Publications | Enrico Capobianco



 

Recently Published

 

Dominietto Marco D., Capobianco Enrico. Expected Impacts of Connected Multimodal Imaging in Precision Oncology. Frontiers in Pharmacology  29 November 2016 , Vol. 7, DOI 10.3389/fphar.2016.00451,  ISBN 1663-9812.

Raju HR, Tsinoremas N, Capobianco E. Emerging non-coding RNA evidences linked to neuropathic pain.  Front Neurol 18 (Neurogenomics). 

Capobianco E. (First Online August 2016) Born to be Big: data and graphs. On their entangled complexity.  Big Data and Information Analytics. American Institute of Mathematical Sciences. Vol. 1, No.2, pp. 2-2,  issn 2380-6966, doi 10.3934/bdia.2016002.

Gherardini L, Capobianco E. Cinti C. Targeting cancer with epidrugs: a precision medicine perspective. Current Pharmaceutical Biotechnology. 2016;17(10):856-65. .

Capobianco E. (2016). Public Science Insights: Rise of Digital Biomarkers and Role in Precision Medicine. Libertas Academica.

Capobianco, E.  Imaging-driven Digital BiomarkersCancer Translational Medicine. 2016; 2(2): 61-3.

El Baroudi M., Cinti C., and Capobianco E..  Pan Cancer Network Inference and Epigenetic Mechanisms.  Evidences from Pathways, Regulatory Cores, Diseases and Drugs.  Cancer Informatics. 2016; 15: 45-64.

Dominietto M. and Capobianco E. The Computational Network Imaging Frontier:  Relevance from shaping Digital Biomarkers in Precision Oncology. Journal of Precision Medicine. 2016; 2(2): 55-6.

Capobianco E. (2015). Common Phenotypes, Diverse Network Signatures: Elucidating Cancer Marker Patterns.  Annals of Translational Medicine.

Salmasi L. and Capobianco E. Use of instrumental variables for building electronic health record-driven models.  Statistical Methods for Medical Research.  First published April 7, 2016.

Ianuale N, Schiavon D, Capobianco, E (2015). Smart Cities, Big Data and Communities: Reasoning from the viewpoint of attractors.  IEEE Access 4, 41-47 Special Section:  Smart Cities. DOI:10.1109/ACCESS.2015.2500733 (with Video)

 

 

Capobianco E and Lio’ P. (2015) Electronic Health Systems: Golden Mine for Precision Medicine?  Current bottlenecks and future opportunities associated with Big Data. Journal of Precision Medicine, Oct-Nov Is. 60-65.

Capobianco. (2015) On digital therapeuticsFrontiers Digital Humanities, published: 10 November 2015 doi: 10.3389/fdigh.2015.00006.

Capobianco E. Cancer Hallmarks through the Network Lens. Cancer Cell & Microenvironment, 2015; 2: e943.

Malusa F, Zaki N, Badidi E, Cinti C, Capobianco E (2015). Time-course Gene Expression Profiling and Networks Dynamics in Demethylated Retinoblastoma cell lineOncotarget, 2015 6(27): 23688-23707.

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, doi: 10.1093/comnet/cnv017. First published online: July 9, 2015.

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 Dermatology2015 Feb 16. doi: 10.1038/jid.2015.47.

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.

Capobianco E. (2015) Computational Multiplexing Imaging: a Network Approach. Suppl. J Nucl Med, 56, 3.

Issac B, Tsinoremas N, Capobianco E. (205) Co-expression profiling and transcriptional netword evidences from RNA-Seq data reveal specific molecular subtype features in breast cancer. Cancer Research, 75 (22 Supplement 2), abs. B1-04-B1-04.

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.

Ianuale N, Schiavon D, Capobianco E. (2015) Smart cities and urban networks: are smart networks what we need? Journal of Management Analytics, 1-10.

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.

