[Jul 2024]  Our paper "Cross-attention enables deep learning on limited omics-imaging-clinical data of 130 lung cancer patients" has been accepted for publication in Cell Reports Methods. 

[March 2024]  Our paper  "Emerging methods for genome-scale metabolic modeling of microbial communities" has been accepted for publication in Trends in Endocrinology and Metabolism. 

[December 2023]  Our paper "Mechanism-aware and multimodal AI: beyond model-agnostic interpretation", has been accepted for publication in Trends in Cell Biology. 

[July 2023]  Our paper "Ten quick tips for avoiding pitfalls in multi-omics data integration analyses" has been accepted for publication in PLOS Computational Biology.

[January 2023] Our paper "Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions" has been accepted for publication in Metabolic Engineering.

[January 2023] Our paper "Glycosylation Spectral Signatures for Glioma Grade Discrimination Using Raman Spectroscopy" has been accepted for publication in BMC Cancer.

[January 2023] Our paper "Metatranscriptomics-guided genome-scale metabolic modelling of microbial communities" has been accepted for publication in Cell Reports Methods.

[November 2022] Our paper "The diagnostic and prognostic potential of the EGFR/MUC4/MMP9 axis in glioma patients" has been accepted for publication in Scientific Reports.

[October 2022] Our paper "Clinical stratification improves the diagnostic accuracy of small omics datasets within machine learning and genome-scale metabolic modelling methods" has been accepted for publication in Computers in Biology and Medicine.

[October 2022] Our paper "Whole-genome sequencing and genome-scale metabolic modeling of Chromohalobacter canadensis 85B to mechanistically explore its salt tolerance and biotechnological use" has been accepted for publication in MicrobiologyOpen.

[October 2022] Our chapter "Machine Learning Methods for Survival Analysis with Clinical and Transcriptomics Data of Breast Cancer" has been published in the book Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology, Springer.

[September 2022] Our paper "Loss of full-length dystrophin expression results in major cell-autonomous abnormalities in proliferating myoblasts" has been published in eLife.

[May 2022] Our book chapter "A Practical Guide to Integrating Multimodal Machine Learning and Metabolic Modeling" has been published in the book Computational Systems Biology in Medicine and Biotechnology, Springer.

[May 2022] Invited talk at the Bioinformatics Institute, A*STAR, Singapore, May 2022 - Talk flyer

[May 2022] The video describing our THYME-funded projects is now online

[Apr 2022] Our paper "A pipeline and comparative study of 12 machine learning models for text classification" has been accepted for publication in Expert Systems with Applications

[Feb 2022] - Our paper "Using Machine Learning as a Surrogate Model for Agent-Based Simulations" has been accepted for publication in PLOS One

[Feb 2022] - I will be leading a Turing Network Development Award by The Alan Turing Institute - EPSRC [news coverage 1] [news coverage 2] [news coverage 3]

[Nov 2021] - I have been invited as a Speaker and Chair of the session on "Artificial Intelligence approaches in neurology" at the 8th European Academy of Neurology Congress - Europe 2022, to be held in Vienna in June 2022

[Sep 2021] - Our paper "Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction" has been accepted for publication in Bioinformatics - Download postprint PDF - Full text access

[Sep 2021] - Our paper "Protocol for Hybrid Flux Balance, Statistical and Machine Learning Analysis of Multi-Omic Data from Cyanobacterium Synechococcus sp. PCC 7002" has been accepted for publication in STAR Protocols

[Sep 2021] - I have been invited to the PNAS early career researcher focus panel, to be held in September 2021.

[Aug 2021] - Our paper "Genome-scale metabolic modelling of SARS-CoV-2 in cancer cells reveals an increased shift to glycolytic energy production" has been accepted for publication in FEBS Letters

[July 2021] - Our paper "Situating Agent-Based Modelling in Population Health Research" has been accepted for publication in Emerging Themes in Epidemiology

[June 2021] - Invited to join the Editorial Board of Frontiers in Systems Biology as an Associate Editor.

[June 2021] - Invited to the Program Committee of CIBB 2021, 15-17 November, 2021

[May 2021] - Invited talk "Predicting optimal engineering strategies through metabolic modelling and machine learning" at the Engineering Biology for High Value Biorenewables workshop, University of York, UK

[May 2021] - Our paper "Modeling Customer Experience in Contact Center through Process Log Mining" has been accepted for publication in ACM Transactions on Intelligent Systems and Technology

[May 2021] - Keynote talk "Deep learning approaches to predict the cell metabolic phenotype"
at the IEEE 10th Joint Symposium on Computational Intelligence (JSCI10), IEEE-CIS Thailand

[Apr 2021] - Our paper "Multimodal regularised linear models with flux balance analysis for mechanistic integration of omics data" has been accepted for publication in Bioinformatics - Full text access - Download postprint PDF - Download supplementary material PDF

[Apr 2021] - Our paper "An integrated approach to adaptive control and supervisory optimisation of HVAC control systems for demand response applications", has been accepted for publication in Energies

[Mar 2021] - Our paper "Dissecting the transcriptome in cardiovascular disease" has been accepted for publication in Cardiovascular Research

[Mar 2021] - Our paper "Integrated multi-omics analysis of ovarian cancer using variational autoencoders" has been accepted for publication in Scientific Reports

[Dec 2020] - Congratulations to Supreeta for successfully defending her PhD thesis viva! Many thanks to Dr Jags Pandhal and Dr The Anh Han for examining the thesis.

