Publication List

Published Papers




  1. Malusa F, Taranta M., Zaki N, Cinti C, Capobianco E. (2015).Time-course Gene Expression Profiling and Networks Dynamics in Demethylated Retinoblastoma cell line. Oncotarget. In press.

  2. Mora A., Taranta M., Zaki N., Cinti C., Capobianco E. (2015). Epigenetically-driven Network Cooperativity: Meta-analysis in Multi-Drug Resistant Osteosarcoma. Journal of Complex Networks. In press

  3. A.Marranci, A.Tuccoli, E. Mercoledi, M. Vitiello, C. Valdes, F. Russo, M. Dal Monte, M. Pellegrini, E. Capobianco, N.Tsinoremas, L.Poliseno. Identification of BRAF 3’UTR isoforms in melanoma. Journal of Investigative Dermatology. 2015 Feb 16. doi: 10.1038/jid.2015.47.

  4. Mora A, Sicari R, Cortigiani L, Carpeggiani C, Picano E, Capobianco E. 2015 Prognostic models in coronary artery disease: Cox and network approaches. R. Soc. Open Sci. 2: 140270.
  5. Kleiman E, Salyakina D, De Heusch M, Hoek KL, Llanes JM, Castro I, Wright JA, Clark ES, Dykxhoorn DM, Capobianco E, Takeda A, Renauld J-C and Khan WN (2015) Distinct transcriptomic features are associated with transitional and mature B-cell populations in the mouse spleen. Front. Immunol. 6:30. doi: 10.3389/fimmu.2015.00030
  6. E. Capobianco and P. Lio’. Comorbidity Networks: Beyond Correlation. Journal of Complex Networks. jcomplexnetw doi: 10.1093/comnet/cnu048. First published online: January 7, 2015.
  7. M.Dominietto, N. Tsinoremas and E. Capobianco (2015) Integrative Analysis of Cancer Imaging Readouts by Networks. Molecular Oncology, 9(1), 1-16. doi: 10.1016/j.molonc.2014.08.013.
  8. Barsanti C, Trivella MG, D'Aurizio R, El Baroudi M, Baumgart M, Groth M, Caruso R, Verde A, Botta L, Cozzi L,  Pitto L,  "Differential regulation of microRNAs in end-stage failing hearts is associated with Left Ventricular Assist Device unloading", (2015) BioMed Research International, Article ID 592512 doi:10.1155/2015/592512




  1. Capobianco E. (2014) RNA-Seq Data: A Complexity Journey. Computational and Structural Biotechnology Journal 11 (19), 123–130.
  2. Capobianco E. and Lio’ P. (Eds.) Comprehensive Systems Biomedicine. E-Book, Special Topic, Frontiers in Genetics, 2014.
  3. Capobianco E. and Trivella MG. (2014) Networks: elucidating experimental data by differential protein-protein interactions. Journal of Computational Systems Biology 1(1): 101.
  4. Capobianco E. and Trivella M.G. (2014). Systems Medicine Road Map: Big Data Complexity in the Medical Arena. Pan European Networks: Science and Technology.
  5. Capobianco E and Lio’ P. (2014). Advances in Translational Biomedicine from Systems Approaches. Editorial article for the Special Topic: Comprehensive Systems Biomedicine.   Frontiers in Genetics, doi: 10.3389/fgene.2014.00273.
  6. Chiavacci E,Cremisi F,Guzzolino E, Cellerino A,Baumgart M,D'Aurizio R, Pitto L, (2104) miR-19a replacement rescues cardiac and fin defects in zebrafish model of holt-oram syndrome. Cardiovascular Research 103 (suppl 1): S99 doi:10.1093/cvr/cvu095.1
  7. El Baroudi, M., La Sala, D., Cinti, C., and Capobianco, E. Pathway landscape and regulatory networks of epigenetic regulation in breast cancer and melanoma cell lines. Theoretical Biology and Medical Modelling, 11(Suppl 1):S8.
  8. Raju HB, Englander Z, Capobianco C, Tsinoremas NF and Lerch JK Identification of potential therapeutic targets in a model of neuropathic pain Front. Genet., 23 May 2014 | doi: 10.3389/fgene.2014.00131
  9. Capobianco E, Mora A, La Sala D, Roberti A, Zaki N, Badidi E, Taranta M and Cinti C. Separate and Combined Effects of DNMT and HDAC Inhibitors in Treating Human Multi-Drug Resistant Osteosarcoma HosDXR150 Cell Line PLoS ONE 9(4): e95596. doi:10.1371/journal.pone.0095596
  10. Mora A, Taranta M, Zaki N, Badidi E, Cinti C and Capobianco E (2014) Ensemble inference by integrative cancer networks. Front. Genet. 5:59. doi: 10.3389/fgene.2014.00059
  11. Pelosi G, Rocchiccioli S, Cecchettini A, Viglione F, Puntoni M, Parodi O, Capobianco E and Trivella MG (2014) Inflammation blood and tissue factors of plaque growth in an experimental model evidenced by a systems approach. Front. Genet. 5:70. doi: 10.3389/fgene.2014.00070.
  12. Valdes, C. and Capobianco, E. (2013) Methods to detect transcribed pseudogenes: RNA-Seq discovery allows learning through features. Methods in Molecular Biology, 1167:157-83.
  13. Zaki N and Mora A - A comparative analysis of computational approaches and algorithms for protein subcomplex identification. Scientific Reports 4, Art. 4262 doi:10.1038/srep04262


