Claudio Angione

j39   P. Kar, M. Saleh-E-In, N. Jaishee, A. Anandraj, E. Kormuth, B. Vellingiri, C. Angione, P. Rahman, S. Pillay, A. Sen, D. Naidoo, A. Roy, Y. Choi, "Computational profiling of natural compounds as promising inhibitors against the spike proteins of SARS-CoV-2 wild type and the variants of concern, viral cell-entry process, and cytokine storm in COVID-19", Journal of Cellular Biochemistry, 2022

j38   C. Angione*, E. Silverman*, E. Yaneske*, "Using Machine Learning as a Surrogate Model for Agent-Based Simulations", PLOS One, 17(2):e0263150 2022

j37   G. Pio, P. Mignone, G. Magazzù, G. Zampieri, M. Ceci, C. Angione, "Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction", Bioinformatics, 38(2):487-493, 2022 - Download postprint PDF - Full text access

j36   S. Vijayakumar, C. Angione, "Protocol for Hybrid Flux Balance, Statistical and Machine Learning Analysis of Multi-Omic Data from Cyanobacterium Synechococcus sp. PCC 7002", STAR Protocols, 2(4):100837, 2021

j35   E. Yaneske*, G. Zampieri*, L. Bertoldi, G. Benvenuto, C. Angione, "Genome-scale metabolic modelling of SARS-CoV-2 in cancer cells reveals an increased shift to glycolytic energy production", FEBS Letters, 595(18), 2350-2365, 2021

j34   E. Silverman, U. Gostoli, S. Picascia, J. Almagor, M. McCann, R. Shaw, C. Angione, "Situating Agent-Based Modelling in Population Health Research", Emerging Themes in Epidemiology, 2021

j33   G. Magazzù, G. Zampieri, C. Angione, "Multimodal regularised linear models with flux balance analysis for mechanistic integration of omics data", Bioinformatics, 37(20), 3546-3552, 2021 - Full text access - Download postprint PDF - Download supplementary material PDF

j32   T. Fu, G. Zampieri, D. Hodgson, C. Angione, Y. Zeng, "Modeling Customer Experience in Contact Center through Process Log Mining", ACM Transactions on Intelligent Systems and Technology, 12(4):48, 2021 - Download PDF

j31   A. Adegbenro, M. Short, C. Angione, "An integrated approach to adaptive control and supervisory optimisation of HVAC control systems for demand response applications", Energies, 2021

c28   A. Occhipinti, C. Angione, "A Computational Model of Cancer Metabolism for Personalised Medicine", Cambridge Medicine Journal, Building Bridges in Medical Science, 2021

j30   E.L. Robinson, A.H. Baker, M. Brittan, I. McCracken, G. Condorelli, C. Emanueli, K.P. Srivastava, C. Gaetano, T. Thum, M. Vanhaverbeke, C. Angione, S. Heymans, Y. Devaux*, T. Pedrazzini*, F. Martelli*, "Dissecting the transcriptome in cardiovascular disease", Cardiovascular Research, cvab117, 2021

j29   M.T. Hira, M.A. Razzaque, C. Angione, J. Scrivens, S. Sawan, M. Sarker, "Integrated multi-omics analysis of ovarian cancer using variational autoencoders", Scientific Reports, 11:6265, 2021

j28   A. Occhipinti, Y. Hamadi, H. Kugler, C. M. Wintersteiger, B. Yordanov, C. Angione, "Discovering essential multiple gene effects through large scale optimization: an application to human cancer metabolism", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(6), 2339-2352, 2021

j27   S. Vijayakumar, P.K.S.M. Rahman, C. Angione, "A hybrid flux balance analysis and machine learning pipeline elucidates the metabolic response of cyanobacteria to different growth conditions", iScience, 23(12), 2020

j26   C. Culley, S. Vijayakumar, G. Zampieri, C. Angione, "A mechanism-aware and multi-omic machine learning pipeline characterizes yeast cell growth", PNAS, 117(31): 18869-18879, 2020 - [News release 1] [News release 2] - Download PDF

c27   M. Mugnaini, R. Deacon, G. Zampieri, P. Vanderklish, C. Angione, E. Kropff, P. Cogram, "From genes to cognition: Octodon degus, an animal model for AD translational research", Alzheimer's & Dementia, 16(S3)e047726, 2020

b2   S. O’Sullivan, F. Jeanquartier, C Jean-Quartier, A. Holzinger, D. Shiebler, P. Moon, C. Angione, "Developments in AI and machine learning for neuroimaging", Artificial Intelligence and Machine Learning for Digital Pathology, Springer, 2020

j25   G. Zampieri, S. Vijayakumar, E. Yaneske, C. Angione, "Machine and deep learning meet genome-scale metabolic modelling", PLOS Computational Biology, 15(7): e1007084, 2019

