baldassarri baronchelli barrat caglioti castellano cattuto complexity dattoli evolutionary_dynamics granular_media granular_media herrmann information_theory innovation_dynamics kreyon language_dynamics loreto mari mukherjee petri pietronero puglisi quantum_optics self_organization servedio statistical_physics techno_social_systems tria zapperi zippers
2013 |
Tria, Francesca; Pompei, Simone; Loreto, Vittorio Dynamically correlated mutations drive human Influenza A evolution Journal Article SCIENTIFIC REPORTS, 3 , 2013. Abstract | Links | BibTeX | Tag: biology, evolutionary_dynamics, loreto, pompei, tria @article{b, title = {Dynamically correlated mutations drive human Influenza A evolution}, author = {Francesca Tria and Simone Pompei and Vittorio Loreto}, url = {http://www.nature.com/srep/2013/130919/srep02705/full/srep02705.html}, year = {2013}, date = {2013-01-01}, journal = {SCIENTIFIC REPORTS}, volume = {3}, publisher = {NATURE PUBLISHING GROUP}, abstract = {Human Influenza A virus undergoes recurrent changes in the hemagglutinin (HA) surface protein, primarily involved in the human antibody recognition. Relevant antigenic changes, enabling the virus to evade host immune response, have been recognized to occur in parallel to multiple mutations at antigenic sites in HA. Yet, the role of correlated mutations (epistasis) in driving the molecular evolution of the virus still represents a challenging puzzle. Further, though circulation at a global geographic level is key for the survival of Influenza A, its role in shaping the viral phylodynamics remains largely unexplored. Here we show, through a sequence based epidemiological model, that epistatic effects between amino acids substitutions, coupled with a reservoir that mimics worldwide circulating viruses, are key determinants that drive human Influenza A evolution. Our approach explains all the up-to-date observations characterizing the evolution of H3N2 subtype, including phylogenetic properties, nucleotide fixation patterns, and composition of antigenic clusters.}, keywords = {biology, evolutionary_dynamics, loreto, pompei, tria}, pubstate = {published}, tppubtype = {article} } Human Influenza A virus undergoes recurrent changes in the hemagglutinin (HA) surface protein, primarily involved in the human antibody recognition. Relevant antigenic changes, enabling the virus to evade host immune response, have been recognized to occur in parallel to multiple mutations at antigenic sites in HA. Yet, the role of correlated mutations (epistasis) in driving the molecular evolution of the virus still represents a challenging puzzle. Further, though circulation at a global geographic level is key for the survival of Influenza A, its role in shaping the viral phylodynamics remains largely unexplored. Here we show, through a sequence based epidemiological model, that epistatic effects between amino acids substitutions, coupled with a reservoir that mimics worldwide circulating viruses, are key determinants that drive human Influenza A evolution. Our approach explains all the up-to-date observations characterizing the evolution of H3N2 subtype, including phylogenetic properties, nucleotide fixation patterns, and composition of antigenic clusters. |
2012 |
Pompei, Simone; Loreto, Vittorio; Tria, Francesca Phylogenetic Properties of RNA Viruses Journal Article PLOS ONE, 7 , pp. e44849-1–e44849-10, 2012. Abstract | Links | BibTeX | Tag: evolutionary_dynamics, loreto, phylogeny, pompei, tria @article{b, title = {Phylogenetic Properties of RNA Viruses}, author = {Simone Pompei and Vittorio Loreto and Francesca Tria}, url = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044849}, year = {2012}, date = {2012-01-01}, journal = {PLOS ONE}, volume = {7}, pages = {e44849-1--e44849-10}, abstract = {A new word, phylodynamics, was coined to emphasize the interconnection between phylogenetic properties, as observed for instance in a phylogenetic tree, and the epidemic dynamics of viruses, where selection, mediated by the host immune response, and transmission play a crucial role. The challenges faced when investigating the evolution of RNA viruses call for a virtuous loop of data collection, data analysis and modeling. This already resulted both in the collection of massive sequences databases and in the formulation of hypotheses on the main mechanisms driving qualitative differences observed in the (reconstructed) evolutionary patterns of different RNA viruses. Qualitatively, it has been observed that selection driven by the host immune response induces an uneven survival ability among co-existing strains. As a consequence, the imbalance level of the phylogenetic tree is manifestly more pronounced if compared to the case when the interaction with the host immune system does not play a central role in the evolutive dynamics. While many imbalance metrics have been introduced, reliable methods to discriminate in a quantitative way different level of imbalance are still lacking. In our work, we reconstruct