Home Research Network Bioinformatics A. Zanzoni

Andreas Zanzoni

Interested in understanding the molecular basis of human disease using network-based approaches.

 

Current research interests

- The role of Protein-RNA interactions in cell networks (A*MIDEX 2015-2016)

- Host-microbe interactions and chronic diseases

- Protein interaction networks and cancer proteomics

- Regulatory sites and signal transduction

 

Publications

2016

Zanzoni A, Brun C. Integration of quantitative proteomics data and interaction networks: identification of dysregulated cellular functions during cancer progression. Methods. 93:103-109. doi: 10.1016/j.ymeth.2015.09.014. PubMed PMID: 26386316.

Zanzoni A. Computational network biology approach to uncover novel genes related to Alzheimer’s disease. Methods in Molecular Biology. 1303:435-46. doi: 10.1007/978-1-4939-2627-5_26. PubMed PMID: 26235083.

2015

Zanzoni A, Chapple CE, Brun C. Relationship between extreme multifunctional proteins, human diseases and comorbidities from a network perspective. Frontiers in Physiology. 6:171 doi: 10.3389/fphys.2015.00171. PubMed PMID: 26157390.

Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M. Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 16(Suppl 9):S1 doi:10.1186/1471-2105-16-S9-S1. PubMed PMID: 26050789.

Panek J, Chetouhi C, El Alaoui H, Texier C, Langin T, de Bekker C, Bonhomme L, Urbach S, Demettre E, Misse D, Holzmuller P, Hughes DP, Zanzoni A, Brun C, Biron DG. Cross-talk in host-parasite associations: what do past and recent proteomics tools tell us? Infection, Genetics and Evolution. doi: 10.1016/j.meegid.2015.04.015. PubMed PMID: 25913042.

Via A and Zanzoni A#. A prismatic view of protein phosphorylation in health and disease. Frontiers in Genetics. 6:131. doi:10.3389/fgene.2015.00131PubMed PMID: 25904935.

Arroyo R, Suñé G, Zanzoni A, Duran-Frigola M, Alcalde V, Stracker TH, Soler-Lopéz M, Aloy P. Systematic identification of molecular links between core and candidate genes in breast cancer. Journal of Molecular Biology. 2015 Mar 27; 427(6 Pt B):1436-50. doi: 10.1016/j.jmb.2015.01.014. PubMed PMID: 25640309.

Via A, Uyar B, Brun C, Zanzoni A#. How pathogens use linear motifs to perturb host cell networks. Trends in Biochemical  Sciences. 2015 Jan; 40(1):36-48. doi: 10.1016/j.tibs.2014.11.001. PubMed PMID: 25475989.

2014

Panek J, El Alaoui H, Mone A, Urbach S, Demettre E, Texier C, Brun C, Zanzoni A, Peyretaillade E, Parisot N, Lerat E, Peyret P, Delbac F, Biron DG. Hijacking of host cellular functions by an intracellular parasite, the microsporidian Anncaliia algerae. PLoS One. 2014 Jun 26; 9(6):e100791. doi: 10.1371/journal.pone.0100791. PubMed PMID: 24967735.

Klus P, Bolognesi B, Agostini F, Marchese D, Zanzoni A, Tartaglia GG. The cleverSuite Approach for Protein Characterization: Predictions of Structural Properties, Solubility, Chaperone Requirements and RNA-Binding Abilities. Bioinformatics 2014 Jun 1; 30(11):1601-8. doi: 10.1093/bioinformatics/btu074. PubMed PMID: 24493033.

2013

Zanzoni A*, Marchese D*, Agostini F, Bolognesi B, Cirillo D, Botta-Orfila M, Livi CM, Rodriguez-Mulero S, Tartaglia GG. Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. Nucleic Acids Research 2013 Dec; 41(22):9987-98. doi: 10.1093/nar/gkt794. PubMed PMID: 24003031.

Agostini F, Zanzoni A, Klus P, Marchese D, Cirillo D, Tartaglia GG. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics 2013 Nov; 29(22): 2928-2930. doi:10.1093/bioinformatics/btt495. PubMed PMID: 23975767.

2012

Soler-López M, Badiola N, Zanzoni A, Aloy P. Towards Alzheimer's root cause: ECSIT as an integrating hub between oxidative stress, inflammation and mitochondrial dysfunction. Hypothetical role of the adapter protein ECSIT in familial and sporadic Alzheimer's disease pathogenesis. Bioessays 2012 Jul; 34(7):532-41. doi: 10.1002/bies.201100193. PubMed PMID: 22513506.

2011

Soler-López M*, Zanzoni A*, Lluís R, Stelzl U, Aloy P. Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. Genome Research 2011 Mar; 21(3):364-76. doi: 10.1101/gr.114280.110. PubMed PMID: 21163940.

Zanzoni A#, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A. Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Research 2011 Jan; 39(Database issue):D268-71. doi: 10.1093/nar/gkq936. PubMed PMID: 20965970.

2009

Zanzoni A, Soler-López M, Aloy P. A network medicine approach to human disease. FEBS Letters 2009 Jun; 583(11):1759-65. doi: 10.1016/j.febslet.2009.03.001. PubMed PMID: 19269289.

2008

Pache RA, Zanzoni A, Naval J, Mas JM, Aloy P. Towards a molecular characterisation of pathological pathways. FEBS Letters 2008 Apr; 582(8):1259-65. doi: 10.1016/j.febslet.2008.02.014. PubMed PMID: 18282477.

Chatr-Aryamontri A, Zanzoni A, Ceol A, Cesareni G. Searching the protein interaction space through the MINT database. Methods in Molecular Biology 2008; 484:305-17. doi: 10.1007/978-1-59745-398-1_20. PubMed PMID: 18592188.

2001 - 2007

Zanzoni A#, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M. Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Research 2007; 35(Database issue):D229-31. PubMed PMID: 17142231.

Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics 2005; 6:194. PubMed PMID: 16076399.

Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M. pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Research 2005; 33(Web Server issue):W133-7. PubMed PMID: 15980442.

Via A, Zanzoni A, Helmer-Citterich M. Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics 2005; 21(4):551-3. PubMed PMID: 15454411.

Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Research 2004; 32(Database issue):D240-4. PubMed PMID: 14681403.

Ferrè F, Via A, Ausiello G, Brannetti B, Zanzoni A, Helmer-Citterich M. Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information. Computational Functional Genomics 2003; 4(4):416-9. doi: 10.1002/cfg.304. PubMed PMID: 18629081.

Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS Letters 2002; 513(1):135-40. PubMed PMID: 11911893.

Brannetti B, Zanzoni A, Montecchi-Palazzi L, Cesareni G, Helmer-Citterich M. iSPOT: a web tool for the analysis and recognition of protein domain specificity. Computational Functional Genomics 2001; 2(5):314-8. doi: 10.1002/cfg.104. PubMed PMID: 18629248.

* equal contribution. # corresponding author.