c26   C. Culley, S. Vijayakumar, G. Zampieri, C. Angione, "Combining metabolic modelling with machine learning accurately predicts yeast growth rate", IWBDA 2019: 11th International Workshop on Bio-Design Automation, University of Cambridge, UK, 8-10 July, 2019

j24   C. Angione, "Human systems biology and metabolic modelling: a review - from disease metabolism to precision medicine", BioMed Research International, article ID 8304260, 2019

j23   A. Di Stefano, M. Scatá, S. Vijayakumar, C. Angione, A. La Corte, P. Lió, "Social Dynamics Modeling of Chrono-nutrition", PLOS Computational Biology, 15(1): e1006714, 2019

j22   A. Occhipinti, F. Eyassu, T.J. Rahman, P.K.S.M. Rahman, C. Angione, "In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production", PeerJ, 6046, 2018 - [News release 1] - Featured in Phys.org - In the top 5 most viewed PeerJ Synthetic Biology articles published in 2018

j21   A. Mancini, F. Eyassu, M. Conway, A. Occhipinti, P. Lió, C. Angione, S. Pucciarelli, "CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design", BMC Bioinformatics, 19(S15):442, 2018

j20   E. Yaneske, C. Angione, "The poly-omics of ageing through individual-based metabolic modelling", BMC Bioinformatics, 19(S14):415, 2018

c25   G. Zampieri, C. Angione, "Integrated computational extraction of cross-cancer poly-omic signatures", IWBDA 2018: 10th International Workshop on Bio-Design Automation, Berkeley, CA, 30 July - 3 August, 2018

c24   E. Yaneske, C. Angione, "Mechanistic effects of influenza in bronchial cells through poly-omic genome-scale modelling", IWBDA 2018: 10th International Workshop on Bio-Design Automation, Berkeley, CA, 30 July - 3 August, 2018

j19   C. Angione, "Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism", Bioinformatics, btx562, 34(3):494-501, 2018 - Featured in OmicTools

j18   S. Vijayakumar, M. Conway, P. Lió, and C. Angione, "Seeing the wood for the trees: a forest of methods for optimisation and omic-network integration in metabolic modelling", Briefings in Bioinformatics, 19(6):1218-1235, 2018

b1   S. Vijayakumar, M. Conway, P. Lió, and C. Angione, "Optimisation of multi-omic genome-scale models: methodologies, hands-on tutorial and perspectives", Metabolic Network Reconstruction and Modeling, Springer, 2018 - Featured in Atlas of Science

c23   G. Zampieri, M. Coggins, G. Valle, C. Angione, "A poly-omics machine-learning method to predict metabolite production in CHO cells", IECM-2, 2017 - Featured in Phys.org

j17   F. Eyassu, C. Angione, "Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism", Royal Society Open Science, 4 (10), 170360, 2017

c22   S. Vijayakumar, C. Angione, "Poly-omic statistical methods describe cyanobacterial metabolic adaptation to fluctuating environments", in Proceedings of IWBDA 2017: 9th International Workshop on Bio-Design Automation, University of Pittsburgh, PA, August 8-11, 2017

c21   E. Yaneske, C. Angione, "A data- and model-driven analysis reveals the multi-omic landscape of aging", in Proceedings of IWBBIO 2017: 5th International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain, April 26-28, LNCS vol. 10208, pp 145-154, Springer, 2017

c20   S. Vijayakumar, C. Angione, "Multi-omic data integration elucidates Synechococcus adaptation mechanisms to fluctuations in light intensity and salinity", in Proceedings of IWBBIO 2017: 5th International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain, April 26-28, LNCS vol. 10208, pp 220-229, Springer, 2017

j16   S. Saheb Kashaf, C. Angione, and P. Lió, "Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization", BMC Systems Biology, 11(1):25, 2017

j15   C. Angione, M. Conway, and P. Lió, "Multiplex methods provide effective integration of multi-omic data in genome-scale models", BMC Bioinformatics, 17:83, 2016 - Featured in Atlas of Science

c19   A. Occhipinti, C. Angione, P. Lió, "Using survival analysis to identify disrupted metabolic pathways in breast cancer", in Proceedings of ICSB 2016: International Conference on Systems Biology, Barcelona, Spain, September 16-20, 2016

c18   C. Angione, P. Lió, S. Pucciarelli, B. Can, M. Conway, M. Lotti, H. Bokhari, A. Mancini, U. Sezerman, and A. Telatin, "Bioinformatics challenges and potentialities in studying extreme environments", LNBI vol. 9874, 2016

j14   M. Conway, C. Angione, and P. Lió, "Iterative multi-level calibration of metabolic networks", Current Bioinformatics, 11(1):93-105, 2016

