Publications

 

2015

  • Mora, A., Sicari, R., Cortigiani, L., Carpeggiani, C., Picano, E., Capobianco, E. (2014). Prognostic Models in Coronary Artery Disease – Cox and Network Approaches. Royal Society Open Science. In press.
  • E. Kleiman, D. Salyakina, M. de Heusch, K.L. Hoek, I. Castro, J.A. Wright, E.S. Clark, J.M. Llanes, D. Dykxhoorn, E. Capobianco, J.C. Renauld, W.N. Khan (2014). Dynamic Transcriptional Program Fosters Peripheral Tolerance and Functional Specialization of Mature Splenic B cell Populations. Frontiers in Immunology. In press.
  • A.Marranci, A.Tuccoli, E. Mercoledi, M. Vitiello, C. Valdes, F. Russo, M. Dal Monte, M. Pellegrini, E. Capobianco, N.Tsinoremas, L.Poliseno (2014) Identification of BRAF 3’UTR isoforms in melanoma. Journal of Investigative Dermatology. In press.
  • E. Capobianco and P. Lio’. Comorbidity: Beyond Correlation. Journal of Complex Networks. doi: 10.1093/comnet/cnu048 First published online:Jan 7, 2015.

2014

  • Clarke B, Valdes C, Dobra A, Clarke J. A Bayes Testing Approach to Metagenomic Profiling in Bacteria. Statistics and Its Interface. 2014, In press.
  • Capobianco E. and Lioí P. (Eds.) Comprehensive Systems Biomedicine. E-Book, Special Topic, Frontiers in Genetics, 2014. http://journal.frontiersin.org/ResearchTopic/1569.
  • Issac B, Galoian K, Guettouche T, Navarro L and Temple HT.Genome-wide mRNA and miRNA expression data analysis to screen for markers involved in sarcomagenesis in human chondrosarcoma cell lines. Genomics Data, 2014, 2:320-324.
  • Capobianco E. RNA-Seq Data: a Complexity Journey. Computational and Structural Biotechnology Journal, 2014, 11(19): 123-130.
  • Capobianco E, Lioí P. Advances in Translational Biomedicine from Systems Approaches. Frontiers Genetics, 2014, 5:273.
  • Wang JC, Ross L, Mahon LW, Owen R, Hemmat M, Wang BT, El Naggar M, Kopita KA, Randolph LM, Chase JM, Matas Aguilera MJ, Siles JL, Church JA, Hauser N, Shen JJ, Jones MC, Wierenga KJ, Jiang Z, Haddadin M, Boyar FZ, Anguiano A, Strom CM, Sahoo T. Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility. Eur J Hum Genet. 2014 Aug. 13. doi: 10.1038/ejhg.2014.153.
  • Capobianco E, Trivella MG. Systems Medicine Road Map: Shaping Data Complexity towards Cultural Diversity. Pan European Networks: Science and Technology, 2014, 128-9.
  • Capobianco E, Trivella MG. Networks: Elucidating Experimental Data by Differential Protein-Protein Interactions. Journal of Computational Systems Biology 2014, 1(1): 101.
  • Capobianco E, Tsinoremas N. Health or Disease ñ Why does Dark Matter matter more? Journal of Investigative Genomics 2014, 1(1): 00002.
  • Raju HR, Englander ZA, Capobianco E, Tsinoremas N, Lerch JK. Identification of therapeutic targets in a modelof neuropathic pain. Frontiers in Genetics, 2014, 5: 131.
  • Capobianco E, Mora A, La Sala D, Roberti A, Zaki N, Taranta, M, Cinti C. Separate and combined effects of of de-methylating and de-acetylating agents in the treatment of human multi-drug resistant osteosarcoma cell lines. PlOS ONE 2014, 9(4): e95596.
  • El Baroudi M, La Sala D, Cinti C, Capobianco E. Pathway landscape and regulatory networks of epigenetic regulation in breast cancer and melanoma. Theoretical Biology and Medical Modelling, 2014, 11(Suppl 1): S8.
  • Pelosi G, Rocchiccioli S, Cecchettini A, Viglione F, Puntoni M, Parodi O, Capobianco E, Trivella MG. Inflammation blood and tissue factors of plaque growth in an experimental model evidenced by a systems approach. Frontiers Genetics 2014, 5:70.
  • Mora A, Taranta M, Zaki N, Badidi E, Cinti C, Capobianco E. Ensemble inference by integrative cancer networks. Frontiers Genetics, 2014, 5:59.
  • Valdes C, Capobianco E. Methods to detect transcribed pseudogenes: RNA-Seq discovery allows learning through features. In: Pseudogenes. Functions and Protocols (L. Poliseno Ed.). Methods in Molecular Biology, 2014, 1167. Springer Protocols, Humana Press.
  • Ashlock BM, Ma Q, Issac B, Mesri EA. Productively infected murine Kaposiís sarcoma-like tumors define new animal models for studying and targeting KSHV oncogeneis and replication. PLoS One. 2014, 9(1):e87324.

