Computer Laboratory

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(Photos on Cambridge exam "lifestyle")

Pietro Lio'

I am a Reader in Computational Biology in the Computer Laboratory which is the department of Computer Science of the University of Cambridge and I am a member of the Artificial Intelligence group of the Computer Laboratory.
I have a MA from Cambridge, one PhD in Complex Systems and Non Linear Dynamics (School of Informatics, dept of Engineering of the University of Firenze, Italy) and one PhD in (Theoretical) Genetics (University of Pavia, Italy).
I am affiliated to Cambridge Computational Biology Institute. I am member of Cambridge Neuroscience, Cambridge Centre for Science and Policy, ACM (Association for Computing Machinery) VPH (Virtual Physiologycal Human) and SMB (society for mathematical biology).
Office: FC20; tel: +44 (0)1223-763604; E_mail: Pietro.Lio at  cl.cam.ac.uk
I am interested in Machine Learning and computational models in health Big Data.
I am happy to receive enquiries for PhD applications.
I have successfully completed the equality and diversity essentials.


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Bioinformatics Software tools: Metrade (with Dr Claudio Angione, multi-omic integration), Cytohic (with Y. Shavit; DNA conformation capture), Dapper (with Dr S. Haider; mass spectra),  chromoR (with Y. Shavit; DNA conformation capture), Fishical (with Dr Y. Shavit, Calibration Fish-HIC), LDA (drug repositioning pathways analysis, with N. Pratanwanich), ComoR (with Dr M. Moni; data fusion), CytoCom (with Dr M. Moni; data visualisation); Nuchart (with Dr I. Merelli; data fusion); Pogo (with Dr M. Moni, data fusion), PASSML (with Dr N. Goldman, phylogenetic inference and protein structure).

Recent Papers

Methods in Computational Biology and BioMedicine

Veličković P. Lio', P.  (2016)  Muxstep: an open-source C++ multiplex HMM library for making inferences on multiple data types, Bioinformatics.

Sansom C., Castiglione F., Liò, P. (2016) Metabolic disorders: how can systems modelling help?. Lancet Endocrinology pii: S2213-8587(16)00047-4. doi: 10.1016/S2213-8587(16)00047-4.

Schwarz, E et al.,  (2016) Protein interaction networks link schizophrenia risk loci to synaptic function. Schizophrenia Bulletin.

Nardi F., Liò, P., Frati F. (2016) Animal inference on human mitochondrial diseases. Computational Biology and Chemistry, Comput Biol Chem. 2016 Feb 16;62:17-28. doi: 10.1016/j.compbiolchem.2016.02.002.

Bartocci E, Lio', P. (2016) Computational modeling, formal analysis and tools for systems biology. Plos Computational Biology. 12(1): e1004591. doi:10.1371/journal.pcbi.1004591.

Capobianco E. and Liò, P. (2015).  Electronic Health Systems: Golden Mine for Precision Medicine? The Journal of Precision Medicine (in press) http://www.thejournalofprecisionmedicine.com/wp-content/uploads/2015/10/ENRICO.pdf

Claudio Angione and Pietro Lio' (2015) Predictive analytics of environmental adaptability in multi-omic network models. Scientific Reports Oct 20;5:15147. doi: 10.1038/srep15147.

S. Haider, Z. Lipinszki, M. R Przewloka, Y. Ladak, P.P. D'Avino, Y. Kimata, P. Lio' and D. M. Glover (2015) DAPPER: A data-mining resource for protein-protein interactions. BioData Mining 2015, 8:30.

Veličković P. Lio', P.  (2015)  Molecular multiplex network inference using Gaussian mixture hidden Markov models. Journal of Complex Networks 2015; doi: 10.1093/comnet/cnv029

Shavit, Y., Merelli I, Milanesi L. & Lio', P. (2015)  How computer science can help in understanding the 3D genome architecture. Briefings in Bioinformatics, 2015, Brief Bioinform. Oct 3. pii: bbv085

Moni, MA, Haoming Xu, Liò, P (2015).  Network regularised Cox regression and multiplex network models to predict disease comorbidities and survival of cancer. Computational Biology and Chemistry (in press).

