Digital Biology Unit

Publications

Journal articles

2021

H. Wang, E. Pujos-Guillot, B. Comte, J.L. De Miranda, V. Spiwok, I. Chorbev, F. Castiglione, P. Tieri, S. Watterson, R. McAllister, T. De Melo Malaquias, M. Zanin, T.S. Rai, and H. Zheng. Deep learning in systems medicine. Briefings in Bioinformatics, 22(2):1543–1559, 2021.

P. Stolfi and F. Castiglione. Emulating complex simulations by machine learning methods. BMC Bioinformatics, 22, 2021.

A. Ravoni. Long-term behaviours of autocatalytic sets. Journal of Theoretical Biology, 529, 2021.

C. Ragone, C. Manolio, B. Cavalluzzo, A. Mauriello, M.L. Tornesello, F.M. Buonaguro, F. Castiglione, L. Vitagliano, E. Iaccarino, M. Ruvo, M. Tagliamonte, and L. Buonaguro. Identification and validation of viral antigens sharing sequence and structural homology with tumor-associated antigens (taas). Journal for ImmunoTherapy of Cancer, 9(5), 2021.

C. Pirazzini, T. Azevedo, L. Baldelli, A. Bartoletti-Stella, G. Calandra-Buonaura, A. Dal Molin, G.M. Dimitri, I. Doykov, P. Gómez-Garre, S. Hägg, J. Häallqvist, C. Halsband, W. Heywood, S. Jesús, J. Jylhävä, K.M. Kwiatkowska, M.A. Labrador-Espinosa, C. Licari, M.G. Maturo, G. Mengozzi, G. Meoni, M. Milazzo, M.T. Periñán-Tocino, F. Ravaioli, C. Sala, L. Sambati, S. Schade, S. Schreglmann, S. Spasov, L. Tenori, D. Williams, L. Xumerle, E. Zago, K.P. Bhatia, S. Capellari, P. Cortelli, P. Garagnani, H. Houlden, P. Liò, C. Luchinat, M. Delledonne, K. Mills, P. Mir, B. Mollenhauer, C. Nardini, N.L. Pedersen, F. Provini, S. Strom, C. Trenkwalder, P. Turano, M.G. Bacalini, C. Franceschi, A. Adarmes- Gomez, M. Bonilla-Toribio, C. Boninsegna, M. Broli, D. Buiza-Rueda, M. Carríon-Claro, R. Cilea, R. Clayton, A.D. Molin, S. De Luca, P. De Massis, R. Escuela-Martin, G. Fabbri, A. Gabellini, C. Giu- liani, P. Guaraldi, I. Huertas, D. Macias, S. Macrì, F. Magrinelli, J.F.M. Rodríguez, F. Mignani, S.A. Nassetti, C.L.M. Scaglione, C. Tejera-Parrado, F. Valzania, and R.V. Ortega. A geroscience approach for parkinson's disease: Conceptual framework and design of propag-ageing project. Mechanisms of Ageing and Development, 194, 2021.

C. Nardini, V. Osmani, P.G. Cormio, A. Frosini, M. Turrini, C. Lionis, T. Neumuth, W. Ballensiefen, E. Borgonovi, and G. D'Errico. The evolution of personalized healthcare and the pivotal role of european regions in its implementation. Personalized Medicine, 18(3):283–294, 2021.

D. Lai, S. Wang, Z. Chong, W. Wu, and C. Nardini. Task-oriented attributed network embedding by multi-view features. Knowledge-Based Systems, 232, 2021.

D. Lai, Z. Liu, J. Huang, Z. Chong, W. Wu, and C. Nardini. Attention based subgraph classification for link prediction by network re-weighting. pages 3171–3175, 2021.

P. Di Lena, C. Sala, and C. Nardini. Estimage: A webserver hub for the computation of methylation age. Nucleic Acids Research, 49(W1):W199–W206, 2021.

D. Deb, S. Basak, T. Kar, U. Narsaria, F. Castiglione, A. Paul, A. Pandey, and A.P. Srivastava. Im- munoinformatics based designing a multi-epitope vaccine against pathogenic chandipura vesiculovirus. Journal of Cellular Biochemistry, 2021.F. Castiglione, D. Deb, A.P. Srivastava, P. Liò, and A. Liso. From infection to immunity: Understanding the response to sars-cov2 through in-silico modeling. Frontiers in Immunology, 12, 2021.