2013

  • E. Capobianco (2013) Protein Networks Tomography. Targeting Cancer and Associated Morbidities. Systems Biomedicine. In press.
  • M. Orsini, A. Travaglione, E. Capobianco (2013) Cancer Markers: Integratively Annotated Classification. Gene, accepted.
  • Capobianco, E., (2013) Multiscale fragPIN Modularity. ISRN Genomics, Art 307608.
  • El Baroudi, M., La Sala, D., Cinti, C., Capobianco E. “DAC-driven Integrative Network Regulation and Pathway Coordination in Breast Cancer”, IWBBIO 2013 (International Work-Conference on Bioinformatics and Biomedical Engineering), Granada, 18-20 March 2013, pg413
  • Orsini, M. and Capobianco, E. (2013) MiRWare: A MiRNA-mRNA warehouse for inference on cancer regulation. MicroRNA. Accepted for publication
  • Orsini, M., Travaglione, A., and Capobianco, E. Warehousing Re-annotated Cancer Genes for Biomarker Meta-analysis. Computer Methods and Programs in Biomedicine: Volume 111, Issue 1, July 2013, Pgs. 166-180
  • Han H, Bourboulia D, Jensen-Taubman S, Issac B, Wei B and Stetler-Stevenson WG (2013), An endogenous inhibitor of angiogenesis inversely correlates with side population phenotype and function in human lung cancer cells. (Accepted for publication in Oncogene (NPG))
  • Comparative analysis of genome sequences from four strains of the Buchnera aphidicola Mp endosymbiont of the green peach aphid, Myzus persicae, BMC Genomics. Zhijie Jiang, Derek H. Jones, Sawsan Khuri,  Nicholas F. Tsinoremas, Tania Wyss, Georg Jander, Alex C. C. Wilson. Accepted.

2012

  • Wierenga KJ, Jiang Z, Yang AC, Mulvihill JJ, Tsinoremas NF. A clinical evaluation tool for SNP arrays, especially for autosomal recessive conditions in offspring of consanguineous parents. Genet Med. 2012 Oct 25. doi: 10.1038/gim.2012.136. PMID: 23100014
  • Capobianco, E., (2012) Constrained Network Modularity. ISRN Biomathematics, Art 192031.
  • Capobianco, E., (2012) Ten challenges for Systems Medicine. Frontiers in Genetics (sect Statistical Genetics and Methodology), 3, Art 193.
  • Capobianco, E., (2012) Dynamic Networks in Systems Medicine. Frontiers in Genetics (sect Bioinformatics and Computational Biology), 3, Art 185
  • Capobianco, E., Travaglione, A., Marras, E. (2012) Modularity Configurations in Biological Networks with Embedded Dynamics.Invited Book chapter in ‘Statistical and Machine Learning Approaches for Network Analysis’. M. Dehmer and SC Basak (Eds.), Wiley, NJ USA, pg 109-129.
  •  Bourboulia D, Han H, Jensen-Taubman S, Gavil N, Issac B,  Wei B, Neckers L, and Stetler-Stevenson WG (2013) TIMP-2 modulates cancer cell transcription profile and enhances E-cadherin/beta-catenin complex expression in A549 lung cancer cells.  Oncotarget, (Advance Publications 2012)
  •  Johnson S, Issac B, Zhao S, Bisht M, Celiku O, Tofilon P, Camphausen K and Shankavaram U (2012), StRAP: an integrated resource for profiling high-throughput cancer genomic data from stress response studies. PLoS ONE 7(12):e51693. PMID: 23284744
  •  Wierenga, K.J., Jiang, Z., Yang, A., Mulvihill, J.J. Tsinoremas, N.F. “A clinicalevaluation tool for SNP arrays, especially for autosomal recessive conditions in offspring of consanguinity” Genetics in Medicine. 2012 Oct. 25 doi:10.1038/gim.2012.136
  • Winters, K.A., Jiang, Z., Xu, W., Li, S., Ammous, Z., Jayakar, P., Wierenga, K.J. “Re-assigned Diagnosis of D4ST1-Deficient Ehlers-Danlos syndrome (Adducted Thumb-Clubfoot Syndrome) After Initial Diagnosis of Marden-Walker Syndrome” Am. J. Med. Genet. 2012 Sep. 14 doi:10.1002/ajmg.a.35613
  • Jing, Y., Kovacs, K., Kurisetty, V., Jiang, Z., Tsinoremas, N., Merchan, J.R. “Role of Plasminogen Activator Inhibitor-1 in Urokinase?s Paradoxical In vivo Tumor suppressing or Promoting Effects” Mol. Cancer Res. 2012 Aug. 21 doi:10.1158/15141-7786.MCR-12-0145
  • Bravo-Egana, V., Rosero, S., Klein, D., Jiang, Z., Vargas, N., Tsinoremas, N., Doni, M., Podetta, M., Ricordi, C., Molano, R.D., Pileggi, A., Pastori, R.L. “Inflammation-Mediated Regulation of MicroRNA Expression in Transplanted Pancreatic Islets” Journal of Transplantation, Vol. 2012, Article ID 723614, 15 pages, 2012. doi:10.1155/2012/723614