Felicetti, L., Femminella, M., Reali, G., Lio', P.  (2015)  Applications of molecular communications to medicine: a survey. Nano Communication Networks (in press).

, M, Angione, C., Lio’ P. (2015) Iterative multi level calibration of metabolic networks. Current Bioinformatics. In press.

Angione C, Costanza J. , Carapezza G., Lio' P, Nicosia G. (2015)  Multi-target analysis and design of mitochondrial metabolism. PLoS ONE 10(9): e0133825. doi:10.1371/journal.pone.0133825

Castellani et al, Lio’ P. (2015)  Systems medicine of inflammaging. Briefings in Bioinformatics, Aug 24. pii: bbv062.

Ascolani G., Occhipinti A., Lio’ P. (2015) Modelling circulating tumour cells for personalised survival prediction in metastatic breast cancer. Plos Computational Biology May 15;11(5):e1004199. doi: 10.1371/journal.pcbi.1004199. eCollection 2015.

Angione C, Pratanwanich N., Lio’ P. (2015) A hybrid of metabolic flux analysis and Bayesian factor modeling for multi-omics temporal pathway activation. ACS Synthetic Biology, 10.1021/sb5003407

Bosi, et al.  MeDuSa: a multi-draft based scaffolder. (2015) Bioinformatics. 2015 Mar 25. pii: btv171 (pubmed/25810435).

Smedley et al. (2015) The BioMart Community Portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research, Apr 20. pii: gkv350.

Iuliano A., Occhipinti A, Angelini C., De Feis I. and Lio’ P. (2015) Network-based survival analysis methods for pathway detection in cancer. Lecture Notes in Computer Science LNCS 8623 (in press).

Boutorh A, Pratanwanich N, Guessoum A. and Lio’ P. (2015) Drug repurposing by optimizing mining of genes target association. Lecture Notes in Computer Science LNCS 8623 (in press).

Capobianco E. and Liò, P. (2015).  Comorbidity Networks: beyond disease correlations. The Journal of Complex Networks ,  jcomplexnetw (2015) doi: 10.1093/comnet/cnu048

Moni MA, Liò P (2015). How to build personalised multi-omics comorbidity profiles. Frontiers in Cell and Developmental Biology, section Systems Biology. Front. Cell Dev. Biol. doi: 10.3389/fcell.2015.00028.

Moni, MA, Haoming Xu, Liò, P (2014). CytoCom: a Cytoscape app to visualise, query and analyse disease comorbidity networks. Bioinformatics 31:969-71.

Capobianco E. and Liò, P. (2014).  Advances in translational biomedicine from systems approaches. Frontiers in Genetics, 14 August 2014 doi: 10.3389/fgene.2014.00273 (Editorial)

Korhonen A., Guo Y, Yetisgen-Yildiz M., Stenius U., Narita M. and Lio’ P. (2015) Improving Literature-Based Discovery with Text Mining Lecture Notes in Computer Science LNCS 8623

Pratanwanich, N. and Liò, P. (2014) Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. Computational Biology and Chemistry. 53:144-52. doi: 10.1016/j.compbiolchem.2014.08.019

Pratanwanich, N. and Liò, P. (2014) Who Wrote This? Textual Modeling with Authorship Attribution in Big Data. ICDM 2nd Workshop for High Dimensional Data Mining.

Moni, M.A. and Lio`, P. (2014) Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies. BMC Bioinformatics 2014, 15:333

Felicetti, L., Femminella, M., Reali, G., Lio', P.  (2014) Effect of Aging, Disease vs Health Conditions in the design of Nano-Communications in Blood Vessels Springer book on Modeling, Methodologies and Tools for Molecular and Nano-scale Communications.

Azad S, Lio P. (2014) Emerging trends of malaria-dengue geographical coupling in the Southeast Asia region. J Vector Borne Dis. 51(3):165-71.

Moni M.A. and Liò, P. (2014). ComoR: a software for disease comorbidity risk assessment. Journal of Clinical Bioinformatics 2014, 4:8  doi:10.1186/2043-9113-4-8.

