 15):442. Epub 2018 Nov 30.

School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.

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November 2018

Bioinformatics methodologies for coeliac disease and its comorbidities.

Brief Bioinform 2018 Nov 16. Epub 2018 Nov 16.

Computer Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge, UK.

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November 2018

Neural network fusion: a novel CT-MR Aortic Aneurysm image segmentation method.

Proc SPIE Int Soc Opt Eng 2018 Mar;10574

Department of Computer Science and Technology, University of Cambridge, Cambridge, UK.

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March 2018

A study on multi-omic oscillations in Escherichia coli metabolic networks.

BMC Bioinformatics 2018 07 9;19(Suppl 7):194. Epub 2018 Jul 9.

NeuRoNe Lab, DISA-MIS, University of Salerno, Via Giovanni Paolo II 132, Salerno, 84084 Fisciano, Italy.

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July 2018

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

BMC Bioinformatics 2018 07 9;19(Suppl 7):184. Epub 2018 Jul 9.

Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte Orientale, 15121, Alessandria, Italy.

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July 2018

Combining Pathway Identification and Breast Cancer Survival Prediction via Screening-Network Methods.

Front Genet 2018 14;9:206. Epub 2018 Jun 14.

Computer Laboratory, University of Cambridge, Cambridge, United Kingdom.

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June 2018

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

Bioinformatics 2018 09;34(17):2944-2950

Department of Computer Science and Technology, University of Cambridge, UK.

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September 2018

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

Sci Rep 2018 03 22;8(1):5005. Epub 2018 Mar 22.

University of Cambridge, Computer Laboratory, Cambridge, CB3 0FD, UK.

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March 2018

Simultaneous Transients of Intracranial Pressure and Heart Rate in Traumatic Brain Injury: Methods of Analysis.

Acta Neurochir Suppl 2018 ;126:147-151

Brain Physics Laboratory, Division of Neurosurgery, Department of Clinical Neuroscience, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.

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July 2018

Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis.

Nat Commun 2017 12 11;8(1):2045. Epub 2017 Dec 11.

Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK.

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December 2017

Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-on Tutorial, and Perspectives.

Methods Mol Biol 2018 ;1716:389-408

Department of Computer Science and Information Systems, Teesside University, Middlesbrough, Tees Valley TS1 3BX, UK.

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July 2018

Genetic Profiling and Comorbidities of Zika Infection.

J Infect Dis 2017 09;216(6):703-712

Computer Laboratory, University of Cambridge,United Kingdom.

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September 2017

Global gene expression profiling and senescence biomarker analysis of hESC exposed to HO induced non-cytotoxic oxidative stress.

Stem Cell Res Ther 2017 07 5;8(1):160. Epub 2017 Jul 5.

Avantea srl, Laboratory of Reproductive Technologies, Via Porcellasco 7/F, Cremona, 26100, Italy.

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July 2017

Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling.

Brief Bioinform 2018 11;19(6):1218-1235

Department of Computer Science and Information Systems, Teesside University, UK.

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November 2018

DrugClust: A machine learning approach for drugs side effects prediction.

Comput Biol Chem 2017 Jun 30;68:204-210. Epub 2017 Mar 30.

Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge, UK.

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June 2017

Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization.

BMC Syst Biol 2017 02 16;11(1):25. Epub 2017 Feb 16.

Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge, CB3 0FD, UK.

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February 2017

The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer.

Front Genet 2016 15;7:194. Epub 2016 Nov 15.

Institute of Biomedical Technologies, Italian National Research Council Milan, Italy.

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November 2016

The Impact of Heterogeneity and Awareness in Modeling Epidemic Spreading on Multiplex Networks.

Sci Rep 2016 11 16;6:37105. Epub 2016 Nov 16.

University of Catania, Dipartimento di Ingegneria Elettrica, Elettronica e Informatica, Catania, 95125, Italy.

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November 2016

Distance-Based Opportunistic Mobile Data Offloading.

Sensors (Basel) 2016 Jun 15;16(6). Epub 2016 Jun 15.

Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.

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June 2016

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

Bioinformatics 2016 08 13;32(16):2562-4. Epub 2016 Apr 13.

Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK.

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August 2016

Protein Interaction Networks Link Schizophrenia Risk Loci to Synaptic Function.

Schizophr Bull 2016 11 7;42(6):1334-1342. Epub 2016 Apr 7.

Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.

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November 2016

Animal inference on human mitochondrial diseases.

Comput Biol Chem 2016 06 16;62:17-28. Epub 2016 Feb 16.

Computer Laboratory, University of Cambridge, Cambridge, UK. Electronic address:

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June 2016

Multiplex methods provide effective integration of multi-omic data in genome-scale models.

BMC Bioinformatics 2016 Mar 2;17 Suppl 4:83. Epub 2016 Mar 2.

Computer Laboratory - University of Cambridge, Cambridge, UK.

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March 2016

Metabolic disorders: how can systems modelling help?

Lancet Diabetes Endocrinol 2016 Apr 12;4(4):306. Epub 2016 Feb 12.