M.Dominietto, N. Tsinoremas, and E. Capobianco (2015) Integrative Analysis of Cancer Imaging Readouts by Networks. Molecular Oncology, 9(1), 1-16.

 

Previous Publications  (2014 and before)

Capobianco E. and Trivella M.G. (2014). Systems Medicine Road Map: Shaping Data Complexity towards Cultural DiversityPan European Networks: Science and Technology, pp. 128-9.

Capobianco E. and Lio’ P. (Eds.) Comprehensive Systems Biomedicine. E-Book, Special Topic, Frontiers in Genetics, 2014.

Capobianco E. (2014) RNA-Seq Data: a Complexity Journey. Computational and Structural Biotechnology Journal, 11(19), 123-130.

Capobianco E. and Trivella M.G. (2014).  Networks: Elucidating Experimental Data by Differential Protein-Protein Interactions. Journal of Computational Systems Biology, 1(1): 101.

Capobianco E and Lio’ P. Advances in Translational Biomedicine from Systems ApproachesEditorial article for the Special Topic: Comprehensive Systems Biomedicine. Frontiers Genetics, 14 August 2014 | doi: 10.3389/fgene.2014.00273.

Capobianco, E. and Tsinoremas, N. (2014). Health or Disease – Why does Dark Matter matter more? Journal of Investigative Genomics, 1(1), 00002.

H.R. Raju, Z.A. Englander, E. Capobianco, N. Tsinoremas, J.K. Lerch. (2014) Identification of therapeutic targets in a model of neuropathic pain. Frontiers in Genetics, doi:
10.3389/fgene.2014.00131.

Capobianco, E., Mora, A., La Sala D., Roberti A., Zaki N., Taranta, M. and Cinti C. (2014) 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,
9(4), e95596.

Mora A, Taranta M, Zaki N, Badidi E, Cinti C and Capobianco E (2014) Ensemble inference by integrative cancer networks. Frontiers Genetics, 5:59. doi: 10.3389/fgene.2014.00059.

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 approachFrontiers Genetics,
5:70. doi: 10.3389/fgene.2014.00070.

El Baroudi, M., La Sala, D., Cinti, C., and Capobianco, E. (2104) Pathway landscape and regulatory networks of epigenetic regulation in breast cancer and melanoma. Theoretical Biology and Medical Modelling, 11(Suppl 1):S8.

Valdes, C. and Capobianco, E. (2014) Methods to detect transcribed pseudogenes: RNA-Seq discovery allows learning through features. In: Pseudogenes. Functions and Protocols (L. Poliseno Ed.). Methods in Molecular Biology, 1167. Springer Protocols, Humana Press.

Capobianco, E. (2013) Protein Networks Tomography – Targeting Cancer and Associated Morbidities. Systems Biomedicine, 1(3), 1-17.

Capobianco, E. and Lio’, P. (2013) Comorbidity: a multidimensional approach. Trends in Molecular Medicine, Cell Press, 19(9) September 2013, 515–21.

Orsini, M., Travaglione, A. and Capobianco, E. (2103) Warehousing re-annotated cancer genes for Biomarker meta-analysis. Computer Methods and Programs in Biomedicine, III, 166-180.

Orsini, M. and Capobianco, E. (2103) MiRWare: A MiRNA-mRNA warehouse for inference on cancer regulationMicrorna, 2(2), pp. 148-155(8).

Orsini, M. Travaglione, A. Capobianco, E. (2013) Cancer Biomarkers: Integratively Re-annotated ClassificationGene, 530(2):257-65.

Capobianco, E. (2012) Multiscale fragPIN Modularity. ISRN Genomics, 2012, Art 307608.

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.

Marras, E. Travaglione, A., and Capobianco, E. (2011)Multiscale Characterization of Signaling Network Dynamics through Features. Statistical Applications in Genetics and Molecular Biology, Vol. 10: Iss. 1, Article 53, 2011.

Capobianco, E. (2011). On network entropy in bio-interactome applications. Journal of Computational Science, 2 (2011) 144-152.