Pratanwanich, N. and Liò, P. (2014) Pathway-based Bayesian inference of drug-disease interactions. Molecular BioSystems Jun;10(6):1538-48. doi: 10.1039/c4mb00014e.


Ascolani, G. and Liò, P. (2014) Modeling TGF-beta in early stages of cancer tissue dynamics. Plos One 9(2):e88533

Capobianco E. and Liò, P. (2013), Comorbidity: a multidimensional approach. Trends in Molecular Medicine  Sep;19(9):515-21

Vicenzi, E., Liò, P., & Poli, G. (2013). The puzzling role of CXCR4 in human immunodeficiency virus infection. Theranostics, 3(1), 18-25. doi:10.7150/thno.5392

Bartocci, E., Liò, P., Merelli, E., & Paoletti, N. (2012). Multiple Verification in Complex Biological Systems: The Bone Remodelling Case Study. T. Comp. Sys. Biology, 14, 53-76. doi:10.1007/978-3-642-35524-0_3

Liò, P., Merelli, E., & Paoletti, N. (2012). Disease processes as hybrid dynamical systems. EPTCS 92, 2012, pp. 152-166. doi:10.4204/EPTCS.92.11

Liò, P., Paoletti, N., Moni, M. A., Atwell, K., Merelli, E., & Viceconti, M. (2012). Modelling osteomyelitis.. BMC Bioinformatics, 13 Suppl 14, S12. doi:10.1186/1471-2105-13-S14-S12

Paoletti, N., Liò, P., Merelli, E., & Viceconti, M. (2012). Multilevel computational modeling and quantitative analysis of bone remodeling. IEEE/ACM Trans Comput Biol Bioinform, 9(5), 1366-1378. doi:10.1109/TCBB.2012.51

Felicetti, L., Femminella, M., Reali, G., Lio', P.   Endovascular Mobile Sensor Network for Detecting Circulating Tumoral Cells.  9th International Conference on Body Area Networks. BODYNETS - 9th International Conference on Body Area Networks, September 29–October 1, 2014, London,
    http://dx.doi.org/10.4108/icst.bodynets.2014.256917

L. Felicetti, M. Femminella, G. Reali, P. Lio', A Molecular Communication System in Blood Vessels for Tumor Detection, ACM NANOCOM 2014, Atlanta, Georgia, USA, May 13-14, 2014 - DOI: 10.1145/2619955.2619978

L. Felicetti, M. Femminella, G. Reali, P. Lio', Book chapter Effect of Aging, Disease vs Health Conditions in the design of Nano-Communications in Blood Vessels, published in the Springer book "Modeling, Methodologies and Tools for Molecular and Nano-scale Communications", Springer nanocom 2014

Methods for MultiOmic data integration


Angione C, Conway M. and Pietro Lio' (2016) Multiplex methods provide effective integration of multi-omic data in genome-scale models. BMC Bioinformatics. 17 Suppl 4:83. doi: 10.1186/s12859-016-0912-1.

Shavit Y., Walker B., Lio' P (2015) Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration. Bioinformatics 2015 Dec 17. pii: btv736.

Bardozzo F, Lio P and Tagliaferri R, (2015) Multi omic oscillations in bacterial pathways. IJCNN2015, Dublin.

Hamey F., Shavit Y., Maciulyte V., Town C., Lio' P. and Tosi S. (2015) Automated Detection of Fluorescent Probes in Molecular Imaging. Lecture Notes in Computer Science LNCS 8623

I Merelli, F Tordini, M Drocco, M Aldinucci,  P Liò, L Milanesi (2015) Integrating Multi-omics features exploiting Chromosome Conformation Capture data. Frontiers in genetics Feb 11;6:40. doi: 10.3389/fgene.2015.00040. eCollection 2015.

M Fondi, P Liò (2015) Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology. Microbiological Research Feb;171:52-64. doi: 10.1016/j.micres.2015.01.003. Epub 2015 Jan 7.

Shavit, Y., Hamey F. & Lio', P. (2014) FisHical: an R package for iterative FISH-based calibration of Hi-C data. Bioinformatics Jul 23. pii: btu491.