  1. Magi A, Tattini L, Cifola I, D'Aurizio R, Benelli M, Mangano E, Battaglia C, Bonora E, Kurg A, Seri M, Magini P, Giusti B, Romeo G, Pippucci T, De Bellis G, Abbate R, Gensini GF, EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biology  2013 Oct 30; 14(10):R120.
  2. Capobianco, E. and Lio', P. (2013) Comorbidity: a multidimensional approach. Trends Mol Med. 2013 Sep;19(9):515-21. doi: 10.1016/j.molmed.2013.07.004.
  3. Lagana', A., Russo, F., Veneziano, D., Di Bella, S., Giugno, R., Pulvirenti, A., Croce, C.M., and Ferro, A. (2013). Extracellular circulating viral microRNAs: current knowledge and perspectives. Frontiers in Genetics, 4, Art. 120.
  4. Capobianco, E. (2013) Protein Network Tomography Targeting Cancer and Associated Morbidities. Systems Biomedicine, 1:3, pg 1-18
  5. Orsini, M., Travaglione, A., and Capobianco, E. (2013) Cancer markers: integratively annotated classification. Gene. 530(2):257-65. doi: 10.1016/j.gene.2013.07.020. Epub 2013 Aug 6
  6. Orsini, M. and Capobianco, E. (2013) Mirware. A MiRNA-mRNA warehouse for inference on their coordination. MicroRNA, 2 (3), 148-155.
  7. Orsini, M., Travaglione, A., and Capobianco, E. (2013) Warehousing re-annotated cancer genes for biomarker meta-analysis. Computer Methods and Programs in Biomedicine III, 166-180.
  8. Capobianco, E. (2013) Multiscale fragPIN modularity. ISRN Genomics, Vol 13, Article 307608. doi:10.1155/2013/307608.


  1. Capobianco, E. (2012) Dynamic networks in systems medicine. Frontiers in Genetics, Vol 3, Art 185, pg 1-2, doi: 10.3389/fgene.2012.00185
  2. Capobianco, E. (2012) Ten challenges for systems medicine. Frontiers in Genetics, Vol 3, Art 193, pg 1-4, doi: 10.3389/fgene.2012.00193
  3. Capobianco, E. (2012) Constrained Network Modularity. ISRN Biomathematics, Vol 12, Art 192031, pg 1-7, doi:10.5402/2012/192031.
  4. Bosia, C., Osella, M., El Baroudi, M., Cora, D., Caselle, M. (2012) Gene autoregulation via intronic microRNAs and its functions, BMC Systems Biology 6:131.




Riba, A., Bosia, C., El Baroudi, M., Ollino, L. and Caselle, M. (2013) A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes.



Dominietto, M, Tsinoremas, N, and Capobianco E. Computational Multiplexing Imaging: a Network Approach. AACR-SNMMI State-of-the-Art Molecular Imaging in Cancer Biology and Therapy Joint Conference. Poster presentation, San Diego Febr 11-14, 2015.

Issac, B Tsinoremas, N, Capobianco, E. Co-expression profiling and transcriptional network evidences from RNA-Seq data reveal specific molecular sub-type features in breast cancer. AACR-Computational and Systems Biology of Cancer Poster presentation, San Francisco Febr 8-11, 2015.

Capobianco, E. Translating cancer data and models to clinical practice. IPAM – UCLA, USA - Febr 10-14, 2014, Invited poster.

El Baroudi, M., La Sala, D., Cinti, C., Capobianco E. (2013) DAC-driven Integrative Network Regulation and Pathway Coordination in Breast Cancer, IWBBIO 2013 (International Work-Conference on Bioinformatics and Biomedical Engineering), Granada, March 18-20, pg413

Chiavacci E,Cremisi F,Guzzolino E,Cellerino A,Baumgart M,D'Aurizio R, Pitto L (2014) "miR-19a replacement rescues cardiac and fin defects in zebrafish model of holt-oram syndrome", FCVB 2014 (Frontiers in Cardiovascular Biology meeting), Barcelona, June 4-6

D'Aurizio R,Tattini L,Pippucci T,Pellegrini M,Magi A (2014) "Exploiting whole-exome sequencing data to identify copy number variants", BITS 2014 (Bioinformatics Italian Society Annual Meeting), Rome, Feb 26-28


Technical Reports

IIT TR-14-2012 – September 2012: Bosia, C., Osella, M., El Baroudi, M., Cora, D., Caselle, M. Gene autoregulation via intronic microRNAs and its functions.

IIT TR-21/2012 – December 2012: El Baroudi, M., La Sala, D., Cinti, C., Capobianco E. Pathway landscape and regulatory networks of epigenetically modified Breast Cancer genes.