Marras, E., Travaglione, A., and Capobianco, E. (2011). Protein Interactomic Manifold Learning. Journal of Computational Biology, 18(1) – 81-96.

Travaglione, A., Marras, E., Capobianco, E. (2011). Dynamic Modularization Assessment in Affine Protein Interaction Networks. BiosimBiostatistics, Bioinformatics, and Biomathematics, 2(3) 2011 137-156.

Rocchiccioli, S., Congiu, E., Boccardi, C., Citti, L., Callipo, L., Lagana’, A., Capobianco, E. (2010). A proteomic study of microgravity cardiac effects: feature maps of label-free LC-MALDI data for differential expression analysis. Molecular Biosystems, DOI:10.1039/C0MB00065E.

Marras, E., Travaglione, A., Chaurasia, G., Futschik, M., and Capobianco, E. (2010). Inferring Modularity from Human Protein Interactome Classes. BMC Systems Biology, 4:102.

Marras, E., Travaglione, A., and Capobianco, E. (2010). Sub-Modular Resolution Analysis by Network Mixture Models. Statistical Applications in Genetics and Molecular Biology, 9(1), Art 19.

Marullo, O., Soggiu, A., Capobianco, E. (2010). Two-dimensional Electrophoresis Gel Images Scan for decomposition and depletion analysis. Advances in Adaptive Data Analysis, Vol 2(3), 359-371.

Orsini, M. and Capobianco, E. (2010). Coupling genomic expression with copy number variation in brain cancer regulation  studies. Biosim – Biostatistics, Bioinformatics, and Biomathematics, 1(1), 2010, 55.

Capobianco, E. (2010). Gene Feature Interference Deconvolution. Mathematical Biosciences, 227, 136-146.

Soggiu, A., Marullo, O., Roncada, P., and Capobianco, E. (2009). Backing up 2DGE Depletion with Source Separation and Multiscale Decomposition Methods. Biophysical Reviews and Letters, vol. 4(4), 319-330, 2009.

Popa, E., Capobianco, E., de Beer, R., van Ormondt, D., Graveron-Demilly, D. (2009). In Vivo quantitation of metabolites with an incomplete model function. Measurement
Science Technology
, IOP Press, 20, 2009, 104032 (Special Issue Imaging Systems and Techniques).

Capobianco, E. (2009). Aliasing in gene feature detection by projective methods. Journal of Bioinformatics and Computational Biology, 2009, 7(4), 685-700.

Soggiu, A., Marullo, O., Roncada, P., Capobianco, E. (2009). Empowering spot detection in 2DE images by wavelet denoising. In Silico Biology, 9 0011, 2009.

Capobianco, E. (2009). Entropy Embedding and Fluctuation Analysis in Genomic Manifolds. Communications in Nonlinear Science and Numerical Simulation, 14, 2602-18.

Marras, E. and Capobianco, E. (2009). Mining Protein-Protein Interaction Networks: Denoising EffectsJournal of Statistical Mechanics: Theory and Experiments, P01006.

Capobianco, E. (2008) Kernel Methods and Flexible Inference for Complex Stochastic Dynamics. Physica A: Statistical Mechanics and Applications, 387(16-17), 4077-98.

Marras, E. and Capobianco, E. (2008) Advances in Human Protein Interactome Inference. Functional and Operational Statistics, S. Dabo-Niang and F. Ferraty Eds., Physica- Verlag, Heidelberg 89-94.

Capobianco, E. (2008). Cascade Systems Denoising and Greedy Calibrated Approximation. Journal of Interdisciplinary Mathematics, 11(3): 429-442.

Capobianco, E. (2008). Dimensionality Reduction and Greedy Learning of Convoluted Stochastic Dynamics. Nonlinear Analysis, Real World Appl Series B, 9(5): 1928-41.