Shavit, Y., & Lio', P. (2014). Combining wavelet changepoint and Bayes Factor for analysing chromosomal interactions data. Molecular BioSystems 10(6):1576-85.

Taffi M., Paoletti N., Liò P., Pucciarelli S., Marini M. (2015) Bioaccumulation modelling and sensitivity analysis for discovering key players in contaminated food webs: the case study of PCBs in the Adriatic Sea.  Ecological Modelling 306:205-215 04 Jun 2015       doi:10.1016/j.ecolmodel.2014.11.030 (Best Young Researcher Award at ISEM 2016).

Taffi, M., Paoletti, N. , Angione, C., Pucciarelli, S., Marini, M., Liò, P. (2014) Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis. Frontiers in Genetics, section Systems Biology.  5: 319.Published online Sep 12, 2014. doi:  10.3389/fgene.2014.00319 (see also related editorial).

F. Tordini, M. Drocco, C. Misale, L. Milanesi, P. Liò, I. Merelli, and M. Aldinucci, Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II, in Proc. of Intl. Euromicro PDP 2015: Parallel Distributed and network-based Processing, Turku, Finland, 2015.

F. Tordini, M. Drocco, C. Misale, P. Liò, I. Merelli, M. Aldinucci: NuChart-II: the road to a fast and scalable tool for Hi-C data analysis, in International Journal of High Performance Computing Application, 2015. (submitted)

F. Tordini, I. Merelli, P. Liò, M. Aldinucci and L. Milanesi: NuchaRt: embedding High-Performance Computing in R for augmented DNA Exploration, in Proc. of the 12th Intl. meeting on Computational Intelligence methods for Bionformatics and Biostatistics (CIBB), Naples, Italy, 2015. (To appear)

M. Drocco, C. Misale, G. P. Pezzi, F. Tordini, and M. Aldinucci: “Memory- Optimised Parallel Processing of Hi-C Data,” in Proc. of Intl. Euromicro PDP 2015: Parallel Distributed and network-based Processing, Turku, Finland,
2015

Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Pietro Liò, and Luciano Milanesi. Integrating multi-omic features exploiting chromosome conformation capture data. Frontiers in Genetics, 6(40), 2015

Fabio Tordini, Maurizio Drocco, Claudia Misale, Luciano Milanesi, Pietro Liò, Ivan Merelli, and Marco Aldinucci. Parallel exploration of the nuclear chromosome conformation with NuChart-II. In Proc. of Intl. Euromicro PDP 2015: Parallel Distributed and network-based Processing. IEEE, March 2015.

I. Merelli, P. Liò, L. Milanesi (2014). Describing the genes social networks relying on chromosome conformation capture data. EMBnet.journal, 19:73-75, oct. 2013. ISSN 2226-6089.

Bartoszek, K & Lio', P. (2014)  A Novel algorithm to reconstruct phylogenies using gene frequencies and expression data.  Proceedings of 2014 International Conference on Bioinformatics and Biomedical Technology. Gdansk 14-16 May, 2014.

F.  Tordini, M. Drocco, I. Merelli, P. Li` o, L. Milanesi, and M. Aldinucci: “NuChart-II: a graph-based approach for the analysis and interpretation of Hi-C Data,” in Proc. of the 11th Intl. meeting on Computational Intelligence methods for Bionformatics and Biostatistics (CIBB), Cambridge, UK, 2014

Merelli I, Liò P, Milanesi L (2013) NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations. PLoS ONE 8(9): e75146. doi:10.1371/journal.pone.0075146

Shavit, Y., & Lio', P. (2013). CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks. Bioinformatics, 29(9), 1206-1207. doi:10.1093/bioinformatics/btt120

Liò, P., Angelini, C., De Feis, I., & Nguyen, V. A. (2012). Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.. PLoS One, 7(9), e42489. doi:10.1371/journal.pone.0042489

Methods in Synthetic Biology

Angione C, Costanza J. , Carapezza G., Lio' P, Nicosia G. (2015) Analysis and Design of Molecular Machines, Theoretical Computer Science (in press).