p6   C. Angione, M. Conway, and P. Lió "Multiplex multi-omic networks", in CompleNet 2016: 7th Workshop on Complex Networks, Dijon, France, March 23-25, 2016 [>120 submissions, acceptance rate ~20%]

j13   C. Angione and P. Lió, "Predictive analytics of environmental adaptability in multi-omic network models", Scientific Reports, 5:15147, 2015
[Download model]

j12   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "Multi-target analysis and design of mitochondrial metabolism", PLoS One, 10(9):e0133825, 2015 - Featured in Le Scienze - Scientific American

j11   C. Angione, N. Pratanwanich, and P. Lió, "A hybrid of metabolic flux analysis and Bayesian factor modeling for multi-omics temporal pathway activation", ACS Synthetic Biology, 4(8):880-889, 2015

j10   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "Analysis and Design of Molecular Machines", Theoretical Computer Science, 599:102-117, 2015

c17   C. Angione, "Phenomics validation of the Escherichia coli underground metabolic reconstruction", in Proceedings of NETTAB 2015 - 15th International Workshop on Network Tools and Applications in Biology, Bari, Italy, October 14-16, 2015

c16   C. Angione, S. Pucciarelli, B. Simionati, and P. Lió, "Measuring adaptation to extreme environments with a multi-omic approach", in Proceedings of CIBB 2015 - Computational Intelligence methods for Bioinformatics and Biostatistics, Naples, Italy, September 10-12, 2015

c15   M. Taffi, C. Angione, N. Paoletti, S. Pucciarelli, M. Marini, and P. Lió "Bioengineering metabolic pathways of PCBs degrading bacteria for the optimisation of ecological functions", in 6th european Bioremediation conference, Chania, Crete, Volume: ISBN 978-960-8475-23-6, 2015

j9   M. Taffi, N. Paoletti, C. Angione, S. Pucciarelli, M. Marini and P. Lió, "Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis", Frontiers in Genetics - Systems Biology, 5:319, 2014 - Featured in Basler and Simeonidis' commentary article - Won the MCED modelling award 2016 [Download model]

j8   C. Angione, A. Occhipinti, and G. Nicosia, "Satisfiability by Maxwell-Boltzmann and Bose-Einstein Statistical Distributions", ACM Journal of Experimental Algorithmics, 1.4(19), 2014

c14   C. Angione, P. Lió, "Discovering the Escherichia coli nutritional phase space from a compendium of environmental conditions", in Proceedings of NETTAB 2014 - 14th International Workshop on Network Tools and Applications in Biology, Turin, Italy, October 15-17, 2014

c13   C. Angione, N. Pratanwanich, and P. Lió, "A hybrid of multi-omics FBA and Bayesian factor modeling to identify pathway crosstalks", in Proceedings of the 6th International Workshop on Bio-Design Automation (IWBDA), Boston, MA, June 11-12, 2014

p5   C. Angione, E. Bartocci, L. Bortolussi, P. Lió, A. Occhipinti and G. Sanguinetti, "Bayesian Design for Whole Cell Synthetic Biology Models", in HSB 2014 - the Third International Workshop on Hybrid Systems Biology, Vienna, Austria, July 23-24, 2014

j7   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Design and strain selection criteria for bacterial communication networks", Nano Communication Networks, 4(4):155-163, 2013

j6   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Pareto Optimality in Organelle Energy Metabolism Analysis", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(4):1032-1044, 2013

j5   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "A Design Automation Framework for Computational Bioenergetics in Biological Networks", Molecular BioSystems, 9(10):2554-2564, 2013

c12   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "Identifiability Analysis to Characterize Mitochondrial Diseases", in Proceedings of the 5th International Workshop on Bio-Design Automation (IWBDA) at Imperial College, London, UK, July 12-13, 2013

c11   J. Costanza, C. Angione, G. Carapezza, P. Lió, and G. Nicosia, "Multi-objective Optimisation of Escherichia coli for Direct Production of 1,4-butanediol", in Proceedings of the 5th International Workshop on Bio-Design Automation (IWBDA) at Imperial College, London, UK, July 12-13, 2013

c10   J. Costanza, C. Angione, G. Carapezza, P. Lió, and G. Nicosia, "Pareto-based Gene and Pathway Sieve for Biofuel Production", in Proceedings of the 5th International Workshop on Bio-Design Automation (IWBDA) at Imperial College, London, UK, July 12-13, 2013

c9   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Multi-objective design for bacterial communication networks", in Proceedings of IEEE ICC'13 - Workshop MoNaCom - The 3rd IEEE International Workshop on Molecular and Nanoscale Communications. Budapest, Hungary, June 9-13, 2013

c8   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Pareto epsilon-Dominance and Identifiable Solutions for BioCAD Modeling", in Proceedings of DAC 2013 - The 50th ACM/EDAC/IEEE Design Automation Conference. Austin, Texas, USA, June 2-6, 2013