Pieroni, E., de la Fuente van Bentem, S., Mancosu, G., Capobianco, E., Hirt, H., and de la Fuente, A. (2008). Protein networking: insights into global functional organization of proteomes. Proteomics, 8(4):799-816.

Capobianco, E. (2008). Model validation for gene selection and regulation maps. Functional and Integrative Genomics, 8(2):87-99.

Capobianco, E. (2006). Statistical Embedding in Complex Biosystems. Journal of Integrative Bioinformatics, 3(2), Hofestadt, Topel (Eds.), Shaker-Verlag, pp. 117-35.

Capobianco, E. (2005). Mining Time-dependent Gene Features. Journal of Bioinformatics and Computational Biology, 3(5), 1191-1205.

Capobianco, E. (2005). Robustness versus Redundancy in Biological Systems. Fluctuation and Noise Letters, 5(3), L375-L385.

Capobianco, E. (2004). On Support Vector Machines and Sparse Approximation for Random ProcessesNeurocomputing, 56, 39-60.

Capobianco, E. (2003). Functional Approximation in Multi-scale Complex Systems. Advances in Complex Systems, 6(2), 177-204.

Capobianco, E. (2003). Computationally efficient atomic representations for non-stationary stochastic processesInternational Journal on Wavelets, Multiresolution and Information Processing, 1(3), 325-351.

Capobianco, E. (2003). Independent Multi-resolution Component Analysis and Matching Pursuit. Computational Statistics and Data Analysis, 42(3), 385-402.

 

Proceedings

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, p. 413.

Travaglione, A., Marras,E., Capobianco, E. (2010). Time-scale analysis from fragmented protein interactome networks. Proceedings Computational Systems Biology (WCSB  2010).

Popa E., Capobianco E., de Beer R., van Ormondt D., Graveron-Demilly D. (2009) In vivo quantitation of metabolites with an incomplete model function.  Measurement Science and Technology, 20 (10), 104032.

Marras, E. and Capobianco, E. (2009). Inference by mixture models in protein interactome networks. WCSB 2009 Proceedings, TICSP series # 48, 119-122.

Marras, E. and Capobianco, E. (2009). Network Mixture Models: an Introduction and Application to Protein Interactomes. Institute Mathematics and its Applications – IMA, preprint series 2230.

Marras, E. and Capobianco, E. (2008) Exploring Protein Interactome Features. WCSB 2008 Proceedings, TICSP Series n. 41, 105-108.

Popa, E. Capobianco, E. de Beer, R., van Ormondt, D., Graveron-Demilly, D. (2008) Lineshape estimation in in vivo MRS without using a reference signal.  IEEE-IST (Imaging Systems and Techniques) Proceedings, 315-320.

H Rabeson, E Capobianco, R de Beer, D van Ormondt. Correction for B0-inhomogeneity and Eddy Current effects without using a reference line.  12ème congrès du GRAMM. 2008

 

Rabeson, H., Ratiney, H., Cudalbu, C., Cavassila, S., Capobianco, E., de Beer, R., van Ormondt, D., and Graveron-Demilly, D. (2006). Signal Disentanglement in In Vivo MR Spectroscopy: by semi-parametric processing or by measurement? ProRISC, IEEE Benelux, Veldhoven, NL.

Ratiney, H., Capobianco, E., de Beer, R., van Ormondt, D., and Graveron-Demilly.D., (2006). Error Bounds for Semi-Parametric Estimation in MRS. Proc. Int. Soc. Mag. Res. Med., 14th Scient. Meet., Seattle, WA (US) 3237, 6-2.

Ratiney, H., Capobianco, E., Sdika, M., Rabeson, H., Cudalbu, C. Cavassila, S., de Beer, R., van Ormondt, D., and Graveron-Demilly, D. (2005). Semiparametric Estimation in In-vivo MR Spectroscopy. ProRISK, IEEE Benelux, Veldhoven, The Netherlands, 658-667.