and analyze the phylogenetic trees of six RNA viruses, with a special emphasis on the human Influenza A virus, due to its relevance for vaccine preparation as well as for the theoretical challenges it poses due to its peculiar evolutionary dynamics. We focus in particular on topological properties. We point out the limitation featured by standard imbalance metrics, and we introduce a new methodology with which we assign the correct imbalance level of the phylogenetic trees, in agreement with the phylodynamics of the viruses. Our thorough quantitative analysis allows for a deeper understanding of the evolutionary dynamics of the considered RNA viruses, which is crucial in order to provide a valuable framework for a quantitative assessment of theoretical predictions.}, keywords = {evolutionary_dynamics, loreto, phylogeny, pompei, tria}, pubstate = {published}, tppubtype = {article} } A new word, phylodynamics, was coined to emphasize the interconnection between phylogenetic properties, as observed for instance in a phylogenetic tree, and the epidemic dynamics of viruses, where selection, mediated by the host immune response, and transmission play a crucial role. The challenges faced when investigating the evolution of RNA viruses call for a virtuous loop of data collection, data analysis and modeling. This already resulted both in the collection of massive sequences databases and in the formulation of hypotheses on the main mechanisms driving qualitative differences observed in the (reconstructed) evolutionary patterns of different RNA viruses. Qualitatively, it has been observed that selection driven by the host immune response induces an uneven survival ability among co-existing strains. As a consequence, the imbalance level of the phylogenetic tree is manifestly more pronounced if compared to the case when the interaction with the host immune system does not play a central role in the evolutive dynamics. While many imbalance metrics have been introduced, reliable methods to discriminate in a quantitative way different level of imbalance are still lacking. In our work, we reconstruct and analyze the phylogenetic trees of six RNA viruses, with a special emphasis on the human Influenza A virus, due to its relevance for vaccine preparation as well as for the theoretical challenges it poses due to its peculiar evolutionary dynamics. We focus in particular on topological properties. We point out the limitation featured by standard imbalance metrics, and we introduce a new methodology with which we assign the correct imbalance level of the phylogenetic trees, in agreement with the phylodynamics of the viruses. Our thorough quantitative analysis allows for a deeper understanding of the evolutionary dynamics of the considered RNA viruses, which is crucial in order to provide a valuable framework for a quantitative assessment of theoretical predictions. |
2011 |
Pompei, Simone; Tria, Francesca; Loreto, Vittorio On the accuracy of language trees Journal Article PLOS ONE, 6(6) , 2011. Links | BibTeX | Tag: evolutionary_dynamics, loreto, phylogeny, pompei, tria @article{b, title = {On the accuracy of language trees}, author = {Simone Pompei and Francesca Tria and Vittorio Loreto}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79958041006&partnerID=65&md5=22335465a4b96cbddf4bbc9cefd7b7a8 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000291355500005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a}, year = {2011}, date = {2011-01-01}, journal = {PLOS ONE}, volume = {6(6)}, publisher = {San Francisco, CA : Public Library of Science}, keywords = {evolutionary_dynamics, loreto, phylogeny, pompei, tria}, pubstate = {published}, tppubtype = {article} } |
2010 |
Caglioti, Emanuele; Loreto, Vittorio; Pompei, Simone; Tria, Francesca Distance-based Phylogenetic algorithms: new insights and applications Journal Article MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, 20 , pp. 1511–1532, 2010. Links | BibTeX | Tag: caglioti, evolutionary_dynamics, loreto, phylogeny, pompei, tria @article{b, title = {Distance-based Phylogenetic algorithms: new insights and applications}, author = {Emanuele Caglioti and Vittorio Loreto and Simone Pompei and Francesca Tria}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-77957171910&partnerID=65&md5=41f74dd5dff0e500c1061a8d02fcd6c8 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000282218000006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a}, year = {2010}, date = {2010-01-01}, journal = {MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES}, volume = {20}, pages = {1511--1532}, publisher = {World Scientific Publishing Company:PO Box 128, Farrer Road, Singapore 912805 Singapore:011 65 6 4665775, EMAIL: journal@wspc.com.sg, INTERNET: http://www.wspc.com.sg, http://www.worldscinet.com, Fax: 011 65 6 4677667}, keywords = {caglioti, evolutionary_dynamics, loreto, phylogeny, pompei, tria}, pubstate = {published}, tppubtype = {article} } |
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