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) 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.


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

Recent Papers

Methods in Computational Biology and BioMedicine

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

Ascolani G., Occhipinti A., Lio’ P. (2015) Modelling circulating tumour cells for personalised survival prediction in metastatic breast cancer. Accepted in Plos Computational Biology.

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, accepted.

Bosi, ..Lio', Fondi, et al.  MeDuSa: a multi-draft based scaffolder. (2015) Bioinformatics. Accepted

Kasprzyk et al. (2015) The BioMart Community Portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research.

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, Haoming Xu, Liò, P (2014). CytoCom: a Cytoscape app to visualise, query and analyse disease comorbidity networks. Bioinformatics (in press).

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)

Moni MA, Liò P (2014). How to build personalised multi-omics comorbidity profiles. Frontiers of Systems biology.

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

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.

Tagliaferriffi 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 (in press).

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. Lió, 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, 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.

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.

Methods in Ethics and Awareness of Genome and ICT technologies

Bianchi, L., Fernandes, P., Pietro 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

Hyoungshick Kim, Wei Ming Khoo and Pietro Lio' 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

           

Editorial & Departmental Administration
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