Capobianco, E. (2005). Robustness versus Redundancy in Biological Systems (short version). American Institute of Physics, Unsolved Problems of Noise and Fluctuations in Physics, Biology, and High Technology, L. Reggiani et. al (Eds.), Conf. Proceedings Vol. 800, pp. 361-367.

Capobianco, E. (2005). Denoising and Dimensionality Reduction of Genomic Data. SPIE Proc., Fluctuation and Noise in Biological, Biophysical, and Biomedical Systems III, N.G. Stocks, D. Abbott, R.P. Morse (Eds.), vol. 5841 (SPIE, WA, 2005), pp. 69-80.

 

Other Publications in my Name

Electronic Journal of Theoretical Physics, 4(15), 165-180, 2007.

SPIE Proc., Complex dynamics and Fluctuations in Biomedical Photonics IV, 6436,2007.

Journal of Numerical Analysis, Industrial and Applied Mathematics (JNAIAM), 1(2) 147-174, 2007.

Electronic Journal of Theoretical Physics, 3 (11), 85-109, 2006.

Physica A, 340 (1-3), 340-346, 2004

Nonlinear Phenomena in Complex Systems. 7(4), 314-331, 2004.

Fractals, 12(2), 179-195, 2004.

Physica A, 344, 122-127, 2004.

Computational Economics 23 (3), 219-237, 2004.

Physica A, 319, 495-518, 2003.

Comput. Stat Data Anal. 42 (3), 386-402, 2003.

IEEE Proc. PhysCon 2003, Physics & Control, pp. 222-227. S.Petersburg, RU, Aug 20-22, 2003.

SPIE Proc., ICA, Wavelets NN, 5102, pp. 360-370. Orlando, Fl, April 21-25, 2003.

Quantitative Finance 2(2), 91-110.

The European Physical Journal B, 27(2), 201-212, 2002.

Neurocomputing 48(4), 779-806, 2002.

EURASIP Journal on Applied Signal Processing, 2, 1-7, 2001.

ENUMATH (4th European Numerical Mathematics and Advanced Applications) Proc. (Springer). Ischia, IT, July 23-28, pp. 391-408, 2001.

Nonlinear Estimation and Classification, pp. 273-285. Proc. (Springer-Verlag) of Workshop at MSRI, Berkeley, March 19-29, 2001.

International Journal of Theoretical and Applied Finance, 4(3), 511-534, 2001.

Artificial Neural Nets and Genetic Algorithms, pp. 426-430 (Springer-Verlag). Proc. of International Conf. in Prague (Czech Rep.), 2001.

Computational Statistics and Data Analysis, 32, 443-454, 2000.

Methodology and Computing in Applied Probability, I(4), 423-443, 1999.

Badanja Operacyjne I Decyzje, 2, 15-25, 1999.

Badanja Operacyjne I Decyzje, 1, 21-33, 1999.

Methodology and Computing in Applied Probability, I(4), 423-443, 1999.

Stochastic Modelling and Applications, I(1), 44-59, 1998.

Chapter in: Mathematics of Neural Networks; Models, Algorithms and Applications, S.W.Ellacott, J.C.Mason and I.J.Anderson (Eds) Kluwer Ac. Pub., pp. 140-147, 1997.

Computing Science and Statistics, (Interface Foundation of North America) 29 (2), pp. 95-101, 1997. Proc. 2nd IASC World Conf., Pasadena, CA (US), 02/19-22/1997.

Neural Networks World: International Journal on Neural and Mass Parallel Computing and Information Systems, 7 (4-5), 439-450, 1997.

International Journal of Modelling and Simulation, 17, 137-142, 1997.

Applied Stochastic Models and Data Analysis, 12 (4), 265-279, 1996.

CISS’96, Proc. Conf. Inf. Sciences and Statistics, Princeton Un, 1037-42, 1996.

NNSP’95, Neural Networks for Signal Processing Proc. IEEE, MIT Press, 87-94, 1995.

Complex Systems, 9, 477-490, 1995.

CCS
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