M Fondi, P Liò (2015) Genome-Scale Metabolic Network Reconstruction, Bacterial Pangenomics, Methods in Molecular Biology Volume 1231, 233-256

Angione C., Bartocci E., Bortolussi L., Lió P., Occhipinti A., Sanguinetti G.,  (2014) Bayesian Design for Whole Cell Synthetic Biology Models. Proceedings HSB. Third International Workshop on Hybrid Systems Biology Vienna, Austria, July 23-24, 2014 at CAV 2014.

Vitaly Petrov, Sasitharan Balasubramaniam, Rahmi Lale, Dmitri Moltchanov, Pietro Lio’, Yevgeni Koucheryavy (2014)  Forward and Reverse Coding for Chromosome Transfer in Bacterial Nanonetworks Nano Communication Networks 5:  1-2.  March-April.

Angione, C., Pratanwanich, N. and Pietro Lió, P.  A hybrid of multi-omics FBA and Bayesian factor modeling to identify pathway crosstalks.  Proceedings IWBDA 2014.

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, 2013

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 Journal, 2(5), 274-288, 2013

Brilli, M., Liò, P., Lacroix, V., & Sagot, M. F. (2013). Short and long-term genome stability analysis of prokaryotic genomes.. BMC Genomics, 14, 309. doi:10.1186/1471-2164-14-309

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


Balasubramaniam, S., & Lio', P. (2013). Multi-hop conjugation based bacteria nanonetworks. IEEE Trans Nanobioscience, 12(1), 47-59. doi:10.1109/TNB.2013.2239657.  Ranked 5th among most popular articles in IEEE Transactions on Nanobioscience. Listed here among IEEECOM Best readings

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

Social Networks, Ethics and Awareness of Genome and ICT technologies

Lu, X and Lió, P. (2015) Privacy Information Security Classification and Comparison between the Westerner and Chinese 2015 International Conference on Identification, Information, and Knowledge in the Internet of Things

Di Stefano, A.,  Scata' M. , Lió, P. et al. (2015) Quantifying the Role of Homophily in Human Cooperation Using Multiplex Evolutionary Game Theory. PLoS One. 2015 Oct 23;10(10):e0140646. doi: 10.1371/journal.pone.0140646.

Alessandro Di Stefano, Aurelio La Corte, Pietro Lió , Marialisa Scatá (2015) Bio-Inspired ICT for Big Data Management in Healthcare. in Intelligent Agents in Data-intensive Computing, editors: Kołodziej, J., Correia, L., Manuel Molina, J. Springer.

Xiaofeng Lu , Pietro Lio , and Pan Hui A Content Dissemination Model for Mobile Internet to Minimize Load on Cellular Network Electronics, Communications and Networks IV, Proceedings of the 4TH Internationa Conference on Electronics, Communications and Networks, 12 – 15 December 2014, Beijing, China Edited by Amir Hussain and Mirjana Ivanovic CRC Press 2015, Pages 289–294. Print ISBN: 978-1-138-02830-2

 Bianchi, L., Fernandes, P., Lió, P. Improving Collective Awareness and Education about the Privacy and Ethical Issues Connected with the Genome Technologies. Proceedings of the International Conference on The Future of Education. Florence, Italy 13 - 14 June 2013

H. Kim, W. M. Khoo and Pietro Lio' (2012) Polymorphic Attacks against Sequence-based Software Birthmarks, SSP: The 2nd ACM SIGPLAN Workshop on Software Security and Protection, held in conjunction with ACM PLDI, Beijing, China, 2012

Stajano, F., Bianchi, L., Lio', P., Korff, D., Forensic Genomics: kin privacy, driftnets and other open questions. Workshop on Privacy in Electronic Society (WPES), Alexandria (VA), USA, October 2008. See: https://dais.cs.uiuc.edu/wpes08/

Bianchi, L., Lio', P. (2007) Forensic DNA and bioinformatics. Brief Bioinform (2007) 8 (2): 117-128.
doi: 10.1093/bib/bbm006

           

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