S. Basak, D. Deb, U. Narsaria, T. Kar, F. Castiglione, I. Sanyal, P.D. Bade, and A.P. Srivastava. In silico designing of vaccine candidate against clostridium difficile. Scientific Reports, 11(1), 2021.

L. Baldelli, S. Schade, S. Jesús, S.R. Schreglmann, L. Sambati, P. Gómez-Garre, C. Halsband, G. Calandra-Buonaura, A.D. Adarmes-Gmez, F. Sixel-öring, C. Zenesini, C. Pirazzini, P. Garagnani, M.G. Bacalini, K.P. Bhatia, P. Cortelli, B. Mollenhauer, C. Franceschi, H. Houlden, P. Liò, C. Luchinat, M. Delledonne, K. Mills, N.L. Pedersen, T. Azevedo, A. Bartoletti-Stella, M. Bonilla-Toribio, D. Buiza- Rueda, S. Capellari, M. Carriòn-Claro, R. Clayton, A. Dal Molin, G.M. Dimitri, I. Doykov, C. Giuliani, S. Hägg, J. Hällqvist, W. Heywood, I. Huertas, J. Jylháv, M.A. Labrador-Espinosa, C. Licari, D. Macias, F. Magrinelli, J.F.M. Rodríguez, M.G. Maturo, G. Mengozzi, G. Meoni, M. Milazzo, C. Nardini, N.L. Pedersen, M.T. Periñán Tocino, F. Ravaioli, C. Sala, S. Spasov, C. Tejera-Parrado, L. Tenori, T. Paola, D. Williams, L. Xumerle, E. Zago, M. Broli, D. Buiza-Rueda, P. De Massis, R. Escuela-Martin, G. Fabbri, A. Gabellini, P. Guaraldi, H. Houlden, S. Macrì, S.A. Nassetti, C.L.M. Scaglione, F. Valzania, C. Rosaria, F. Mignani, R.V. Ortega, C. Boninsegna, S. De Luca, P. Mir, C. Trenkwalder, and F. Provini. Heterogeneity of prodromal parkinson symptoms in siblings of parkinson disease patients. npj-Parkinson's Disease, 7(1), 2021.

2020

P. Stolfi, I. Valentini, M. C. Palumbo, P. Tieri, A. Grignolio, and F. Castiglione. Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices. BMC Bioinformatics, 21, 2020.

P. Stolfi, L. Manni, M. Soligo, D. Vergni, and P. Tieri. Designing a network proximity-based drug repurposing strategy for covid-19. Frontiers in Cell and Developmental Biology, 8, 2020.

P. Stolfi and F. Castiglione. Emulation of dynamic multi-output simulator of risk of type-2 diabetes. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Seoul, Korea (South), 2020, pp. 1289-1294.

C. Sala, P. Di Lena, D.F. Durso, A. Prodi, G. Castellani, and C. Nardini. Evaluation of pre-processing on the meta-analysis of dna methylation data from the illumina humanmethylation450 beadchip platform. PLoS ONE, 15(3), 2020.

A. Ravoni and L. Angelani. Lattice model for active flows in microchannels. Physical Review E, 102(6), 2020.

A. Ravoni. Impact of composition on the dynamics of autocatalytic sets. BioSystems, 198, 2020.

M.G. Maturo, M. Soligo, G. Gibson, L. Manni, and C. Nardini. The greater inflammatory path- way—high clinical potential by innovative predictive, preventive, and personalized medical approach. EPMA Journal, 11(1), 2020.

P.D. Lena, C. Sala, A. Prodi, and C. Nardini. Methylation data imputation performances under different representations and missingness patterns. BMC Bioinformatics, 21(1), 2020.

T. Kar, U. Narsaria, S. Basak, D. Deb, F. Castiglione, D.M. Mueller, and A.P. Srivastava. A candidate multi-epitope vaccine against sars-cov-2. Scientific Reports, 10(1), 2020.

M. Bernardi and P. Stolfi. A dominance test for measuring financial connectedness. European Journal of Finance, 26(2-3):119–141, 2020.

2019

X. Zhou, V. Devescovi, Y. Liu, J.E. Dent, and C. Nardini. Host-microbiome synergistic control on sphingolipid metabolism by mechanotransduction in model arthritis. Biomolecules, 9(4), 2019.

P. Stolfi, I. Valentini, M. C. Palumbo, P. Tieri, A. Grignolio and F. Castiglione. Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), San Diego, CA, USA, 2019, pp. 2214-2221.

