Digital Biology Unit

Publications

  • F. Castiglione and F. xxxx. Immune System etc. CRC Press, Boca Raton (2015), p. 274. ISBN 978-1-4665-9748-8
  • Marilda Sotomayor, David Perez-Castrillo and F. Castiglione (Eds.). Complex etc. and Agent-Based Models. Springer US, Aug 21, 2020. ISBN 978-1-07-160367-3
  • 1 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.
  • 2 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.

1. 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.


2 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.


3 F. Castiglione, D. Ghersi, and F. Celada.

In-silico analysis of the 'memory anti-naïve' effect in anti-viral cross-reactive responses.

In Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, volume 2017-January, pages 1433-1437, 2017.


4 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.


5 F. Castiglione, E. Mancini, M. Pedicini, and A.S. Jarrah.

Quantitative modelling approaches, volume 1-3.

Amsterdam, Netherlands ; Cambridge, MA, United States : Elsevier, 2018.

6

A. Celestini, M. Cianfriglia, E. Mastrostefano, A. Palma, F. Castiglione, and P. Tieri.

Critical nodes reveal peculiar features of human essential genes and protein interactome.

In Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019, pages 2121-2128, 2019.

7

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.

8

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.

9

D. Deb, S. Basak, T. Kar, U. Narsaria, F. Castiglione, A. Paul, A. Pandey, and A.P. Srivastava.

Immunoinformatics based designing a multi-epitope vaccine against pathogenic chandipura vesiculovirus.

Journal of Cellular Biochemistry, 2021.

10

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.

11

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 expression profile and selective upregulation of igfbp6.

Oncotarget, 8(37):60826-60840, 2017.

12

A. Madonia, C. Melchiorri, S. Bonamano, M. Marcelli, C. Bulfon, F. Castiglione, M. Galeotti, D. Volpatti, 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.

13

T. Mendes, F. Castiglione, P. Tieri, and L. Felicori.

Systems and Synthetic Biology Applied to Health.

2017.

14

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.

15

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.

16

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.

17

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.

18

M. Pedicini, M.C. Palumbo, and F. Castiglione.

Computing hierarchical transition graphs of asynchronous genetic regulatory networks.

Communications in Computer and Information Science, 830:88-103, 2018.

19

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.

20

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.

21

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.

22

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.

23

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.

24

P. Stolfi and F. Castiglione.

Emulation of dynamic multi-output simulator of risk of type-2 diabetes.

pages 1289-1294, 2020.

25

P. Stolfi and F. Castiglione.

Emulating complex simulations by machine learning methods.

BMC Bioinformatics, 22, 2021.

26

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.

pages 2214-2221, 2019.

27

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.

28

P. Tieri, L. Farina, M. Petti, L. Astolfi, P. Paci, and F. Castiglione.

Network inference and reconstruction in bioinformatics, volume 1-3.

2018.

29

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.

30

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.