[Nov 2020] - Our paper "A hybrid flux balance analysis and machine learning pipeline elucidates the metabolic response of cyanobacteria to different growth conditions" has been accepted for publication in iScience

[Oct 2020] - Our THYME case study on using AI and microbial community modelling to improve the efficacy of probiotics in the gut

[Aug 2020] - Associate Editor for BMC Bioinformatics

[Jun 2020] - Our paper "A mechanism-aware and multi-omic machine learning pipeline characterizes yeast cell growth" has been accepted for publication in PNAS - [news release 1] [news release 2] - Download PDF (postprint)

[Jun 2020] - Invited to join the Editorial Board of BioMed Research International

[Feb 2020] - Guest Editor, MDPI Metabolites. Special issue on "Metabolic Modelling: Methods, Applications and Future Perspectives"

[Feb 2020] - Our paper "Discovering essential multiple gene effects through large scale optimization: an application to human cancer metabolism" has been accepted for publication in IEEE/ACM Transactions on Computational Biology and Bioinformatics

[Nov 2019] - Talk at the AI and Blockchain Event, Teesside University, UK

[Nov 2019] - Seminar "Combining metabolic modelling and machine learning for mechanism-aware predictions of cell behaviour" at the Department of Biology, University of York, UK

[Oct 2019] - Talk "Integrating transcriptomic data with metabolic modelling and machine learning for mechanistic insights into cell behaviour" at the EU CardioRNA COST Action meeting, Istanbul, Turkey

[Sep 2019] - Keynote talk "Exploiting machine/deep learning and in silico mechanistic modelling in biotechnology" at the Data-Driven Decision Making for Bioprocessing event, Fujifilm Diosynth Biotechnologies, UK

[Aug 2019] - Invited to the Program Committee of AAAI-20, New York, USA, February 7-12, 2020

[July 2019] - Paper "Machine and deep learning meet genome-scale metabolic modelling" now published in PLOS Computational Biology

[June 2019] - Our extended abstract "Combining metabolic modelling with machine learning accurately predicts yeast growth rate" has been accepted for publication in the Proceedings of IWBDA 2019, University of Cambridge, UK, 8-10 July, 2019

[May 2019] - Our BBSRC CBMNet Proof of Concept case study

[May 2019] - Paper "Human systems biology and metabolic modelling: a review - from disease metabolism to precision medicine" accepted for publication in BioMed Research International

[May 2019] - Congratulations to Kanika Saini and Mahmud Naina for the 2019 runner-up prize from the British Computer Society for our project "Machine learning and multi-omic modelling of lung cancer" at ExpoTees!

[May 2019] - Talk at Final CBMNet event - University of Sheffield, UK, May 2019

[Jan 2019] - Talk at NorthernBUG meeting - Newcastle University, UK, January 2019

[Dec 2018] - Paper "Social Dynamics Modeling of Chrono-nutrition" accepted for publication in PLOS Computational Biology

[Dec 2018] - Paper "In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production" published in PeerJ - Featured in Phys.org

[Nov 2018] - Paper "The poly-omics of ageing through individual-based metabolic modelling" published in BMC Bioinformatics

[May 2018] - Talk "Integrating machine learning and metabolic modelling for biomedicine and biotechnology" at Demystifying Maths and Stats for Bioscientists - A Short Course Supported by BBSRC, Newcastle University, UK

[Feb 2018] - GEMsplice featured in OmicTools

[Feb 2018] - Invited to the Program Committee of CIBB 2018, Universidade Nova de Lisboa, Portugal, September 6-8, 2018

[Jan 2018] - Invited to the Program Committee of VEMDP 2018 @ CAV 2018, part of FLoC 2018, University of Oxford, UK, July 19, 2018

[Dec 2017] - Our work on combining machine learning and metabolic modelling featured in Phys.org

[Dec 2017] - Talk "Machine-learning driven analysis and optimisation of metabolic networks" at the CBMNet Event: Factories for advanced biomanufacturing, University of Sheffield, UK

[Dec 2017] - Invited to the Program Committee of IJCAI-ECAI-18, Stockholm, Sweden, July 13-19, 2018

[Nov 2017] - Paper "A poly-omics machine-learning method to predict metabolite production in CHO cells" accepted for IECM-2

[Nov 2017] - Book chapter "Optimisation of multi-omic genome-scale models: methodologies, hands-on tutorial and perspectives" published in Metabolic Network Reconstruction and Modeling, Springer, 2017

[Oct 2017] - Poster "A poly-omics machine-learning method to predict protein production in CHO cells" at BioProNET 4th annual science meeting, University of Warwick, UK

[Oct 2017] - Paper "Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism" accepted for publication in Royal Society Open Science