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April 2016

Computational Modeling, Formal Analysis, and Tools for Systems Biology.

PLoS Comput Biol 2016 Jan 21;12(1):e1004591. Epub 2016 Jan 21.

Computer Laboratory, University of Cambridge, Cambridge, United Kingdom.

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January 2016

Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration.

Bioinformatics 2016 04 17;32(8):1121-9. Epub 2015 Dec 17.

Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK.

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April 2016

Network regularised Cox regression and multiplex network models to predict disease comorbidities and survival of cancer.

Comput Biol Chem 2015 Dec 19;59 Pt B:15-31. Epub 2015 Oct 19.

Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK. Electronic address:

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December 2015

Quantifying the Role of Homophily in Human Cooperation Using Multiplex Evolutionary Game Theory.

PLoS One 2015 23;10(10):e0140646. Epub 2015 Oct 23.

Dipartimento di Ingegneria Elettrica, Elettronica e Informatica (DIEEI), Università degli Studi di Catania, Catania, Italy.

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June 2016

Predictive analytics of environmental adaptability in multi-omic network models.

Sci Rep 2015 Oct 20;5:15147. Epub 2015 Oct 20.

Computer Laboratory - University of Cambridge, UK.

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October 2015

DAPPER: a data-mining resource for protein-protein interactions.

BioData Min 2015 24;8:30. Epub 2015 Sep 24.

Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK.

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September 2015

Multi-Target Analysis and Design of Mitochondrial Metabolism.

PLoS One 2015 16;10(9):e0133825. Epub 2015 Sep 16.

Department of Mathematics and Computer Science-University of Catania, Catania, Italy.

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May 2016

Bayesian Melding Approach to Estimate the Reproduction Number for Tuberculosis Transmission in Indian States and Union Territories.

Asia Pac J Public Health 2015 Oct 16;27(7):723-32. Epub 2015 Jul 16.

University of Cambridge, Cambridge, UK.

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October 2015

How to build personalized multi-omics comorbidity profiles.

Front Cell Dev Biol 2015 24;3:28. Epub 2015 Jun 24.

Computer Laboratory, University of Cambridge Cambridge, UK.

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July 2015

Modelling circulating tumour cells for personalised survival prediction in metastatic breast cancer.

PLoS Comput Biol 2015 May 15;11(5):e1004199. Epub 2015 May 15.

University of Cambridge, Computer Laboratory, Cambridge, United Kingdom.

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May 2015

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Authors:
Damian Smedley Syed Haider Steffen Durinck Luca Pandini Paolo Provero James Allen Olivier Arnaiz Mohammad Hamza Awedh Richard Baldock Giulia Barbiera Philippe Bardou Tim Beck Andrew Blake Merideth Bonierbale Anthony J Brookes Gabriele Bucci Iwan Buetti Sarah Burge Cédric Cabau Joseph W Carlson Claude Chelala Charalambos Chrysostomou Davide Cittaro Olivier Collin Raul Cordova Rosalind J Cutts Erik Dassi Alex Di Genova Anis Djari Anthony Esposito Heather Estrella Eduardo Eyras Julio Fernandez-Banet Simon Forbes Robert C Free Takatomo Fujisawa Emanuela Gadaleta Jose M Garcia-Manteiga David Goodstein Kristian Gray José Afonso Guerra-Assunção Bernard Haggarty Dong-Jin Han Byung Woo Han Todd Harris Jayson Harshbarger Robert K Hastings Richard D Hayes Claire Hoede Shen Hu Zhi-Liang Hu Lucie Hutchins Zhengyan Kan Hideya Kawaji Aminah Keliet Arnaud Kerhornou Sunghoon Kim Rhoda Kinsella Christophe Klopp Lei Kong Daniel Lawson Dejan Lazarevic Ji-Hyun Lee Thomas Letellier Chuan-Yun Li Pietro Lio Chu-Jun Liu Jie Luo Alejandro Maass Jerome Mariette Thomas Maurel Stefania Merella Azza Mostafa Mohamed Francois Moreews Ibounyamine Nabihoudine Nelson Ndegwa Céline Noirot Cristian Perez-Llamas Michael Primig Alessandro Quattrone Hadi Quesneville Davide Rambaldi James Reecy Michela Riba Steven Rosanoff Amna Ali Saddiq Elisa Salas Olivier Sallou Rebecca Shepherd Reinhard Simon Linda Sperling William Spooner Daniel M Staines Delphine Steinbach Kevin Stone Elia Stupka Jon W Teague Abu Z Dayem Ullah Jun Wang Doreen Ware Marie Wong-Erasmus Ken Youens-Clark Amonida Zadissa Shi-Jian Zhang Arek Kasprzyk

Nucleic Acids Res 2015 Jul 20;43(W1):W589-98. Epub 2015 Apr 20.

Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia

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July 2015

A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation.

ACS Synth Biol 2015 Aug 27;4(8):880-9. Epub 2015 Apr 27.

Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, United Kingdom.

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August 2015

MeDuSa: a multi-draft based scaffolder.