A. Presbitero, E. Mancini, F. Castiglione, V.V. Krzhizhanovskaya, and R. Quax. Game of neutrophils: Modeling the balance between apoptosis and necrosis. BMC Bioinformatics, 20, 2019.

A. Presbitero, E. Mancini, F. Castiglione, V.V. Krzhizhanovskaya, and R. Quax. Evolutionary game theory can explain the choice between apoptotic and necrotic pathways in neutrophils. pages 1401–1405, 2019.

V. Prana, P. Tieri, M.C. Palumbo, E. Mancini, and F. Castiglione. Modeling the effect of high calorie diet on the interplay between adipose tissue, inflammation, and diabetes. Computational and Mathematical Methods in Medicine, 2019, 2019.

P. Di Lena, C. Sala, A. Prodi, and C. Nardini. Missing value estimation methods for dna methylation data. Bioinformatics, 35(19):3786–3793, 2019.

H.A.L. De Ribeiro, T.U. Maioli, L.M. De Freitas, P. Tieri, and F. Castiglione. A mathematical model of murine macrophage infected with leishmania sp. pages 1425–1430, 2019.

L.M. De Freitas, T.U. Maioli, H.A.L. De Ribeiro, P. Tieri, and F. Castiglione. A mathematical model of chagas disease infection predicts inhibition of the immune system. pages 1374–1379, 2019.

F. Castiglione, D. Ghersi, and F. Celada. Computer modeling of clonal dominance: Memory-anti-naïve and its curbing by attrition. Frontiers in Immunology, 10(JUL), 2019.

M.G. Bacalini, C. Franceschi, D. Gentilini, F. Ravaioli, X. Zhou, D. Remondini, C. Pirazzini, C. Giuliani, E. Marasco, N. Gensous, A.M. Di Blasio, E. Ellis, R. Gramignoli, G. Castellani, M. Capri, S. Strom, C. Nardini, M. Cescon, G.L. Grazi, and P. Garagnani. Molecular aging of human liver: An epige- netic/transcriptomic signature. Journals of Gerontology - Series A Biological Sciences and Medical Sciences, 74(1):1–8, 2019.

2018

P. Stolfi, M. Bernardi, and L. Petrella. The sparse method of simulated quantiles: An application to portfolio optimization. Statistica Neerlandica, 72(3):375–398, 2018.

M. Pedicini, M.C. Palumbo, and F. Castiglione. Computing hierarchical transition graphs of asyn- chronous genetic regulatory networks. Communications in Computer and Information Science, 830:88– 103, 2018.

M.C. Palumbo, M. Morettini, P. Tieri, F. Diele, M. Sacchetti, and F. Castiglione. Personalizing physical exercise in a computational model of fuel homeostasis. PLoS Computational Biology, 14(4), 2018.

A. Palma, A.S. Jarrah, P. Tieri, G. Cesareni, and F. Castiglione. Gene regulatory network modeling of macrophage differentiation corroborates the continuum hypothesis of polarization states. Frontiers in Physiology, 9, 2018.

C. Nardini, J.-F. Moreau, N. Gensous, F. Ravaioli, P. Garagnani, and M.G. Bacalini. The epigenetics of inflammaging: The contribution of age-related heterochromatin loss and locus-specific remodelling and the modulation by environmental stimuli. Seminars in Immunology, 40:49–60, 2018.

A. Ciabattini, C. Nardini, F. Santoro, P. Garagnani, C. Franceschi, and D. Medaglini. Vaccination in the elderly: The challenge of immune changes with aging. Seminars in Immunology, 40:83–94, 2018.

X. Zhou, G. Meng, C. Nardini, and H. Mei. Systemic evaluation of cellular reprogramming processes exploiting a novel r-tool: Eegc. Bioinformatics, 33(16):2532–2538, 2017.

2017

M. Zanin, I. Chorbev, B. Stres, E. Stalidzans, J. Vera, P. Tieri, F. Castiglione, D. Groen, H. Zheng, J. Baumbach, J.A. Schmid, J. Basilio, P. Klimek, N. Debeljak, D. Rozman, and H.H.H.W. Schmidt. Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. Briefings in Bioinformatics, 20(3):1057–1062, 2017.

