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 hold 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, 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


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Bioinformatics Software: Cytohic (with Shavit; DNA conformation capture), Dapper (with Dr S. Haider; mass spectra),   chromoR (with Shavit; DNA conformation capture), Fishical (Calibration HIC), LDA (drugs repositioning-pathways), ComoR (with Moni; data fusion); PASSML (phylogenetic inference and protein structure).

Recent Papers

Computational Biology and BioMedicine

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)

Pratanwanich, N. and Liò, P. Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. Computational Biology and Chemistry. in press.

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 2014 Feb 20;9(2):e88533

Capobianco E. and Liò, P. (2013), Comorbidity: a multidimensional approach. Trends in Molecular Medicine 2013 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.

Felicetti, L., Femminella, M., Reali, G., Lio', P.  Modeling, Methodologies and Tools for Molecular and Nano-scale Communications. 2014 Springer.

Felicetti, L., Femminella, M., Reali, G., Lio', P. A Molecular Communication System in Blood Vessels for Tumor Detection. ACM NANOCOM 2014

MultiOmic data integration (particularly on nuclear data analysis)


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.

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.

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

Synthetic Biology

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(1), 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

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

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

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/

           

Editorial & Departmental Administration
Interesting Conferences
Valigie (personal)