Bioinformatics 2015 Aug 25;31(15):2443-51. Epub 2015 Mar 25.

Department of Biology, ComBo, Florence Computational Biology Group, Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019 Sesto F.no, Italy.

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August 2015

Analyzing seasonality of tuberculosis across Indian states and union territories.

J Epidemiol Glob Health 2015 Dec 18;5(4):337-46. Epub 2015 Mar 18.

Computer Laboratory, William Gates Building 15, JJ Thomson Avenue, Cambridge CB3 0FD, University of Cambridge, UK.

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December 2015

Integrating multi-omic features exploiting Chromosome Conformation Capture data.

Front Genet 2015 11;6:40. Epub 2015 Feb 11.

Bioinformatics Unit, Institute of Biomedical Technologies, Italian National Research Council Milan, Italy.

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February 2015

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology.

Microbiol Res 2015 Feb 7;171:52-64. Epub 2015 Jan 7.

University of Cambridge, Computer Laboratory, 15 JJ Thomson Avenue, CB3 0FD Cambridge, UK.

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February 2015

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

Bioinformatics 2015 Mar 7;31(6):969-71. Epub 2014 Nov 7.

Computer Laboratory, University of Cambridge, Cambridge, UK and Department of CSE, Pabna University of Science and Technology, Pabna, Bangladesh.

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March 2015

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

BMC Bioinformatics 2014 Oct 24;15:333. Epub 2014 Oct 24.

Computer Laboratory, University of Cambridge, William Gates Building, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK.

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October 2014

Genome-scale metabolic network reconstruction.

Methods Mol Biol 2015 ;1231:233-56

Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence, Italy,

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June 2015

Emerging trends of malaria-dengue geographical coupling in the Southeast Asia region.

J Vector Borne Dis 2014 Sep;51(3):165-71

School of Basic Sciences, Indian Institute of Technology, Mandi, Himachal Pradesh, India.

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September 2014

Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation.

Comput Biol Chem 2014 Dec 24;53 Pt A:144-52. Epub 2014 Aug 24.

Computer Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0FD, United Kingdom. Electronic address:

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December 2014

Advances in translational biomedicine from systems approaches.

Front Genet 2014 14;5:273. Epub 2014 Aug 14.

Computer Laboratory, Cambridge University Cambridge, UK.

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September 2014

FisHiCal: an R package for iterative FISH-based calibration of Hi-C data.

Bioinformatics 2014 Nov 23;30(21):3120-2. Epub 2014 Jul 23.

Computer Laboratory, University of Cambridge, Cambridge CB3 0FD and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK.

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November 2014

comoR: a software for disease comorbidity risk assessment.

J Clin Bioinforma 2014 23;4. Epub 2014 May 23.

Computer Laboratory, University of Cambridge, William Gates Building, 15 JJ Thomson Avenue, Cambridge CB3 0FD, UK.

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July 2014

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

Environ Microbiol 2015 Mar 30;17(3):751-66. Epub 2014 Jun 30.

Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, Florence, 50019, Italy; ComBo, Florence Computational Biology Group, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, Florence, 50019, Italy.

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March 2015

Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data.

Mol Biosyst 2014 Jun 7;10(6):1576-85. Epub 2014 Apr 7.

Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK.

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June 2014

Pathway-based Bayesian inference of drug-disease interactions.

Mol Biosyst 2014 Jun 3;10(6):1538-48. Epub 2014 Apr 3.

University of Cambridge, JJ Thomson Avenue, CB3 0FD, UK.

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June 2014

Modeling TGF-β in early stages of cancer tissue dynamics.

PLoS One 2014 20;9(2):e88533. Epub 2014 Feb 20.

Computer Laboratory, Cambridge University, Cambridge, United Kingdom.

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January 2015

MtPAN(3): site-class specific amino acid replacement matrices for mitochondrial proteins of Pancrustacea and Collembola.

Mol Phylogenet Evol 2014 Jun 10;75:239-44. Epub 2014 Feb 10.

Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy. Electronic address:

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June 2014

Pareto optimality in organelle energy metabolism analysis.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jul-Aug;10(4):1032-44

University of Catania, Catania.

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August 2014

NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

PLoS One 2013 19;8(9):e75146. Epub 2013 Sep 19.

Institute for Biomedical Technologies, National Research Council, Segrate (Milan), Italy.

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June 2014

Comorbidity: a multidimensional approach.

Trends Mol Med 2013 Sep 12;19(9):515-21. Epub 2013 Aug 12.

Center for Computational Science (CCS), Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Laboratory of Integrative Systems Medicine (LISM), Institute of Clinical Physiology (IFC), National Research Council (CNR), Pisa 56124, Italy.

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September 2013

A design automation framework for computational bioenergetics in biological networks.

Mol Biosyst 2013 Oct;9(10):2554-64

Computer Laboratory, University of Cambridge, William Gates Building, 15 JJ Thomson Avenue, Cambridge, UK.

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October 2013

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

BMC Genomics 2013 May 8;14:309. Epub 2013 May 8.

INRIA, Grenoble Rhône-Alpes, Lyon, France.

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May 2013