[Sep 2017] - Paper "Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism" accepted for publication in Bioinformatics

[Sep 2017] - Talk at the BBSRC IBCarb workshop on Bioactive Polysaccharides, University of Cambridge, UK

[Aug 2017] - Invited talk and tutorial: "Integrating transcriptomic and codon usage data for better therapeutic target characterisation of Clostridium difficile", MIMOmics Summer School 2017, University of Cambridge, UK

[Feb 2017] - Talk at King's College London

[Jan 2017] - Paper "Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization" accepted for publication in BMC Systems Biology

[Jan 2017] - Invited to the Program Committee of Complex Networks 2017, Université de Lyon, France

[Dec 2016] - Invited to the Program Committee of CIBB 2017, the 14th conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, University of Cagliari, Italy

[Sep 2016] - Marianna Taffi and our paper "Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis" won the MCED Award for Innovative Contributions to Ecological Modelling

[Sep 2016] - Paper "Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis" selected for a spotlight talk at MASAMB 2016, University of Cambridge, UK

[Sep 2016] - Invited to the Program Committee of MASAMB 2016, the 26th workshop on Mathematical and Statistical Aspects of Molecular Biology, University of Cambridge, UK

[Aug 2016] - Paper "Multiplex methods provide effective integration of multi-omic data in genome-scale models" featured in Atlas of Science

[Jul 2016] - Project Condition-specific engineering of Pseudomonas metabolism with TeeGene Biotech, funded by BBSRC CBMNet, £20K

[Jul 2016] - Italy Made Me 2016 research award - Italian Embassy, London UK [news coverage 1] [news coverage 2 - in Italian] [news coverage 3 - in Italian]

[Jul 2016] - Paper "Using survival analysis to identify disrupted metabolic pathways in breast cancer" accepted for oral presentation at ICSB 2016: International Conference on Systems Biology, Barcelona, Spain, September 16-20

[Jun 2016] - Paper "Bioinformatics challenges and potentialities in studying extreme environments" accepted for publication in LNBI vol. 9874

[May 2016] - My project "Multivariate machine learning for lung cancer big data" won the hackathon for Roy Castle lung cancer foundation held at Sunderland Software Centre and Barclays Headquarters, London, UK

[May 2016] - ABTA Doctoral Researcher Award 2016, UCL London, UK

[Mar 2016] - Invited talk at The UK's National Biologics Manufacturing Centre, Darlington, UK

[Feb 2016] - Invited talk at ECMTB 2016 - European Conference on Mathematical and Theoretical Biology, Nottingham, UK, July 11-15, 2016

[Feb 2016] - I am Chair of the Tool Track at CMSB 2016 - 14th International Conference on Computational Methods in Systems Biology, 21-23 September 2016, Computer Laboratory, University of Cambridge, UK

[Feb 2016] - I am in the Program Committee of Complex Networks 2016 - 5th International Workshop on Complex Networks and their Applications, 30 November - 02 December 2016, Milan, Italy

[Feb 2016] - Paper "Multiplex methods provide effective integration of multi-omic data in genome-scale models" accepted for publication in BMC Bioinformatics!

[Jan 2016] - Paper "Iterative multi-level calibration of metabolic networks" accepted for publication in Current Bioinformatics!

[Dec 2015] - Paper "Multiplex multi-omic networks" accepted for an oral presentation at CompleNet 2016: 7th Workshop on Complex Networks, Dijon, France, March 23-25, 2016

[Oct 2015] - Paper "Predictive analytics of environmental adaptability in multi-omic network models" accepted for publication in Nature Scientific Reports!

[Sep 2015] - Paper "Multi-target analysis and design of mitochondrial metabolism" accepted for publication in PLoS One!

[Jun 2015] - Paper "A hybrid of metabolic flux analysis and Bayesian factor modeling for multi-omics temporal pathway activation" accepted for publication in ACS Synthetic Biology!

[Feb 2015] - Paper "Analysis and Design of Molecular Machines" accepted for publication in Theoretical Computer Science!

Paper "Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis" accepted for publication in Frontiers in Genetics - Systems Biology! (and featured in Basler and Simeonidis' commentary article)

Paper "Bose-Einstein Condensation in Satisfiability Problems" featured in Le Scienze - Scientific American

Paper "Satisfiability by Maxwell-Boltzmann and Bose-Einstein Statistical Distributions" accepted for publication in ACM Journal of Experimental Algorithmics!

Heidelberg Laureate Forum! Abel-, Fields-, Nevanlinna- and Turing- Laureates!
I am one of the 100 students invited across all the undergraduates, graduates and post-graduates worldwide! [list of participating Laureates] [photo gallery]
[with Vincent Cerf] [scientific concert]
[talking with Charles Bachman (pardon my back)]
[laureates parade] [laureates parade 2]
[Image Film]

American Chemical Society Introducing our authors!

Best paper award at The Alan Turing Centenary Conference in Manchester!
Award presented by Sir Roger Penrose! [photo] [photo] [photo] [photo]

Anile Prize 2011 for the best thesis at the Department of Mathematics and Computer Science of the University of Catania!