j4   C. Angione, A. Occhipinti, G. Stracquadanio, and G. Nicosia, "Bose-Einstein Condensation in Satisfiability Problems", European Journal of Operational Research, 227(1):44-54, 2013 - Featured in Le Scienze - Scientific American

j3   G. Carapezza, R. Umeton, J. Costanza, C. Angione, G. Stracquadanio, A. Papini, P. Lió, G. Nicosia, "Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability and Sensitivity Analysis", ACS Synthetic Biology, 2(5):274-288, 2013

p4   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "Pareto Front and Identifiability Analysis to Characterize Mitochondrial Diseases", in Mitochondrial Disease: Translating biology into new treatments, Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, October 2-4, 2013

p3   J. Costanza, G. Carapezza, C. Angione, P. Lió, G. Nicosia. "Reducing atmospheric CO2 by optimizing the consumption from synthetic organisms", in SB 6.0 Biobricks at Imperial College - London, UK. July 9-11, 2013

t3   C. Angione, E. Camilo, J. Harvey, P. Beltrao, "Post-translational modifications: a call to arms for computational biologists". Department of Applied Mathematics and Theoretical Physics, University of Cambridge, 2013

j2   C. Angione, P. Lió, and G. Nicosia, "How to Compute with Metabolism in Bacteria?", ERCIM News, 12, 2012

j1   J. Costanza, G. Carapezza, C. Angione, P. Lió, and G. Nicosia, "Robust Design of Microbial Strains", Bioinformatics, 28(23):3097-3104, 2012

c7   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Rational Design of Organelle Compartments in Cells", in Proceedings of NETTAB 2012 - Twelfth International Workshop on Network Tools and Applications in Biology - Workshop focused on Integrated Bio-Search, Como, Italy, November 14-16, 2012, EMBnet Journal

c6   J. Costanza, G. Carapezza, C. Angione, P. Lió, and G. Nicosia, "Multi-objective Optimisation, Sensitivity and Robustness Analysis in FBA modeling", in Proceedings of CMSB 2012 - The 10th Conference on Computational Methods in Systems Biology. The Royal Society, London, UK. October 3-5, 2012, Springer LNCS

c5   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "The Role of the Genome in the Evolution of the Computational Complexity of Metabolic Machines", in Proceedings of the European Conference in Complex Systems - ECCS'12, Brussels, September 3-7, 2012, Springer Complexity

c4   C. Angione, G. Carapezza , J. Costanza, P. Lió, and G. Nicosia, "Computing with Metabolic Machines", in Proceedings of Turing100: The Alan Turing Centenary Conference. University of Manchester, UK. June 22-26, 2012, pp. 1-15. Best paper award presented by Sir Roger Penrose [photo1] [photo2] [photo3] [photo4]

c3   J. Costanza, C. Angione, P. Lió, and G. Nicosia, "Are Bacteria Unconventional Computing Architectures?", in Proceedings of CiE 2012: Turing Centenary Conference. University of Cambridge, UK. June 18-23, 2012

c2   J. Costanza, G. Carapezza, C. Angione, R. Umeton, P. Lió, and G. Nicosia, "MetaDesign: Bacterial Strain Design Automation Software", in Proceedings of the 4th International Workshop on Bio-Design Automation (IWBDA) at Design Automation Conference (DAC 2012), San Francisco, CA, USA, June 3-4, 2012, pp. 18-19

p2   C. Angione, A. Occhipinti, G. Nicosia. "Bose-Einstein Condensation in Satisfiability Networks", in NetSci 2012: The International School and Conference on Complex Networks. Northwestern University - Evanston, Illinois. June 18-22, 2012.

p1   J. Costanza, G. Carapezza, C. Angione, P. Lió, G. Nicosia. "Pareto Front Sensitivity in Large Scale Biological Networks", in NetSci 2012: The International School and Conference on Complex Networks. Northwestern University - Evanston, Illinois. June 18-22, 2012.

c1   C. Angione, G. Nicosia, G. Stracquadanio, "Characteristic Phase Transitions and Complex Networks in Random Satisfiability Problems", From Self-Organisation in Living Systems to Sensor and Wireless Networks, 2nd Workshop on Bio-Inspired Design of Networks, BIOWIRE 2009. Pietro Lio', Eiko Yoneki, Jon Crowcroft, Dinesh C. Verma (Eds.). Cambridge, UK, June 11-12, 2009

t2   C. Angione, G. Nicosia, G. Stracquadanio, "Characteristic Phase Transitions and Bose-Einstein Condensation in Networks of Random Satisfiability Problems". University of Catania, 2009

t1   C. Angione, G. Nicosia, G. Stracquadanio, "Chaotic Quicksort: One-dimensional Chaotic Maps to Improve the Performance of Quicksort Algorithms". University of Catania, 2008