H.A.L. Ribeiro, T.U. Maioli, L.M. de Freitas, P. Tieri, and F. Castiglione. Modeling immune response to leishmania species indicates adenosine as an important inhibitor of th-cell activation. Frontiers in Cellular and Infection Microbiology, 7(JUL), 2017.

C. Nardini, V. Devescovi, Y. Liu, X. Zhou, Y. Lu, and J.E. Dent. Corrigendum: Systemic wound healing associated with local sub-cutaneous mechanical stimulation. Scientific reports, 7:46118, 2017.

M. Morettini, M.C. Palumbo, M. Sacchetti, F. Castiglione, and C. Mazzà. A system model of the effects of exercise on plasma interleukin-6 dynamics in healthy individuals: Role of skeletal muscle and adipose tissue. PLoS ONE, 12(7), 2017.

J.-F. Moreau, T. Pradeu, A. Grignolio, C. Nardini, F. Castiglione, P. Tieri, M. Capri, S. Salvioli, J.-L. Taupin, P. Garagnani, and C. Franceschi. The emerging role of ecm crosslinking in t cell mobility as a hallmark of immunosenescence in humans. Ageing Research Reviews, 35:322–335, 2017.

A. Madonia, C. Melchiorri, S. Bonamano, M. Marcelli, C. Bulfon, F. Castiglione, M. Galeotti, D. Vol- patti, F. Mosca, P.-G. Tiscar, and N. Romano. Computational modeling of immune system of the fish for a more effective vaccination in aquaculture. Bioinformatics, 33(19):3065–3071, 2017.

Y. Lu, X. Zhou, and C. Nardini. Dissection of the module network implementation ”lemontree”: En- hancements towards applications in metagenomics and translation in autoimmune maladies. Molecular BioSystems, 13(10):2083–2091, 2017.

A. Liso, S. Castellani, F. Massenzio, R. Trotta, A. Pucciarini, B. Bigerna, P. De Luca, P. Zoppoli, F. Castiglione, M.C. Palumbo, F. Stracci, M. Landriscina, G. Specchia, L.A. Bach, M. Conese, and B. Falini. Human monocyte-derived dendritic cells exposed to hyperthermia show a distinct gene ex- pression profile and selective upregulation of igfbp6. Oncotarget, 8(37):60826–60840, 2017.

D. Lai, X. Shu, and C. Nardini. Link prediction in complex networks via modularity-based belief propagation. Chinese Physics B, 26(3), 2017.

D.F. Durso, M.G. Bacalini, C. Sala, C. Pirazzini, E. Marasco, M. Bonafé, M.F. do Valle, D. Gentilini, G. Castellani, A.M.C. Faria, C. Franceschi, P. Garagnani, and C. Nar- dini. Acceleration of leukocytes' epigenetic age as an early tumorand sex-specific marker of breast and colorectal cancer. Oncotarget, 8(14):23237–23245, 2017.

D.F. Durso, M.G. Bacalini, ́I.F. do Valle, C. Pirazzini, M. Bonaf ́e, G. Castellani, A.M.C. Faria, C. Franceschi, P. Garagnani, and C. Nardini. Aberrant methylation patterns in colorectal cancer: A meta-analysis. Oncotarget, 8(8):12820–12830, 2017.

M.G. Bacalini, P. D'Aquila, E. Marasco, C. Nardini, A. Montesanto, C. Franceschi, G. Passarino, P. Garagnani, and D. Bellizzi. The methylation of nuclear and mitochondrial dna in ageing phenotypes and longevity. Mechanisms of Ageing and Development, 165:156–161, 2017.

In Books

P. Tieri, L. Farina, M. Petti, L. Astolfi, P. Paci, and F. Castiglione. Network inference and reconstruction in bioinformatics, volume 1-3. 2018.

T. Mendes, F. Castiglione, P. Tieri, and L. Felicori. Systems and Synthetic Biology Applied to Health. 2017.

F. Castiglione, E. Mancini, M. Pedicini, and A.S. Jarrah. Quantitative modelling approaches, volume 1-3. Amsterdam, Netherlands ; Cambridge, MA, United States : Elsevier, 2018.

M. Bernardi and P. Stolfi. Robust time-varying undirected graphs. Mathematical and Statistical Methods for Actuarial Sciences and Finance, MAF 2018. 2018.

M. Bernardi and P. Stolfi. Approximate em algorithm for sparse estimation of multivariate location-scale mixture of normals. Mathematical and Statistical Methods for Actuarial Sciences and Finance, MAF 2018. 2018.